1
|
Lucotte EA, Jay P, Rougemont Q, Boyer L, Cornille A, Snirc A, Labat A, Chahine E, Duhamel M, Namias A, Gendelman J, Ma WJ, Hayes RK, Baruri S, Ham JP, Perlin MH, Hood ME, Rodríguez de la Vega RC, Giraud T. Repeated loss of function at HD mating-type genes and of recombination in anther-smut fungi. Nat Commun 2025; 16:4962. [PMID: 40436846 PMCID: PMC12119880 DOI: 10.1038/s41467-025-60222-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Accepted: 05/14/2025] [Indexed: 06/01/2025] Open
Abstract
Basidiomycete fungi typically have two mating-type loci controlling mating compatibility, HD and PR, residing on different chromosomes. Loss-of-function in mating compatibility has been reported at the PR genes in a few heterothallic basidiomycetes, but not for the HD genes. In Microbotryum anther-smut fungi, there have been repeated linkage events between the HD and PR loci through chromosome fusions, leading to non-recombining regions. Here, we found that two sister Microbotryum species parasitizing Dianthus plants, M. superbum and M. shykoffianum, as well as the distantly related M. scorzonerae, have their HD and PR loci on different chromosomes, but with the PR chromosome fused with a part of the ancestral HD chromosome. In addition, recombination suppression has extended stepwise, generating evolutionary strata. In all three species, the HD genes lost their function in mating compatibility, natural diploid strains being often homozygous at the HD locus. Strains could be homozygous for a disrupted HD2 gene, that was hardly expressed during mating. Mating tests confirmed that a single genetic factor controlled mating compatibility and that haploid strains with identical HD alleles could mate and produce hyphae. This study shows that a unifactorial mating-type determinism can evolve, repeatedly, from a bifactorial system, by different mechanisms.
Collapse
Affiliation(s)
- Elise A Lucotte
- Université Paris-Saclay, CNRS, AgroParisTech, Ecologie Société Evolution, Gif sur Yvette, France.
| | - Paul Jay
- Université Paris-Saclay, CNRS, AgroParisTech, Ecologie Société Evolution, Gif sur Yvette, France
- Center for GeoGenetics, University of Copenhagen, Copenhagen, Denmark
| | - Quentin Rougemont
- Université Paris-Saclay, CNRS, AgroParisTech, Ecologie Société Evolution, Gif sur Yvette, France
| | - Loreleï Boyer
- Université Paris-Saclay, CNRS, AgroParisTech, Ecologie Société Evolution, Gif sur Yvette, France
| | - Amandine Cornille
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE-Le Moulon, Gif-sur-Yvette, France
| | - Alodie Snirc
- Université Paris-Saclay, CNRS, AgroParisTech, Ecologie Société Evolution, Gif sur Yvette, France
| | - Amandine Labat
- Université Paris-Saclay, CNRS, AgroParisTech, Ecologie Société Evolution, Gif sur Yvette, France
| | - Elizabeth Chahine
- Université Paris-Saclay, CNRS, AgroParisTech, Ecologie Société Evolution, Gif sur Yvette, France
| | - Marine Duhamel
- Université Paris-Saclay, CNRS, AgroParisTech, Ecologie Société Evolution, Gif sur Yvette, France
| | - Alice Namias
- Université Paris-Saclay, CNRS, AgroParisTech, Ecologie Société Evolution, Gif sur Yvette, France
| | | | - Wen-Juan Ma
- Department of Biology, Amherst College, Amherst, MA, USA
- Department of Biology, Research group of Ecology, Evolution and Genetics, Vrije Universiteit Brussel, Brussels, Belgium
| | - Roxanne K Hayes
- Department of Biology, Program on Disease Evolution, University of Louisville, Louisville, KY, USA
| | - Shikhi Baruri
- Department of Biology, Program on Disease Evolution, University of Louisville, Louisville, KY, USA
| | - Joseph P Ham
- Department of Biology, Program on Disease Evolution, University of Louisville, Louisville, KY, USA
| | - Michael H Perlin
- Department of Biology, Program on Disease Evolution, University of Louisville, Louisville, KY, USA
| | - Michael E Hood
- Department of Biology, Amherst College, Amherst, MA, USA
| | | | - Tatiana Giraud
- Université Paris-Saclay, CNRS, AgroParisTech, Ecologie Société Evolution, Gif sur Yvette, France.
| |
Collapse
|
2
|
Feng B, Li Y, Xu B, Liu H, Steenwyk JL, David KT, Tian X, Gonçalves C, Opulente DA, LaBella AL, Harrison MC, Wolters JF, Shao S, Chen Z, Fisher KJ, Groenewald M, Hittinger CT, Shen XX, Li S, Rokas A, Zhou X, Li Y. Unique trajectory of gene family evolution from genomic analysis of nearly all known species in an ancient yeast lineage. Mol Syst Biol 2025:10.1038/s44320-025-00118-0. [PMID: 40425814 DOI: 10.1038/s44320-025-00118-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2024] [Revised: 04/11/2025] [Accepted: 04/30/2025] [Indexed: 05/29/2025] Open
Abstract
Gene gains and losses are a major driver of genome evolution; their precise characterization can provide insights into the origin and diversification of major lineages. Here, we examined gene family evolution of 1154 genomes from nearly all known species in the medically and technologically important yeast subphylum Saccharomycotina. We found that yeast gene family evolution differs from that of plants, animals, and filamentous ascomycetes, and is characterized by smaller overall gene numbers yet larger gene family sizes for a given gene number. Faster-evolving lineages (FELs) in yeasts experienced significantly higher rates of gene losses-commensurate with a narrowing of metabolic niche breadth-but higher speciation rates than their slower-evolving sister lineages (SELs). Gene families most often lost are those involved in mRNA splicing, carbohydrate metabolism, and cell division and are likely associated with intron loss, metabolic breadth, and non-canonical cell cycle processes. Our results highlight the significant role of gene family contractions in the evolution of yeast metabolism, genome function, and speciation, and suggest that gene family evolutionary trajectories have differed markedly across major eukaryotic lineages.
Collapse
Affiliation(s)
- Bo Feng
- Institute of Marine Science and Technology, Shandong University, Qingdao, 266237, China
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, 266237, China
| | - Yonglin Li
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Center, South China Agricultural University, Guangzhou, 510642, China
| | - Biyang Xu
- Institute of Marine Science and Technology, Shandong University, Qingdao, 266237, China
| | - Hongyue Liu
- Institute of Marine Science and Technology, Shandong University, Qingdao, 266237, China
| | - Jacob L Steenwyk
- Howards Hughes Medical Institute and the Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Kyle T David
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, 37235, USA
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN, 37235, USA
| | - Xiaolin Tian
- Institute of Marine Science and Technology, Shandong University, Qingdao, 266237, China
| | - Carla Gonçalves
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, 37235, USA
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN, 37235, USA
- Associate Laboratory i4HB-Institute for Health and Bioeconomy and UCIBIO-Applied Molecular Biosciences Unit, Department of Life Sciences, NOVA School of Science and Technology, Universidade Nova de Lisboa, Caparica, Portugal
- UCIBIO-i4HB, Departamento de Ciências da Vida, Faculdade de Ciências e Tenologia, Universidade Nova de Lisboa, Caparica, Portugal
| | - Dana A Opulente
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Center for Genomic Science Innovation, Department of Energy (DOE) Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI, 53726, USA
- Biology Department, Villanova University, Villanova, PA, 19085, USA
| | - Abigail L LaBella
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, 37235, USA
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN, 37235, USA
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, North Carolina Research Campus, Kannapolis, NC, 28233, USA
- Center for Computational Intelligence to Predict Health and Environmental Risks (CIPHER), University of North Carolina at Charlotte, Charlotte, NC, 28233, USA
| | - Marie-Claire Harrison
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, 37235, USA
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN, 37235, USA
| | - John F Wolters
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Center for Genomic Science Innovation, Department of Energy (DOE) Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI, 53726, USA
| | - Shengyuan Shao
- Institute of Marine Science and Technology, Shandong University, Qingdao, 266237, China
| | - Zhaohao Chen
- Institute of Marine Science and Technology, Shandong University, Qingdao, 266237, China
| | - Kaitlin J Fisher
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Center for Genomic Science Innovation, Department of Energy (DOE) Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI, 53726, USA
- Department of Biological Sciences, State University of New York at Oswego, Oswego, NY, 13126, USA
| | | | - Chris Todd Hittinger
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Center for Genomic Science Innovation, Department of Energy (DOE) Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI, 53726, USA
| | - Xing-Xing Shen
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Shengying Li
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, 37235, USA.
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN, 37235, USA.
| | - Xiaofan Zhou
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Center, South China Agricultural University, Guangzhou, 510642, China.
| | - Yuanning Li
- Institute of Marine Science and Technology, Shandong University, Qingdao, 266237, China.
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, 266237, China.
| |
Collapse
|
3
|
Giulieri SG, Leroi M, Daniel D, Chean R, Bond K, Walker H, Holmes NE, Mothobi N, Alexander A, Jenney A, Beckett C, Mahony A, Stevens K, Sherry NL, Howden BP. A multi-hospital, clinician-initiated bacterial genomics programme to investigate treatment failure in severe Staphylococcus aureus infections. Nat Commun 2025; 16:4869. [PMID: 40419483 DOI: 10.1038/s41467-025-60045-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2024] [Accepted: 05/13/2025] [Indexed: 05/28/2025] Open
Abstract
Bacterial genomics is increasingly used for infectious diseases surveillance, outbreak detection and prediction of antibiotic resistance. With expanding availability of rapid whole-genome sequencing, bacterial genomics data could become a valuable tool for clinicians managing bacterial infections, driving precision medicine strategies. Here, we present a clinician-driven bacterial genomics framework that applies within-patient evolutionary analysis to identify in real-time microbial genetic changes that have an impact on treatment outcomes of severe Staphylococcus aureus infections, a strategy that is increasingly used in cancer genomics. Our approach uses a combination of bacterial genomics and antibiotic susceptibility testing to identify and track bacterial adaptive mutations that underlie microbiologically documented treatment failure (i.e. ongoing positive cultures [persistent infection] or new positive cultures after initial response [recurrent infection]). We show the potential added value of our approach to clinicians and propose a roadmap for the use of bacterial genomics to advance the management of severe bacterial infections.
Collapse
Affiliation(s)
- Stefano G Giulieri
- Department of Microbiology and Immunology, The University of Melbourne at the Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia.
- Victorian Infectious Disease Service, The Royal Melbourne Hospital, at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia.
- Department of Infectious Diseases and Immunology, Austin Health, Heidelberg, VIC, Australia.
- Centre for Pathogen Genomics, The University of Melbourne, Melbourne, VIC, Australia.
| | - Marcel Leroi
- Department of Infectious Diseases and Immunology, Austin Health, Heidelberg, VIC, Australia
- Department of Pathology, Austin Health, Heidelberg, VIC, Australia
| | - Diane Daniel
- Department of Microbiology and Immunology, The University of Melbourne at the Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at the Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Roy Chean
- Department of Microbiology, Eastern Health, Box Hill, VIC, Australia
- Department of Infectious Diseases, Eastern Health, Box Hill, VIC, Australia
| | - Katherine Bond
- Department of Microbiology and Immunology, The University of Melbourne at the Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
- Victorian Infectious Disease Service, The Royal Melbourne Hospital, at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
- Department of Microbiology, Royal Melbourne Hospital, Parkville, VIC, Australia
| | - Harry Walker
- Dorevitch Pathology, Footscray, VIC, Australia
- Department of Infectious Diseases, Western Health, Footscray, VIC, Australia
| | - Natasha E Holmes
- Department of Infectious Diseases and Immunology, Austin Health, Heidelberg, VIC, Australia
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Nomvuyo Mothobi
- Department of Infectious Diseases, University Hospital Geelong, Geelong, VIC, Australia
- AMR-One Health Working Group, Burnet Institute, Melbourne, VIC, Australia
| | - Adrian Alexander
- Department of Infectious Diseases, The Alfred Hospital, Melbourne, VIC, Australia
| | - Adam Jenney
- Department of Infectious Diseases, The Alfred Hospital, Melbourne, VIC, Australia
- Microbiology Unit, The Alfred Hospital, Melbourne, VIC, Australia
| | | | - Andrew Mahony
- Department of Infectious Diseases and Immunology, Austin Health, Heidelberg, VIC, Australia
- Department of Infectious Diseases, Bendigo Health, Bendigo, VIC, Australia
| | - Kerrie Stevens
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at the Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Norelle L Sherry
- Department of Microbiology and Immunology, The University of Melbourne at the Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
- Department of Infectious Diseases and Immunology, Austin Health, Heidelberg, VIC, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at the Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Benjamin P Howden
- Department of Microbiology and Immunology, The University of Melbourne at the Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
- Department of Infectious Diseases and Immunology, Austin Health, Heidelberg, VIC, Australia
- Centre for Pathogen Genomics, The University of Melbourne, Melbourne, VIC, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at the Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
- Department of Microbiology, Royal Melbourne Hospital, Parkville, VIC, Australia
| |
Collapse
|
4
|
Lemarcis T, Blin A, Cariou M, Derzelle A, Farhat S, Fedosov A, Zaharias P, Zuccon D, Puillandre N. Too Far From Relatives? Impact of the Genetic Distance on the Success of Exon Capture in Phylogenomics. Mol Ecol Resour 2025; 25:e14064. [PMID: 39780767 DOI: 10.1111/1755-0998.14064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2024] [Revised: 12/11/2024] [Accepted: 12/20/2024] [Indexed: 01/11/2025]
Abstract
The exon capture approach allows for sequencing a large number of loci to reconstruct phylogenetic relationships at varying taxonomic levels. In order to efficiently recover the targeted loci, the probes designed to capture the exons need to be genetically sufficiently similar to bind to the DNA, with a proposed limit of 10% of divergence. However, this threshold has never been tested with a specific protocol. We have designed a set of probes to capture 1125 exons in the Neogastropoda (Mollusca, Gastropoda), processed with the same protocol from the field to the DNA sequencing to control for potential bias in DNA quantity and quality. We sequenced 30 different species, including 14 species of Neogastropoda and 16 species of Caenogastropoda non-Neogastropoda. Each species includes five specimens, for a total of 150 specimens, and for four specimens among the 150, DNA extracts were aliquoted in four samples, sequenced separately, to estimate the intraspecific and intraspecimen variability in capture success. Our results confirm the impact of genetic distance on the success of exon capture with a negative linear correlation between the genetic distance and the number of exons captured for each sample. Consequently, designing new capture probes would allow for capturing exons in genetically more distant groups without the need to redesign a new set of exons.
Collapse
Affiliation(s)
- Thomas Lemarcis
- Institut Systématique Evolution Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, EPHE, Sorbonne Université, Université Des Antilles, Paris, France
| | - Amandine Blin
- UAR 2047 DoHNEE : Données de recherche pour l'Histoire Naturelle, l'Ecologie et l'Environnement, Muséum National d'Histoire Naturelle, Centre National de la Recherche Scientifique, Paris, France
| | - Marie Cariou
- UAR 2047 DoHNEE : Données de recherche pour l'Histoire Naturelle, l'Ecologie et l'Environnement, Muséum National d'Histoire Naturelle, Centre National de la Recherche Scientifique, Paris, France
| | - Alessandro Derzelle
- Institut Systématique Evolution Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, EPHE, Sorbonne Université, Université Des Antilles, Paris, France
| | - Sarah Farhat
- Institut Systématique Evolution Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, EPHE, Sorbonne Université, Université Des Antilles, Paris, France
| | - Alexander Fedosov
- Institut Systématique Evolution Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, EPHE, Sorbonne Université, Université Des Antilles, Paris, France
- Zoology Department, Swedish Museum of Natural History, Stockholm, Sweden
| | - Paul Zaharias
- Institut Systématique Evolution Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, EPHE, Sorbonne Université, Université Des Antilles, Paris, France
| | - Dario Zuccon
- Institut Systématique Evolution Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, EPHE, Sorbonne Université, Université Des Antilles, Paris, France
| | - Nicolas Puillandre
- Institut Systématique Evolution Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, EPHE, Sorbonne Université, Université Des Antilles, Paris, France
| |
Collapse
|
5
|
Ma J, Bechsgaard J, Aagaard A, Villesen P, Bilde T, Schierup MH. The genomic consequences and persistence of sociality in spiders. Genome Res 2025; 35:499-511. [PMID: 39978820 PMCID: PMC11960701 DOI: 10.1101/gr.279503.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Accepted: 02/04/2025] [Indexed: 02/22/2025]
Abstract
In cooperatively breeding social animals, a few individuals account for all reproduction. In some taxa, sociality is accompanied by a transition from outcrossing to inbreeding. In concert, these traits reduce effective population size, potentially rendering transitions to sociality "evolutionarily dead-ends." We addressed this hypothesis in a comparative genomic study in spiders, in which sociality has evolved independently at least 23 times, but social branches are recent and short. We present genomic evidence for the evolutionary dead-end hypothesis in a spider genus with three independent transitions to sociality. We assembled and annotated high-quality, chromosome-level reference genomes from three pairs of closely related social and subsocial Stegodyphus species. We timed the divergence between the social and subsocial species pairs to be from 1.3 million to 1.8 million years. Social evolution in spiders involves a shift from outcrossing to inbreeding and from an equal to a female-biased sex ratio, causing severe reductions in effective population size and decreased efficacy of selection. We show that transitions to sociality only had full effect on purifying selection at 119, 260, and 279 kya, respectively, and follow similar convergent trajectories of progressive loss of diversity and shifts to an increasingly female-biased sex ratio. This almost deterministic genomic response to sociality may explain why social spider lineages do not persist. What causes species extinction is not clear, but either could be selfish meiotic drive eliminating the production of males or could be an inability to retain genome integrity in the face of extremely reduced efficacy of selection.
Collapse
Affiliation(s)
- Jilong Ma
- Bioinformatics Research Center, Aarhus University, Aarhus C, DK-8000, Denmark;
- Department of Biology, Aarhus University, Aarhus C, DK-8000, Denmark
| | - Jesper Bechsgaard
- Department of Biology, Aarhus University, Aarhus C, DK-8000, Denmark
| | - Anne Aagaard
- Department of Biology, Aarhus University, Aarhus C, DK-8000, Denmark
| | - Palle Villesen
- Bioinformatics Research Center, Aarhus University, Aarhus C, DK-8000, Denmark
| | - Trine Bilde
- Department of Biology, Aarhus University, Aarhus C, DK-8000, Denmark;
- Center for Ecology and Conservation, University of Exeter, Penryn, TR10 9FE, United Kingdom
| | | |
Collapse
|
6
|
Hu Y, Gan Y, Chen Y, Wang H, Cui X, Shen Y, Shen X. Molecular characterization and prevalence assessment of Durettenema sp. (Nematoda: Trichostrongyloidea) in the great leaf-nosed bats ( Hipposideros armiger) in South China. J Helminthol 2025; 99:e41. [PMID: 40045704 DOI: 10.1017/s0022149x25000227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2025]
Abstract
The viruses associated with bats have generated significant concern; however, there is limited knowledge regarding the endoparasites that affect these mammals. This study involved the collection of seven nematode specimens (three males and four females) from the intestines of Hipposideros armiger in Shaoguan City, Guangdong, China. Next-generation sequencing was employed to obtain the mitochondrial DNA (mtDNA) genome, which was determined to be 14,130 base pairs in length. The mitochondrial genome comprised 12 protein-coding genes, 21 tRNA genes, 2 rRNA genes, and an AT-rich non-coding region. Phylogenetic analyses based on mtDNA sequences indicated that the nematode forms a sister clade to Nematodirus, exhibiting only 74% nucleotide identity. In contrast, the nuclear ITS1 gene demonstrated a high degree of nucleotide identity (98.6%-98.8%) with Durettenema guangdongense. Consequently, the parasitic nematode identified from H. armiger is likely to belong to the genus Durettenema and has been designated as Durettenema sp. 888. Furthermore, an epidemiological investigation revealed the presence of the parasitic nematode infections in H. armiger collected from Guangdong, Guangxi, and Guizhou Provinces. Given the widespread distribution of H. armiger and their tendency to inhabit areas in close proximity to human dwellings, the influence of parasite prevalence on bat population numbers and potential for human and domestic animal transmission of this pathogen warrants further investigation.
Collapse
Affiliation(s)
- Y Hu
- State Key Laboratory for Animal Disease Control and Prevention, Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China
| | - Y Gan
- State Key Laboratory for Animal Disease Control and Prevention, Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China
| | - Y Chen
- State Key Laboratory for Animal Disease Control and Prevention, Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China
| | - H Wang
- State Key Laboratory for Animal Disease Control and Prevention, Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China
| | - X Cui
- State Key Laboratory for Animal Disease Control and Prevention, Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China
| | - Y Shen
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai200240, China
| | - X Shen
- State Key Laboratory for Animal Disease Control and Prevention, Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China
- College of Veterinary Medicine, Yangzhou University, Yangzhou225012, China
| |
Collapse
|
7
|
Olagoke O, Aziz A, Zhu L, Read T, Dean D. Whole-genome automated assembly pipeline for Chlamydia trachomatis strains from reference, in vitro and clinical samples using the integrated CtGAP pipeline. NAR Genom Bioinform 2025; 7:lqae187. [PMID: 39781511 PMCID: PMC11704784 DOI: 10.1093/nargab/lqae187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2024] [Revised: 12/10/2024] [Accepted: 12/18/2024] [Indexed: 01/12/2025] Open
Abstract
Whole genome sequencing (WGS) is pivotal for the molecular characterization of Chlamydia trachomatis (Ct)-the leading bacterial cause of sexually transmitted infections and infectious blindness worldwide. Ct WGS can inform epidemiologic, public health and outbreak investigations of these human-restricted pathogens. However, challenges persist in generating high-quality genomes for downstream analyses given its obligate intracellular nature and difficulty with in vitro propagation. No single tool exists for the entirety of Ct genome assembly, necessitating the adaptation of multiple programs with varying success. Compounding this issue is the absence of reliable Ct reference strain genomes. We, therefore, developed CtGAP-Chlamydia trachomatisGenome Assembly Pipeline-as an integrated 'one-stop-shop' pipeline for assembly and characterization of Ct genome sequencing data from various sources including isolates, in vitro samples, clinical swabs and urine. CtGAP, written in Snakemake, enables read quality statistics output, adapter and quality trimming, host read removal, de novo and reference-guided assembly, contig scaffolding, selective ompA, multi-locus-sequence and plasmid typing, phylogenetic tree construction, and recombinant genome identification. Twenty Ct reference genomes were also generated. Successfully validated on a diverse collection of 363 samples containing Ct, CtGAP represents a novel pipeline requiring minimal bioinformatics expertise with easy adaptation for use with other bacterial species.
Collapse
Affiliation(s)
- Olusola Olagoke
- Departments of Medicine and Pediatrics, Division of Infectious Diseases and Global Health, University of California San Francisco School of Medicine, 550 16th Street, 4th Floor Mission Hall, San Francisco, CA, 94158, USA
| | - Ammar Aziz
- Victorian Infectious Diseases Reference Laboratory, 792 Elizabeth Street, Melbourne, Victoria, 3000, Australia
| | - Lucile H Zhu
- Department of Bioengineering, University of California San Francisco and Berkeley School of Engineering, 306 Stanley Hall, Berkeley, CA, 94720, USA
| | - Timothy D Read
- Departments of Medicine and Genetics, Division of Infectious Diseases, Emory University School of Medicine, 100 Woodruff Circle, Atlanta, GA, 30322, USA
| | - Deborah Dean
- Departments of Medicine and Pediatrics, Division of Infectious Diseases and Global Health, University of California San Francisco School of Medicine, 550 16th Street, 4th Floor Mission Hall, San Francisco, CA, 94158, USA
- Department of Bioengineering, University of California San Francisco and Berkeley School of Engineering, 306 Stanley Hall, Berkeley, CA, 94720, USA
- Bixby Center for Global Reproductive Health, University of California San Francisco, 1001 Potrero Ave, San Francisco, CA, 94110, USA
- Benioff Center for Microbiome Medicine, University of California San Francisco, 513 Parnassus Avenue, S357, San Francisco, CA, 94143, USA
- University of California San Francisco Institute of Global Health Sciences, 550 16th Street, 3rd Floor Mission Hall, San Francisco, CA, 94158, USA
| |
Collapse
|
8
|
Miller EC, Faucher R, Hart PB, Rincón-Sandoval M, Santaquiteria A, White WT, Baldwin CC, Miya M, Betancur-R R, Tornabene L, Evans K, Arcila D. Reduced evolutionary constraint accompanies ongoing radiation in deep-sea anglerfishes. Nat Ecol Evol 2025; 9:474-490. [PMID: 39604701 DOI: 10.1038/s41559-024-02586-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 10/18/2024] [Indexed: 11/29/2024]
Abstract
Colonization of a novel habitat is often followed by phenotypic diversification in the wake of ecological opportunity. However, some habitats should be inherently more constraining than others if the challenges of that environment offer few evolutionary solutions. We examined this push-and-pull on macroevolutionary diversification following habitat transitions in the anglerfishes (Lophiiformes). We constructed a phylogeny with extensive sampling (1,092 loci and ~38% of species), combined with three-dimensional phenotypic data from museum specimens. We used these datasets to examine the tempo and mode of phenotypic diversification. The deep-sea pelagic anglerfishes originated from a benthic ancestor and shortly after experienced rapid lineage diversification rates. This transition incurred shifts towards larger jaws, smaller eyes and a more laterally compressed body plan. Despite these directional trends, this lineage still evolved high phenotypic disparity in body, skull and jaw shapes. In particular, bathypelagic anglerfishes show high variability in body elongation, while benthic anglerfishes are constrained around optimal shapes. Within this radiation, phenotypic evolution was concentrated among recently diverged lineages, notably those that deviated from the archetypical globose body plan. Taken together, these results demonstrate that spectacular evolutionary radiations can unfold even within environments with few ecological resources and demanding physiological challenges.
Collapse
Affiliation(s)
- Elizabeth Christina Miller
- Department of Biology, University of Oklahoma, Norman, OK, USA.
- Department of Ichthyology, Sam Noble Museum of Natural History, Norman, OK, USA.
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA, USA.
- Burke Museum of Natural History and Culture, University of Washington, Seattle, WA, USA.
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA.
| | - Rose Faucher
- Department of Biosciences, Rice University, Houston, TX, USA
| | - Pamela B Hart
- Department of Biology, University of Oklahoma, Norman, OK, USA
- Department of Ichthyology, Sam Noble Museum of Natural History, Norman, OK, USA
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL, USA
| | | | | | - William T White
- CSIRO Australian National Fish Collection, National Research Collections Australia, Hobart, Tasmania, Australia
| | - Carole C Baldwin
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Masaki Miya
- Department of Zoology, Natural History Museum and Institute, Chuo-ku, Chiba, Japan
| | - Ricardo Betancur-R
- Department of Biology, University of Oklahoma, Norman, OK, USA
- Department of Ichthyology, Sam Noble Museum of Natural History, Norman, OK, USA
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Luke Tornabene
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA, USA
- Burke Museum of Natural History and Culture, University of Washington, Seattle, WA, USA
| | - Kory Evans
- Department of Biosciences, Rice University, Houston, TX, USA
| | - Dahiana Arcila
- Department of Biology, University of Oklahoma, Norman, OK, USA
- Department of Ichthyology, Sam Noble Museum of Natural History, Norman, OK, USA
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| |
Collapse
|
9
|
Levy S, Jiang AK, Grant MR, Arp G, Minabou Ndjite G, Jiang X, Hall B. Convergent evolution of oxidized sugar metabolism in commensal and pathogenic microbes in the inflamed gut. Nat Commun 2025; 16:1121. [PMID: 39875389 PMCID: PMC11775122 DOI: 10.1038/s41467-025-56332-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2024] [Accepted: 01/14/2025] [Indexed: 01/30/2025] Open
Abstract
Inflammation-associated perturbations of the gut microbiome are well characterized, but poorly understood. Here, we demonstrate that disparate taxa recapitulate the metabolism of the oxidized sugars glucarate and galactarate, utilizing enzymatically divergent, yet functionally equivalent, gud/gar pathways. The divergent pathway in commensals includes a putative 5-KDG aldolase (GudL) and an uncharacterized ABC transporter (GarABC) that recapitulate the function of their non-homologous counterparts in pathogens. A systematic bioinformatic search for the gud/gar pathway in gut microbes identified 887 species putatively capable of metabolizing oxidized sugars. Previous studies showed that inflammation-derived nitrate, formed by nitric oxide reacting with superoxide, promotes pathogen growth. Our findings reveal a parallel phenomenon: oxidized sugars, also produced from reactions with nitric oxide, serve as alternative carbon sources for commensal microbes. Previously considered a pathogen virulence factor, oxidized sugar metabolism is also present in specific commensals and may contribute to their increased relative abundance in gastrointestinal inflammation.
Collapse
Affiliation(s)
- Sophia Levy
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, College Park, MD, USA
| | - Angela K Jiang
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, College Park, MD, USA
- National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Maggie R Grant
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, College Park, MD, USA
| | - Gabriela Arp
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, College Park, MD, USA
| | - Glory Minabou Ndjite
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, College Park, MD, USA
| | - Xiaofang Jiang
- National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.
| | - Brantley Hall
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, College Park, MD, USA.
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, College Park, MD, USA.
| |
Collapse
|
10
|
Cerqueira de Araujo A, Noel B, Bretaudeau A, Labadie K, Boudet M, Tadrent N, Istace B, Kritli S, Cruaud C, Olaso R, Deleuze JF, Voordouw MJ, Hervet C, Plantard O, Zamoto-Niikura A, Chertemps T, Maïbèche M, Hilliou F, Le Goff G, Chmelař J, Mazák V, Jmel MA, Kotsyfakis M, Medina JM, Hackenberg M, Šimo L, Koutroumpa FA, Wincker P, Kopáček P, Perner J, Aury JM, Rispe C. Genome sequences of four Ixodes species expands understanding of tick evolution. BMC Biol 2025; 23:17. [PMID: 39838418 PMCID: PMC11752866 DOI: 10.1186/s12915-025-02121-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2024] [Accepted: 01/07/2025] [Indexed: 01/23/2025] Open
Abstract
BACKGROUND Ticks, hematophagous Acari, pose a significant threat by transmitting various pathogens to their vertebrate hosts during feeding. Despite advances in tick genomics, high-quality genomes were lacking until recently, particularly in the genus Ixodes, which includes the main vectors of Lyme disease. RESULTS Here, we present the genome sequences of four tick species, derived from a single female individual, with a particular focus on the European species Ixodes ricinus, achieving a chromosome-level assembly. Additionally, draft assemblies were generated for the three other Ixodes species, I. persulcatus, I. pacificus, and I. hexagonus. The quality of the four genomes and extensive annotation of several important gene families have allowed us to study the evolution of gene repertoires at the level of the genus Ixodes and of the tick group. We have determined gene families that have undergone major amplifications during the evolution of ticks, while an expression atlas obtained for I. ricinus reveals striking patterns of specialization both between and within gene families. Notably, several gene family amplifications are associated with a proliferation of single-exon genes-most strikingly for fatty acid elongases and sulfotransferases. CONCLUSIONS The integration of our data with existing genomes establishes a solid framework for the study of gene evolution, improving our understanding of tick biology. In addition, our work lays the foundations for applied research and innovative control targeting these organisms.
Collapse
Affiliation(s)
| | - Benjamin Noel
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
| | | | - Karine Labadie
- Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
| | - Matéo Boudet
- University of Rennes, INRIA, CNRS, IRISA, Rennes, France
- IGEPP, INRAE, Institut Agro, BIPAA, University of Rennes, Rennes, France
| | - Nachida Tadrent
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
| | - Benjamin Istace
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
| | - Salima Kritli
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
| | - Corinne Cruaud
- Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
| | - Robert Olaso
- Centre National de Recherche en Génomique Humaine (CNRGH), Institut de Biologie François Jacob, CEA, Université Paris-Saclay, Evry, France
| | - Jean-François Deleuze
- Centre National de Recherche en Génomique Humaine (CNRGH), Institut de Biologie François Jacob, CEA, Université Paris-Saclay, Evry, France
| | - Maarten J Voordouw
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Canada
| | | | | | - Aya Zamoto-Niikura
- Research Center for Biosafety, Laboratory Animal and Pathogen Bank, National Institute of Infectious Diseases, Tokyo, Japan
| | - Thomas Chertemps
- Institut d'Ecologie Et Des Sciences de L'Environnement de Paris, Sorbonne Université, INRAE, CNRS, IRD, UPEC, Paris, France
| | - Martine Maïbèche
- Institut d'Ecologie Et Des Sciences de L'Environnement de Paris, Sorbonne Université, INRAE, CNRS, IRD, UPEC, Paris, France
| | - Frédérique Hilliou
- Université Côte d'Azur, INRAE, CNRS, ISA, 06903, Sophia Antipolis, France
| | - Gaëlle Le Goff
- Université Côte d'Azur, INRAE, CNRS, ISA, 06903, Sophia Antipolis, France
| | - Jindřich Chmelař
- Department of Medical Biology, Faculty of Science, University of South Bohemia in České Budějovice, Branišovská 31, 37005, České Budějovice, Czech Republic
| | - Vilém Mazák
- Department of Medical Biology, Faculty of Science, University of South Bohemia in České Budějovice, Branišovská 31, 37005, České Budějovice, Czech Republic
| | - Mohamed Amine Jmel
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Branišovská 1160/31, 37005, České Budějovice, Czech Republic
| | - Michalis Kotsyfakis
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Branišovská 1160/31, 37005, České Budějovice, Czech Republic
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, N. Plastira 100, 70013, Heraklion, Crete, Greece
| | - José María Medina
- Dpto. de Genética, Facultad de Ciencias, Universidad de Granada, Campus de Fuentenueva S/N, 18071, Granada, Spain
- Lab. de Bioinformática, Centro de Investigación Biomédica, PTS, Instituto de Biotecnología, Avda. del Conocimiento S/N, 18100, Granada, Spain
| | - Michael Hackenberg
- Dpto. de Genética, Facultad de Ciencias, Universidad de Granada, Campus de Fuentenueva S/N, 18071, Granada, Spain
- Lab. de Bioinformática, Centro de Investigación Biomédica, PTS, Instituto de Biotecnología, Avda. del Conocimiento S/N, 18100, Granada, Spain
| | - Ladislav Šimo
- ANSES, INRAE, Ecole Nationale Vétérinaire d'Alfort, UMR BIPAR, Laboratoire de Santé Animale, 22 Rue Pierre Et Marie Curie, Maisons-Alfort, France
| | - Fotini A Koutroumpa
- INRAE, Université de Tours, UMR1282 Infectiologie Et Santé Publique, 37380, Nouzilly, France
| | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
| | - Petr Kopáček
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Branišovská 1160/31, 37005, České Budějovice, Czech Republic
| | - Jan Perner
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Branišovská 1160/31, 37005, České Budějovice, Czech Republic
| | - Jean-Marc Aury
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
| | | |
Collapse
|
11
|
Hounmanou YMG, Hougbenou BGJ, Dougnon VT, Hammerl JA, Dalsgaard A. Vibrio cidicii genomes recovered from Baltic Sea samples in Denmark. Microbiol Resour Announc 2025; 14:e0112124. [PMID: 39665568 PMCID: PMC11737143 DOI: 10.1128/mra.01121-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2024] [Accepted: 11/25/2024] [Indexed: 12/13/2024] Open
Abstract
We report the genomic characteristics of the human pathogen Vibrio cidicii isolated from seawater and green algae in the Baltic Sea. Initially misidentified as Vibrio vulnificus through culture and MALDI-TOF, whole-genome sequencing (WGS) confirmed them as V. cidicii, highlighting the importance of WGS analysis in accurate classification of emerging pathogens.
Collapse
Affiliation(s)
- Yaovi Mahuton Gildas Hounmanou
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
- Research Unit in Applied Microbiology and Pharmacology of Natural Substances, Laboratory Research in Applied Biology, Polytechnic School of Abomey-Calavi, University of Abomey-Calavi, Abomey-Calavi, Benin
| | - Beau-Gard Jules Hougbenou
- Research Unit in Applied Microbiology and Pharmacology of Natural Substances, Laboratory Research in Applied Biology, Polytechnic School of Abomey-Calavi, University of Abomey-Calavi, Abomey-Calavi, Benin
| | - Victorien Tamegnon Dougnon
- Research Unit in Applied Microbiology and Pharmacology of Natural Substances, Laboratory Research in Applied Biology, Polytechnic School of Abomey-Calavi, University of Abomey-Calavi, Abomey-Calavi, Benin
| | - Jens-Andre Hammerl
- DVG-Consultant Laboratory for Vibrio spp. in Food, Department Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Anders Dalsgaard
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| |
Collapse
|
12
|
Taouk ML, Featherstone LA, Taiaroa G, Seemann T, Ingle DJ, Stinear TP, Wick RR. Exploring SNP filtering strategies: the influence of strict vs soft core. Microb Genom 2025; 11:001346. [PMID: 39812553 PMCID: PMC11734701 DOI: 10.1099/mgen.0.001346] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2024] [Accepted: 12/13/2024] [Indexed: 01/16/2025] Open
Abstract
Phylogenetic analyses are crucial for understanding microbial evolution and infectious disease transmission. Bacterial phylogenies are often inferred from SNP alignments, with SNPs as the fundamental signal within these data. SNP alignments can be reduced to a 'strict core' by removing those sites that do not have data present in every sample. However, as sample size and genome diversity increase, a strict core can shrink markedly, discarding potentially informative data. Here, we propose and provide evidence to support the use of a 'soft core' that tolerates some missing data, preserving more information for phylogenetic analysis. Using large datasets of Neisseria gonorrhoeae and Salmonella enterica serovar Typhi, we assess different core thresholds. Our results show that strict cores can drastically reduce informative sites compared to soft cores. In a 10 000-genome alignment of Salmonella enterica serovar Typhi, a 95% soft core yielded ten times more informative sites than a 100% strict core. Similar patterns were observed in N. gonorrhoeae. We further evaluated the accuracy of phylogenies built from strict- and soft-core alignments using datasets with strong temporal signals. Soft-core alignments generally outperformed strict cores in producing trees displaying clock-like behaviour; for instance, the N. gonorrhoeae 95% soft-core phylogeny had a root-to-tip regression R 2 of 0.50 compared to 0.21 for the strict-core phylogeny. This study suggests that soft-core strategies are preferable for large, diverse microbial datasets. To facilitate this, we developed Core-SNP-filter (https://github.com/rrwick/Core-SNP-filter), an open-source software tool for generating soft-core alignments from whole-genome alignments based on user-defined thresholds.
Collapse
Affiliation(s)
- Mona L. Taouk
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Leo A. Featherstone
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Macroevolution and Macroecology Group, Research, School of Biology, Australian National University, Canberra, ACT, Australia
| | - George Taiaroa
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Torsten Seemann
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Centre for Pathogen Genomics, The University of Melbourne, Melbourne, Victoria, Australia
| | - Danielle J. Ingle
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Centre for Pathogen Genomics, The University of Melbourne, Melbourne, Victoria, Australia
| | - Timothy P. Stinear
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Centre for Pathogen Genomics, The University of Melbourne, Melbourne, Victoria, Australia
| | - Ryan R. Wick
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Centre for Pathogen Genomics, The University of Melbourne, Melbourne, Victoria, Australia
| |
Collapse
|
13
|
Pitot TM, Girard C, Rapp JZ, Somerville V, Culley AI, Vincent WF, Moineau S, Roux S. Viral niche-partitioning: comparative genomics of giant viruses across environmental gradients in a high Arctic freshwater-saltwater lake. ISME COMMUNICATIONS 2025; 5:ycae155. [PMID: 39834781 PMCID: PMC11745019 DOI: 10.1093/ismeco/ycae155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Revised: 11/20/2024] [Accepted: 12/04/2024] [Indexed: 01/22/2025]
Abstract
Giant viruses (GVs; Nucleocytoviricota) impact the biology and ecology of a wide range of eukaryotic hosts, with implications for global biogeochemical cycles. Here, we investigated GV niche separation in highly stratified Lake A at the northern coast of Ellesmere Island, Nunavut, Canada. This lake is composed of a layer of ice-covered freshwater that overlies saltwater derived from the ancient Arctic Ocean, and it therefore provides a broad gradient of environmental conditions and ecological habitats, each with a distinct protist community and rich assemblages of associated GVs. The upper layer (mixolimnion) had measurable light and oxygen, and contained diverse GVs linked to photosynthetic protists, indicating adaptation to surface biotic and abiotic conditions. In contrast, the saline lower layer (monimolimnion), lacking oxygen and light, hosted GVs associated with predicted heterotrophic protists, some of which are known for a predatory lifestyle, and with several viral genes suggesting adaptation to deep-water anaerobic conditions. Our observations underscore the coupling between physical and chemical gradients, microeukaryotes and their associated GVs in Lake A, and provide insight into the potential for GVs to directly and indirectly impact host metabolism. There were similarities between the genetic composition of GVs and the metabolic processes of their potential hosts, implying co-evolution and niche-adaptation within the lake habitats. Notably, we found a greater presence of viral rhodopsins in deeper water layers, suggesting an evolutionary relationship with potential hosts capable of supplementing their energetic needs to thrive in low energy, anoxic conditions.
Collapse
Affiliation(s)
- Thomas M Pitot
- Département de Biochimie, de Microbiologie et de Bio-informatique, Université Laval, 2325 rue de l’Université, Québec, QC G1V0A6, Canada
- Takuvik International Research Laboratory, Université Laval, 2325 rue de l’Université, Québec, QC G1V0A6, Canada
- Centre d’études nordiques (CEN), Université Laval, 2325 rue de l’Université, Québec, QC G1V0A6, Canada
- Institut de Biologie Intégrative et des Systèmes, Université Laval, 2325 rue de l’Université, Québec, QC G1V0A6, Canada
- Department of Energy - Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, United States
| | - Catherine Girard
- Centre d’études nordiques (CEN), Université Laval, 2325 rue de l’Université, Québec, QC G1V0A6, Canada
- Département des Sciences Fondamentales, Université du Québec à Chicoutimi, 555 Boulevard de l'Université, Chicoutimi, QC G7H 2B1, Canada
| | - Josephine Z Rapp
- Centre d’études nordiques (CEN), Université Laval, 2325 rue de l’Université, Québec, QC G1V0A6, Canada
- Département de Biologie, Université Laval, 1045 Avenue de la Médecine, Québec, QC G1V0A6, Canada
- REV Ocean, Oksenøyveien 10, Lysaker 1327, Norway
| | - Vincent Somerville
- Département de Biochimie, de Microbiologie et de Bio-informatique, Université Laval, 2325 rue de l’Université, Québec, QC G1V0A6, Canada
- Institut de Biologie Intégrative et des Systèmes, Université Laval, 2325 rue de l’Université, Québec, QC G1V0A6, Canada
| | - Alexander I Culley
- Takuvik International Research Laboratory, Université Laval, 2325 rue de l’Université, Québec, QC G1V0A6, Canada
- Centre d’études nordiques (CEN), Université Laval, 2325 rue de l’Université, Québec, QC G1V0A6, Canada
- Pacific Biosciences Research Center, 1800 East-West Road Honolulu, HI 96822, United States
| | - Warwick F Vincent
- Takuvik International Research Laboratory, Université Laval, 2325 rue de l’Université, Québec, QC G1V0A6, Canada
- Centre d’études nordiques (CEN), Université Laval, 2325 rue de l’Université, Québec, QC G1V0A6, Canada
- Institut de Biologie Intégrative et des Systèmes, Université Laval, 2325 rue de l’Université, Québec, QC G1V0A6, Canada
- Département de Biologie, Université Laval, 1045 Avenue de la Médecine, Québec, QC G1V0A6, Canada
| | - Sylvain Moineau
- Département de Biochimie, de Microbiologie et de Bio-informatique, Université Laval, 2325 rue de l’Université, Québec, QC G1V0A6, Canada
- Institut de Biologie Intégrative et des Systèmes, Université Laval, 2325 rue de l’Université, Québec, QC G1V0A6, Canada
| | - Simon Roux
- Department of Energy - Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, United States
| |
Collapse
|
14
|
Tyrrell GJ, Croxen M, McCullough E, Li V, Golden AR, Martin I. Group A streptococcal infections in Alberta, Canada 2018-2023. Epidemiol Infect 2024; 153:e35. [PMID: 39711024 PMCID: PMC11869071 DOI: 10.1017/s0950268824001857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2024] [Revised: 11/06/2024] [Accepted: 12/18/2024] [Indexed: 12/24/2024] Open
Abstract
Group A streptococcal or Streptococcus pyogenes infections have been increasing post-COVID-19 pandemic. We describe the epidemiology of S. pyogenes pharyngitis and invasive disease in Alberta, Canada 2018-2023. Positive pharyngitis specimens were identified from throat swabs collected from pharyngitis patients. Invasive S. pyogenes was defined as the isolation of S. pyogenes from a normally sterile site or severe skin infection. S. pyogenes isolates were emm typed. Pharyngitis and invasive disease displayed seasonal trends preceding the COVID-19 pandemic followed by a sharp decrease during COVID-19 intervention measures. After the lifting of interventions, rates of pharyngitis and invasive disease rose. There were 182 983 positive pharyngitis specimens between 2018 and 2023 for a positivity rate of 17.6%. The highest rates occurred in the 0-9 age group in 2023 (41.5%). Invasive disease increased in 2022-2023 driven by emm1 and 12 types. M1UK strain was the most frequent M1 type associated with invasive disease (59% of M1 isolates sequenced). Notably, out of 182 983 pharyngitis cases, there were 111 cases of invasive S. pyogenes detected for an invasive disease rate of 0.06%. This descriptive epidemiology of S. pyogenes pharyngitis and invasive S. pyogenes disease highlights the rapid increase in cases of S. pyogenes occurring in western Canada and illustrates the critical need for a vaccine.
Collapse
Affiliation(s)
- Gregory J. Tyrrell
- Division of Diagnostic and Applied Microbiology, Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB, Canada
- Li Ka Shing Institute of Virology, University of Alberta, Edmonton, AB, Canada
- Alberta Precision Laboratories – Public Health Laboratory, Edmonton, AB, Canada
- Women and Children’s Health Research Institute, University of Alberta, Edmonton, AB, Canada
| | - Matthew Croxen
- Division of Diagnostic and Applied Microbiology, Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB, Canada
- Li Ka Shing Institute of Virology, University of Alberta, Edmonton, AB, Canada
- Alberta Precision Laboratories – Public Health Laboratory, Edmonton, AB, Canada
- Women and Children’s Health Research Institute, University of Alberta, Edmonton, AB, Canada
| | - Emily McCullough
- Alberta Precision Laboratories – Public Health Laboratory, Edmonton, AB, Canada
| | - Vincent Li
- Alberta Precision Laboratories – Public Health Laboratory, Edmonton, AB, Canada
| | - Alyssa R. Golden
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Irene Martin
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| |
Collapse
|
15
|
Rice AM, Troendle EP, Bridgett SJ, Firoozi Nejad B, McKinley JM, Bradley DT, Fairley DJ, Bamford CGG, Skvortsov T, Simpson DA. SARS-CoV-2 introductions to the island of Ireland: a phylogenetic and geospatiotemporal study of infection dynamics. Genome Med 2024; 16:150. [PMID: 39702217 DOI: 10.1186/s13073-024-01409-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 11/07/2024] [Indexed: 12/21/2024] Open
Abstract
BACKGROUND Ireland's COVID-19 response combined extensive SARS-CoV-2 testing to estimate incidence, with whole genome sequencing (WGS) for genome surveillance. As an island with two political jurisdictions-Northern Ireland (NI) and Republic of Ireland (RoI)-and access to detailed passenger travel data, Ireland provides a unique setting to study virus introductions and evaluate public health measures. Using a substantial Irish genomic dataset alongside global data from GISAID, this study aimed to trace the introduction and spread of SARS-CoV-2 across the island. METHODS We recursively searched for 29,518 SARS-CoV-2 genome sequences collected in Ireland from March 2020 to June 2022 within the global SARS-CoV-2 phylogenetic tree and identified clusters based on shared last common non-Irish ancestors. A maximum parsimony approach was used to assign a likely country of origin to each cluster. The geographic locations and collection dates of the samples in each introduction cluster were used to map the spread of the virus across Ireland. Downsampling was used to model the impact of varying levels of sequencing and normalisation for population permitted comparison between jurisdictions. RESULTS Six periods spanning the early introductions and the emergence of Alpha, Delta, and Omicron variants were studied in detail. Among 4439 SARS-CoV-2 introductions to Ireland, 2535 originated in England, with additional cases largely from the rest of Great Britain, United States of America, and Northwestern Europe. Introduction clusters ranged in size from a single to thousands of cases. Introductions were concentrated in the densely populated Dublin and Belfast areas, with many clusters spreading islandwide. Genetic phylogeny was able to effectively trace localised transmission patterns. Introduction rates were similar in NI and RoI for most variants, except for Delta, which was more frequently introduced to NI. CONCLUSIONS Tracking individual introduction events enables detailed modelling of virus spread patterns and clearer assessment of the effectiveness of control measures. Stricter travel restrictions in RoI likely reduced Delta introductions but not infection rates, which were similar across jurisdictions. Local and global sequencing levels influence the information available from phylogenomic analyses and we describe an approach to assess the ability of a chosen WGS level to detect virus introductions.
Collapse
Affiliation(s)
- Alan M Rice
- Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, Belfast, Northern Ireland, BT9 7BL, UK
- Current address: UCD National Virus Reference Laboratory, University College Dublin, Belfield, Dublin 4, D04 E1W1, Ireland
| | - Evan P Troendle
- Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, Belfast, Northern Ireland, BT9 7BL, UK
| | - Stephen J Bridgett
- Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, Belfast, Northern Ireland, BT9 7BL, UK
| | - Behnam Firoozi Nejad
- Geography, School of Natural and Built Environment, Queen's University Belfast, Belfast, Northern Ireland, BT7 1NN, UK
| | - Jennifer M McKinley
- Geography, School of Natural and Built Environment, Queen's University Belfast, Belfast, Northern Ireland, BT7 1NN, UK
| | - Declan T Bradley
- Public Health Agency, Belfast, Northern Ireland, BT2 8BS, UK
- Centre for Public Health, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, Belfast, Northern Ireland, BT12 6BA, UK
| | - Derek J Fairley
- Regional Virus Laboratory, Belfast Health and Social Care Trust, Belfast, Northern Ireland, BT12 6BA, UK
| | - Connor G G Bamford
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, Belfast, Northern Ireland, BT9 5DL, UK
| | - Timofey Skvortsov
- School of Pharmacy, Medical Biology Centre, Queen's University Belfast, Belfast, Northern Ireland, BT9 7BL, UK.
| | - David A Simpson
- Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, Belfast, Northern Ireland, BT9 7BL, UK.
| |
Collapse
|
16
|
Mao B, Zheng Y, Xiao Y, Yang K, Shangguan J, Shen M, Sun H, Fang X, Fu Y. Genome-wide phylogenetic analysis and expansion of gene families involved in detoxification in Smittia aterrima (Meigen)and Smittia pratorum (Goetghebuer) (Diptera, Chironomidae). BMC Genom Data 2024; 25:106. [PMID: 39695974 DOI: 10.1186/s12863-024-01289-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2024] [Accepted: 12/10/2024] [Indexed: 12/20/2024] Open
Abstract
Smittia aterrima (Meigen, 1818) and Smittia pratorum (Goetghebuer, 1927) are important indicator insects for aquatic environments, showing extensive tolerance to the environment. However, the genome-wide phylogenetic relationships and characteristics of the detoxification mechanisms in S. aterrima and S. pratorum remain unclear. Based on the genomes of the two species obtained in our preliminary studies and nine genomes from the NCBI database, we found that chironomids diverged from other mosquitoes approximately 200 million years ago (MYA), and S. aterrima and S. pratorum diverged about 30 MYA according to phylogenetic analysis. Gene family evolution analysis showed significant expansion of 43 and 15 gene families in S. aterrima and S. pratorum, respectively, particularly those related to detoxification pathways. Positive selection analysis reveals that genes under positive selection are crucial for promoting environmental adaptation. Additionally, the detoxification-associated gene families including Cytochrome P450 (CYP), Glutathione S-transferases (GST), ATP-binding cassette (ABC), carboxylesterase (CCE), and UDP-glucuronosyltransferase (UGT) were annotated. Our analysis results show that these five detoxification gene families have significantly expanded in the chironomid genomes. This study highlights the genome evolution of chironomids and their responses to mechanisms of tolerance to environmental challenges.
Collapse
Affiliation(s)
- Bin Mao
- Hubei Key Laboratory of Economic Forest Germplasm Improvement and Resources Comprehensive Utilization, Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Hubei Zhongke Research Institute of Industrial Technology, College of Biology and Agricultural Resources, Huanggang Normal University, Huanggang City, 438000, Hubei, China
| | - Yue Zheng
- Hubei Key Laboratory of Economic Forest Germplasm Improvement and Resources Comprehensive Utilization, Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Hubei Zhongke Research Institute of Industrial Technology, College of Biology and Agricultural Resources, Huanggang Normal University, Huanggang City, 438000, Hubei, China
| | - Yunli Xiao
- Hubei Key Laboratory of Economic Forest Germplasm Improvement and Resources Comprehensive Utilization, Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Hubei Zhongke Research Institute of Industrial Technology, College of Biology and Agricultural Resources, Huanggang Normal University, Huanggang City, 438000, Hubei, China
| | - Kaixia Yang
- Hubei Key Laboratory of Economic Forest Germplasm Improvement and Resources Comprehensive Utilization, Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Hubei Zhongke Research Institute of Industrial Technology, College of Biology and Agricultural Resources, Huanggang Normal University, Huanggang City, 438000, Hubei, China
| | - Jingru Shangguan
- Hubei Key Laboratory of Economic Forest Germplasm Improvement and Resources Comprehensive Utilization, Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Hubei Zhongke Research Institute of Industrial Technology, College of Biology and Agricultural Resources, Huanggang Normal University, Huanggang City, 438000, Hubei, China
| | - Mi Shen
- Hubei Key Laboratory of Economic Forest Germplasm Improvement and Resources Comprehensive Utilization, Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Hubei Zhongke Research Institute of Industrial Technology, College of Biology and Agricultural Resources, Huanggang Normal University, Huanggang City, 438000, Hubei, China
| | - Hao Sun
- Hubei Key Laboratory of Economic Forest Germplasm Improvement and Resources Comprehensive Utilization, Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Hubei Zhongke Research Institute of Industrial Technology, College of Biology and Agricultural Resources, Huanggang Normal University, Huanggang City, 438000, Hubei, China
| | - Xiangliang Fang
- Hubei Key Laboratory of Economic Forest Germplasm Improvement and Resources Comprehensive Utilization, Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Hubei Zhongke Research Institute of Industrial Technology, College of Biology and Agricultural Resources, Huanggang Normal University, Huanggang City, 438000, Hubei, China
| | - Yue Fu
- Hubei Key Laboratory of Economic Forest Germplasm Improvement and Resources Comprehensive Utilization, Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Hubei Zhongke Research Institute of Industrial Technology, College of Biology and Agricultural Resources, Huanggang Normal University, Huanggang City, 438000, Hubei, China.
| |
Collapse
|
17
|
Jagadeesh J, Vembar SS. Evolution of sequence, structural and functional diversity of the ubiquitous DNA/RNA-binding Alba domain. Sci Rep 2024; 14:30363. [PMID: 39638848 PMCID: PMC11621453 DOI: 10.1038/s41598-024-79937-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2024] [Accepted: 11/13/2024] [Indexed: 12/07/2024] Open
Abstract
The DNA/RNA-binding Alba domain is prevalent across all kingdoms of life. First discovered in archaea, this protein domain has evolved from RNA- to DNA-binding, with a concomitant expansion in the range of cellular processes that it regulates. Despite its widespread presence, the full extent of its sequence, structural, and functional diversity remains unexplored. In this study, we employed iterative searches in PSI-BLAST to identify 15,161 unique Alba domain-containing proteins from the NCBI non-redundant protein database. Sequence similarity network (SSN) analysis clustered them into 13 distinct subgroups, including the archaeal Alba and eukaryotic Rpp20/Pop7 and Rpp25/Pop6 groups, as well as novel fungal and Plasmodium-specific Albas. Sequence and structural conservation analysis of the subgroups indicated high preservation of the dimer interface, with Alba domains from unicellular eukaryotes notably exhibiting structural deviations towards their C-terminal end. Finally, phylogenetic analysis, while supporting SSN clustering, revealed the evolutionary branchpoint at which the eukaryotic Rpp20- and Rpp25-like clades emerged from archaeal Albas, and the subsequent taxonomic lineage-based divergence within each clade. Taken together, this comprehensive analysis enhances our understanding of the evolutionary history of Alba domain-containing proteins across diverse organisms.
Collapse
Affiliation(s)
- Jaiganesh Jagadeesh
- Institute of Bioinformatics and Applied Biotechnology, Bengaluru, Karnataka, India
| | | |
Collapse
|
18
|
Boyd JM, Ryan Kaler K, Esquilín-Lebrón K, Pall A, Campbell CJ, Foley ME, Rios-Delgado G, Mustor EM, Stephens TG, Bovermann H, Greco TM, Cristea IM, Carabetta VJ, Beavers WN, Bhattacharya D, Skaar EP, Shaw LN, Stemmler TL. Fpa (YlaN) is an iron(II) binding protein that functions to relieve Fur-mediated repression of gene expression in Staphylococcus aureus. mBio 2024; 15:e0231024. [PMID: 39440976 PMCID: PMC11559061 DOI: 10.1128/mbio.02310-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2024] [Accepted: 09/30/2024] [Indexed: 10/25/2024] Open
Abstract
Iron (Fe) is a trace nutrient required by nearly all organisms. As a result of the demand for Fe and the toxicity of non-chelated cytosolic ionic Fe, regulatory systems have evolved to tightly balance Fe acquisition and usage while limiting overload. In most bacteria, including the mammalian pathogen Staphylococcus aureus, the ferric uptake regulator (Fur) is the primary transcriptional regulator controlling the transcription of genes that code for Fe uptake and utilization proteins. Fpa (formerly YlaN) was demonstrated to be essential in Bacillus subtilis unless excess Fe is added to the growth medium, suggesting a role in Fe homeostasis. Here, we demonstrate that Fpa is essential in S. aureus upon Fe deprivation. Null fur alleles bypassed the essentiality of Fpa. The absence of Fpa abolished the derepression of Fur-regulated genes during Fe limitation. Bioinformatic analyses suggest that fpa was recruited to Gram-positive bacteria and, once acquired, was maintained in the genome as it co-evolved with Fur. Consistent with a role for Fpa in alleviating Fur-dependent repression, Fpa and Fur interacted in vivo, and Fpa decreased the DNA-binding ability of Fur in vitro. Fpa bound Fe(II) in vitro using oxygen or nitrogen ligands with an association constant that is consistent with a physiological role in Fe homeostasis. These findings have led to a model wherein Fpa is an Fe(II) binding protein that influences Fur-dependent regulation through direct interaction.IMPORTANCEIron (Fe) is an essential nutrient for nearly all organisms. If Fe homeostasis is not maintained, Fe may accumulate in the cytosol, which can be toxic. Questions remain about how cells efficiently balance Fe uptake and usage to prevent overload. Iron uptake and proper metalation of proteins are essential processes in the mammalian bacterial pathogen Staphylococcus aureus. Understanding the gene products involved in the genetic regulation of Fe uptake and usage and the physiological adaptations that S. aureus uses to survive in Fe-depleted conditions provides insight into pathogenesis. Herein, we demonstrate that the DNA-binding activity of the ferric uptake regulator transcriptional repressor is alleviated under Fe limitation, but uniquely, in S. aureus, alleviation requires the presence of Fpa.
Collapse
Affiliation(s)
- Jeffrey M. Boyd
- Department of Biochemistry and Microbiology, Rutgers, the State University of New Jersey, New Brunswick, New Jersey, USA
| | - Kylie Ryan Kaler
- Department of Biochemistry and Microbiology, Rutgers, the State University of New Jersey, New Brunswick, New Jersey, USA
| | - Karla Esquilín-Lebrón
- Department of Biochemistry and Microbiology, Rutgers, the State University of New Jersey, New Brunswick, New Jersey, USA
| | - Ashley Pall
- Department of Pharmaceutical Sciences, Wayne State University, Detroit, Michigan, USA
| | - Courtney J. Campbell
- Department of Pharmaceutical Sciences, Wayne State University, Detroit, Michigan, USA
| | - Mary E. Foley
- Department of Biochemistry and Microbiology, Rutgers, the State University of New Jersey, New Brunswick, New Jersey, USA
| | - Gustavo Rios-Delgado
- Department of Biochemistry and Microbiology, Rutgers, the State University of New Jersey, New Brunswick, New Jersey, USA
| | - Emilee M. Mustor
- Department of Molecular Biosciences, University of South Florida, Tampa, Florida, USA
| | - Timothy G. Stephens
- Department of Biochemistry and Microbiology, Rutgers, the State University of New Jersey, New Brunswick, New Jersey, USA
| | - Hannah Bovermann
- Department of Biochemistry and Microbiology, Rutgers, the State University of New Jersey, New Brunswick, New Jersey, USA
| | - Todd M. Greco
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
| | - Ileana M. Cristea
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
| | - Valerie J. Carabetta
- Department of Biomedical Sciences, Cooper Medical School of Rowan University, Camden, New Jersey, USA
| | - William N. Beavers
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Debashish Bhattacharya
- Department of Biochemistry and Microbiology, Rutgers, the State University of New Jersey, New Brunswick, New Jersey, USA
| | - Eric P. Skaar
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Lindsey N. Shaw
- Department of Molecular Biosciences, University of South Florida, Tampa, Florida, USA
| | - Timothy L. Stemmler
- Department of Pharmaceutical Sciences, Wayne State University, Detroit, Michigan, USA
| |
Collapse
|
19
|
Ndjite GM, Jiang A, Ravel C, Grant M, Jiang X, Hall B. Gut Microbial Utilization of the Alternative Sweetener, D-Allulose, via AlsE. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.11.07.622513. [PMID: 39574671 PMCID: PMC11580995 DOI: 10.1101/2024.11.07.622513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/01/2024]
Abstract
D-allulose, a rare sugar with emerging potential as a low-calorie sweetener, has garnered attention as an alternative to other commercially available alternative sweeteners, such as sugar alcohols, which often cause severe gastrointestinal discomfort. D-allulose-6-phosphate 3-epimerase (AlsE) is a prokaryotic enzyme that converts D-allulose-6-phosphate into D-fructose-6-phopshate, enabling its use as a carbon source. However, the taxonomic breadth of AlsE across gut bacteria remains poorly understood, hindering insights into the utilization of D-allulose by microbial communities. In this study, we provide experimental evidence showing that Clostridium innocuum is capable of D-allulose metabolism via a homologous AlsE. A bioinformatics search of 85,202 bacterial genomes identified 116 bacterial species with AlsE homologs, suggesting a limited distribution of AlsE in bacteria. Additionally, Escherichia coli contains a copy of alsE , but it does not grow on D-allulose as a sole carbon source unless alsE is heterologously expressed. A metagenomic analysis revealed that 15.8% of 3,079 adult healthy human metagenomic samples that we analyzed contained alsE , suggesting a limited prevalence of the enzyme in the gut microbiome. These results suggest that the gut microbiome has limited capacity to metabolize D-allulose via alsE , supporting its use as an alternative sweetener with minimal impact on microbial composition and gastrointestinal symptoms. This finding also enables personalized nutrition, allowing diabetic individuals to assess their gut microbiota for alsE , and manage glycemic response while reducing gastrointestinal distress.
Collapse
Affiliation(s)
- Glory Minabou Ndjite
- College of Computer, Mathematical and Natural Sciences, University of Maryland, College Park, Maryland, USA
| | - Angela Jiang
- College of Computer, Mathematical and Natural Sciences, University of Maryland, College Park, Maryland, USA
- National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
| | - Charlotte Ravel
- College of Computer, Mathematical and Natural Sciences, University of Maryland, College Park, Maryland, USA
| | - Maggie Grant
- College of Computer, Mathematical and Natural Sciences, University of Maryland, College Park, Maryland, USA
| | - Xiaofang Jiang
- National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
| | - Brantley Hall
- College of Computer, Mathematical and Natural Sciences, University of Maryland, College Park, Maryland, USA
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, College Park, Maryland, USA
| |
Collapse
|
20
|
Thomy J, Schvarcz CR, McBeain KA, Edwards KF, Steward GF. Eukaryotic viruses encode the ribosomal protein eL40. NPJ VIRUSES 2024; 2:51. [PMID: 39464202 PMCID: PMC11499249 DOI: 10.1038/s44298-024-00060-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2024] [Accepted: 09/20/2024] [Indexed: 10/29/2024]
Abstract
Viruses in the phylum Nucleocytoviricota are large, complex and have an exceptionally diverse metabolic repertoire. Some encode hundreds of products involved in the translation of mRNA into protein, but none was known to encode any of the proteins in ribosomes, the central engines of translation. With the discovery of the eL40 gene in FloV-SA2, we report the first example of a eukaryotic virus encoding a ribosomal protein and show that this gene is also present and expressed in other uncultivated marine giant viruses. FloV-SA2 also encodes a "group II" viral rhodopsin, a viral light-activated protein of unknown function previously only reported in metagenomes. FloV-SA2 is thus a valuable model system for investigating new mechanisms by which viruses manipulate eukaryotic cell metabolism.
Collapse
Affiliation(s)
- Julie Thomy
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, School of Ocean and Earth Science and Technology (SOEST), University of Hawaiʻi at Mānoa, Honolulu, HI USA
- Department of Oceanography, School of Ocean and Earth Science and Technology (SOEST), University of Hawaiʻi at Mānoa, Honolulu, HI USA
| | - Christopher R. Schvarcz
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, School of Ocean and Earth Science and Technology (SOEST), University of Hawaiʻi at Mānoa, Honolulu, HI USA
- Department of Oceanography, School of Ocean and Earth Science and Technology (SOEST), University of Hawaiʻi at Mānoa, Honolulu, HI USA
| | - Kelsey A. McBeain
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, School of Ocean and Earth Science and Technology (SOEST), University of Hawaiʻi at Mānoa, Honolulu, HI USA
- Department of Oceanography, School of Ocean and Earth Science and Technology (SOEST), University of Hawaiʻi at Mānoa, Honolulu, HI USA
| | - Kyle F. Edwards
- Department of Oceanography, School of Ocean and Earth Science and Technology (SOEST), University of Hawaiʻi at Mānoa, Honolulu, HI USA
| | - Grieg F. Steward
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, School of Ocean and Earth Science and Technology (SOEST), University of Hawaiʻi at Mānoa, Honolulu, HI USA
- Department of Oceanography, School of Ocean and Earth Science and Technology (SOEST), University of Hawaiʻi at Mānoa, Honolulu, HI USA
| |
Collapse
|
21
|
Rey Redondo E, Leung SKK, Yung CCM. Genomic and biogeographic characterisation of the novel prasinovirus Mantoniella tinhauana virus 1. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e70020. [PMID: 39392286 PMCID: PMC11467894 DOI: 10.1111/1758-2229.70020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2024] [Accepted: 09/10/2024] [Indexed: 10/12/2024]
Abstract
Mamiellophyceae are a ubiquitous class of unicellular green algae in the global ocean. Their ecological importance is highlighted in studies focused on the prominent genera Micromonas, Ostreococcus, and Bathycoccus. Mamiellophyceae are susceptible to prasinoviruses, double-stranded DNA viruses belonging to the nucleocytoplasmic large DNA virus group. Our study represents the first isolation of a prasinovirus in the South China Sea and the only one to infect the globally distributed genus Mantoniella. We conducted a comparative analysis with previously identified viral relatives, encompassing morphological characteristics, host specificity, marker-based phylogenetic placement, and whole-genome sequence comparisons. Although it shares morphological and genetic similarities with established prasinoviruses, this novel virus showed distinct genetic traits, confining its infection to the species Mantoniella tinhauana. We also explored the global biogeography of this prasinovirus and its host by mapping metagenomic data and analysing their relationship with various environmental parameters. Our results demonstrate a pronounced link between the virus and its host, both found predominantly in higher latitudes in the surface ocean. By gaining an increased understanding of the relationships between viruses, hosts, and environments, researchers can better make predictions and potentially implement measures to mitigate the consequences of climate change on oceanic processes.
Collapse
Affiliation(s)
- Elvira Rey Redondo
- Department of Ocean ScienceThe Hong Kong University of Science and TechnologyHong KongHong Kong SAR
| | - Shara Ka Kiu Leung
- Department of Ocean ScienceThe Hong Kong University of Science and TechnologyHong KongHong Kong SAR
| | - Charmaine Cheuk Man Yung
- Department of Ocean ScienceThe Hong Kong University of Science and TechnologyHong KongHong Kong SAR
| |
Collapse
|
22
|
Chan KO. Next-generation bioinformatics: An ultrafast and user-friendly tool for phylogenomic data exploration. Mol Ecol Resour 2024; 24:e13993. [PMID: 38970356 DOI: 10.1111/1755-0998.13993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2024] [Accepted: 06/26/2024] [Indexed: 07/08/2024]
Abstract
With increasingly large genomic datasets, even routine bioinformatic tasks can be arduous, computationally demanding, and time-consuming. Additionally, most bioinformatic programs do not have a graphical user interface (GUI) and thus, require users to be minimally competent in command-line. These impediments present significant economic and technological barriers for practitioners who do not have access to advanced computational resources and support. In this issue of Molecular Ecology Resources, Handika and Esselstyn (2024) developed an ultrafast and memory-efficient bioinformatic tool, SEGUL, that performs common manipulations and calculations of summary statistics on phylogenomic datasets. SEGUL has two main features that distinguish it from other bioinformatic programs: (1) it is based on the recently emergent, high-performance programming language Rust, and (2) it has a GUI written using Flutter, a cross-platform programming framework that also supports mobile operating systems (mobile iOS, iPadOS and Android). By leveraging and combining the power of Rust and Flutter, SEGUL achieves significantly faster computation times and lower memory usage across different platforms and CPU architectures compared to similar programs. The unique and innovative features of SEGUL pave the way for a new era of bioinformatics that can be more energy-efficient, inclusive, and available to a broader swathe of users.
Collapse
Affiliation(s)
- Kin Onn Chan
- University of Kansas Biodiversity Institute and Natural History Museum, Lawrence, Kansas, USA
| |
Collapse
|
23
|
Handika H, Esselstyn JA. SEGUL: Ultrafast, memory-efficient and mobile-friendly software for manipulating and summarizing phylogenomic datasets. Mol Ecol Resour 2024; 24:e13964. [PMID: 38666432 DOI: 10.1111/1755-0998.13964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 03/18/2024] [Accepted: 04/15/2024] [Indexed: 10/10/2024]
Abstract
Phylogenetic studies now routinely require manipulating and summarizing thousands of data files. For most of these tasks, currently available software requires considerable computing resources and substantial knowledge of command-line applications. We develop an ultrafast and memory-efficient software, SEGUL, that performs common phylogenomic dataset manipulations and calculates statistics summarizing essential data features. Our software is available as standalone command-line interface (CLI) and graphical user interface (GUI) applications, and as a library for Rust, R and Python, with possible support of other languages. The CLI and library versions run native on Windows, Linux and macOS, including Apple ARM Macs. The GUI version extends support to include mobile iOS, iPadOS and Android operating systems. SEGUL leverages the high performance of the Rust programming language to offer fast execution times and low memory footprints regardless of dataset size and platform choice. The inclusion of a GUI minimizes bioinformatics barriers to phylogenomics while SEGUL's efficiency reduces economic barriers by allowing analysis on inexpensive hardware. Our support for mobile operating systems further enables teaching phylogenomics where access to computing power is limited.
Collapse
Affiliation(s)
- Heru Handika
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, USA
| | - Jacob A Esselstyn
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, USA
| |
Collapse
|
24
|
Vakirlis N, Acar O, Cherupally V, Carvunis AR. Ancestral Sequence Reconstruction as a Tool to Detect and Study De Novo Gene Emergence. Genome Biol Evol 2024; 16:evae151. [PMID: 39004885 PMCID: PMC11299112 DOI: 10.1093/gbe/evae151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 06/17/2024] [Accepted: 07/09/2024] [Indexed: 07/16/2024] Open
Abstract
New protein-coding genes can evolve from previously noncoding genomic regions through a process known as de novo gene emergence. Evidence suggests that this process has likely occurred throughout evolution and across the tree of life. Yet, confidently identifying de novo emerged genes remains challenging. Ancestral sequence reconstruction is a promising approach for inferring whether a gene has emerged de novo or not, as it allows us to inspect whether a given genomic locus ancestrally harbored protein-coding capacity. However, the use of ancestral sequence reconstruction in the context of de novo emergence is still in its infancy and its capabilities, limitations, and overall potential are largely unknown. Notably, it is difficult to formally evaluate the protein-coding capacity of ancestral sequences, particularly when new gene candidates are short. How well-suited is ancestral sequence reconstruction as a tool for the detection and study of de novo genes? Here, we address this question by designing an ancestral sequence reconstruction workflow incorporating different tools and sets of parameters and by introducing a formal criterion that allows to estimate, within a desired level of confidence, when protein-coding capacity originated at a particular locus. Applying this workflow on ∼2,600 short, annotated budding yeast genes (<1,000 nucleotides), we found that ancestral sequence reconstruction robustly predicts an ancient origin for the most widely conserved genes, which constitute "easy" cases. For less robust cases, we calculated a randomization-based empirical P-value estimating whether the observed conservation between the extant and ancestral reading frame could be attributed to chance. This formal criterion allowed us to pinpoint a branch of origin for most of the less robust cases, identifying 49 genes that can unequivocally be considered de novo originated since the split of the Saccharomyces genus, including 37 Saccharomyces cerevisiae-specific genes. We find that for the remaining equivocal cases we cannot rule out different evolutionary scenarios including rapid evolution, multiple gene losses, or a recent de novo origin. Overall, our findings suggest that ancestral sequence reconstruction is a valuable tool to study de novo gene emergence but should be applied with caution and awareness of its limitations.
Collapse
Affiliation(s)
- Nikolaos Vakirlis
- Institute for Fundamental Biomedical Research, BSRC “Alexander Fleming”, Vari, Greece
| | - Omer Acar
- Pittsburgh Center for Evolutionary Biology and Medicine, Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Vijay Cherupally
- Pittsburgh Center for Evolutionary Biology and Medicine, Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Anne-Ruxandra Carvunis
- Pittsburgh Center for Evolutionary Biology and Medicine, Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| |
Collapse
|
25
|
Zhang J, Schneller NM, Field MA, Chan CX, Miller DJ, Strugnell JM, Riginos C, Bay L, Cooke I. Chromosomal inversions harbour excess mutational load in the coral, Acropora kenti, on the Great Barrier Reef. Mol Ecol 2024; 33:e17468. [PMID: 39046252 DOI: 10.1111/mec.17468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 06/28/2024] [Accepted: 07/03/2024] [Indexed: 07/25/2024]
Abstract
The future survival of coral reefs in the Anthropocene depends on the capacity of corals to adapt as oceans warm and extreme weather events become more frequent. Targeted interventions designed to assist evolutionary processes in corals require a comprehensive understanding of the distribution and structure of standing variation, however, efforts to map genomic variation in corals have so far focussed almost exclusively on SNPs, overlooking structural variants that have been shown to drive adaptive processes in other taxa. Here, we show that the reef-building coral, Acropora kenti, harbours at least five large, highly polymorphic structural variants, all of which exhibit signatures of strongly suppressed recombination in heterokaryotypes, a feature commonly associated with chromosomal inversions. Based on their high minor allele frequency, uniform distribution across habitats and elevated genetic load, we propose that these inversions in A. kenti are likely to be under balancing selection. An excess of SNPs with high impact on protein-coding genes within these loci elevates their importance both as potential targets for adaptive selection and as contributors to genetic decline if coral populations become fragmented or inbred in future.
Collapse
Affiliation(s)
- Jia Zhang
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, Queensland, Australia
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, Queensland, Australia
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Nadja M Schneller
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, Queensland, Australia
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, Queensland, Australia
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
| | - Matt A Field
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, Queensland, Australia
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, Queensland, Australia
- Immunogenomics Lab, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Cheong Xin Chan
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - David J Miller
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, Queensland, Australia
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, Queensland, Australia
| | - Jan M Strugnell
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, Queensland, Australia
- Centre for Sustainable Tropical Fisheries and Aquaculture, James Cook University, Townsville, Queensland, Australia
- College of Science and Engineering, James Cook University, Townsville, Queensland, Australia
| | - Cynthia Riginos
- School of the Environment, The University of Queensland, Brisbane, Queensland, Australia
- Australian Institute of Marine Science, Townsville, Queensland, Australia
| | - Line Bay
- Australian Institute of Marine Science, Townsville, Queensland, Australia
| | - Ira Cooke
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, Queensland, Australia
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, Queensland, Australia
| |
Collapse
|
26
|
Vakirlis N, Kupczok A. Large-scale investigation of species-specific orphan genes in the human gut microbiome elucidates their evolutionary origins. Genome Res 2024; 34:888-903. [PMID: 38977308 PMCID: PMC11293555 DOI: 10.1101/gr.278977.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 06/12/2024] [Indexed: 07/10/2024]
Abstract
Species-specific genes, also known as orphans, are ubiquitous across life's domains. In prokaryotes, species-specific orphan genes (SSOGs) are mostly thought to originate in external elements such as viruses followed by horizontal gene transfer, whereas the scenario of native origination, through rapid divergence or de novo, is mostly dismissed. However, quantitative evidence supporting either scenario is lacking. Here, we systematically analyzed genomes from 4644 human gut microbiome species and identified more than 600,000 unique SSOGs, representing an average of 2.6% of a given species' pangenome. These sequences are mostly rare within each species yet show signs of purifying selection. Overall, SSOGs use optimal codons less frequently, and their proteins are more disordered than those of conserved genes (i.e., non-SSOGs). Importantly, across species, the GC content of SSOGs closely matches that of conserved ones. In contrast, the ∼5% of SSOGs that share similarity to known viral sequences have distinct characteristics, including lower GC content. Thus, SSOGs with similarity to viruses differ from the remaining SSOGs, contrasting an external origination scenario for most of them. By examining the orthologous genomic region in closely related species, we show that a small subset of SSOGs likely evolved natively de novo and find that these genes also differ in their properties from the remaining SSOGs. Our results challenge the notion that external elements are the dominant source of prokaryotic genetic novelty and will enable future studies into the biological role and relevance of species-specific genes in the human gut.
Collapse
Affiliation(s)
- Nikolaos Vakirlis
- Institute For Fundamental Biomedical Research, B.S.R.C. "Alexander Fleming," Vari 166 72, Greece;
- Institute for General Microbiology, Kiel University, 24118 Kiel, Germany
| | - Anne Kupczok
- Bioinformatics Group, Wageningen University, 6700 PB Wageningen, The Netherlands
| |
Collapse
|
27
|
Efimenko B, Popadin K, Gunbin K. NeMu: a comprehensive pipeline for accurate reconstruction of neutral mutation spectra from evolutionary data. Nucleic Acids Res 2024; 52:W108-W115. [PMID: 38795067 PMCID: PMC11223800 DOI: 10.1093/nar/gkae438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 04/23/2024] [Accepted: 05/09/2024] [Indexed: 05/27/2024] Open
Abstract
The recognized importance of mutational spectra in molecular evolution is yet to be fully exploited beyond human cancer studies and model organisms. The wealth of intraspecific polymorphism data in the GenBank repository, covering a broad spectrum of genes and species, presents an untapped opportunity for detailed mutational spectrum analysis. Existing methods fall short by ignoring intermediate substitutions on the inner branches of phylogenetic trees and lacking the capability for cross-species mutational comparisons. To address these challenges, we present the NeMu pipeline, available at https://nemu-pipeline.com, a tool grounded in phylogenetic principles designed to provide comprehensive and scalable analysis of mutational spectra. Utilizing extensive sequence data from numerous available genome projects, NeMu rapidly and accurately reconstructs the neutral mutational spectrum. This tool, facilitating the reconstruction of gene- and species-specific mutational spectra, contributes to a deeper understanding of evolutionary mechanisms across the broad spectrum of known species.
Collapse
Affiliation(s)
- Bogdan Efimenko
- Center for Mitochondrial Functional Genomics, Immanuel Kant Baltic Federal University, Kaliningrad, Russia
- A.A. Kharkevich Institute for Information Transmission Problems RAS, Moscow, Russia
| | - Konstantin Popadin
- Center for Mitochondrial Functional Genomics, Immanuel Kant Baltic Federal University, Kaliningrad, Russia
| | - Konstantin Gunbin
- Center for Mitochondrial Functional Genomics, Immanuel Kant Baltic Federal University, Kaliningrad, Russia
- A.A. Kharkevich Institute for Information Transmission Problems RAS, Moscow, Russia
- Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia
| |
Collapse
|
28
|
Feng B, Li Y, Liu H, Steenwyk JL, David KT, Tian X, Xu B, Gonçalves C, Opulente DA, LaBella AL, Harrison MC, Wolters JF, Shao S, Chen Z, Fisher KJ, Groenewald M, Hittinger CT, Shen XX, Rokas A, Zhou X, Li Y. Unique trajectory of gene family evolution from genomic analysis of nearly all known species in an ancient yeast lineage. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.05.597512. [PMID: 38895429 PMCID: PMC11185758 DOI: 10.1101/2024.06.05.597512] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Gene gains and losses are a major driver of genome evolution; their precise characterization can provide insights into the origin and diversification of major lineages. Here, we examined gene family evolution of 1,154 genomes from nearly all known species in the medically and technologically important yeast subphylum Saccharomycotina. We found that yeast gene family and genome evolution are distinct from plants, animals, and filamentous ascomycetes and are characterized by small genome sizes and smaller gene numbers but larger gene family sizes. Faster-evolving lineages (FELs) in yeasts experienced significantly higher rates of gene losses-commensurate with a narrowing of metabolic niche breadth-but higher speciation rates than their slower-evolving sister lineages (SELs). Gene families most often lost are those involved in mRNA splicing, carbohydrate metabolism, and cell division and are likely associated with intron loss, metabolic breadth, and non-canonical cell cycle processes. Our results highlight the significant role of gene family contractions in the evolution of yeast metabolism, genome function, and speciation, and suggest that gene family evolutionary trajectories have differed markedly across major eukaryotic lineages.
Collapse
Affiliation(s)
- Bo Feng
- Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao 266237, China
| | - Yonglin Li
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Center, South China Agricultural University, Guangzhou 510642, China
| | - Hongyue Liu
- Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China
| | - Jacob L. Steenwyk
- Howards Hughes Medical Institute and the Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Kyle T. David
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
| | - Xiaolin Tian
- Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China
| | - Biyang Xu
- Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China
| | - Carla Gonçalves
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
- Associate Laboratory i4HB—Institute for Health and Bioeconomy and UCIBIO—Applied Molecular Biosciences Unit, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
- UCIBIO-i4HB, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | - Dana A. Opulente
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Center for Genomic Science Innovation, Department of Energy (DOE) Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI 53726, USA
- Biology Department, Villanova University, Villanova, PA 19085, USA
| | - Abigail L. LaBella
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, North Carolina Research Campus, Kannapolis NC 28223, USA AND Center for Computational Intelligence to Predict Health and Environmental Risks (CIPHER), University of North Carolina at Charlotte, Charlotte, NC, 28233, USA
| | - Marie-Claire Harrison
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
| | - John F. Wolters
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Center for Genomic Science Innovation, Department of Energy (DOE) Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI 53726, USA
| | - Shengyuan Shao
- Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China
| | - Zhaohao Chen
- Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China
| | - Kaitlin J. Fisher
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Center for Genomic Science Innovation, Department of Energy (DOE) Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI 53726, USA
- Department of Biological Sciences, State University of New York at Oswego, Oswego, NY, 13126, USA
| | | | - Chris Todd Hittinger
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Center for Genomic Science Innovation, Department of Energy (DOE) Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI 53726, USA
| | - Xing-Xing Shen
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
| | - Xiaofan Zhou
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Center, South China Agricultural University, Guangzhou 510642, China
| | - Yuanning Li
- Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao 266237, China
| |
Collapse
|
29
|
Paremskaia AI, Volchkov PY, Deviatkin AA. IAVCP (Influenza A Virus Consensus and Phylogeny): Automatic Identification of the Genomic Sequence of the Influenza A Virus from High-Throughput Sequencing Data. Viruses 2024; 16:873. [PMID: 38932165 PMCID: PMC11209090 DOI: 10.3390/v16060873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 04/27/2024] [Accepted: 05/28/2024] [Indexed: 06/28/2024] Open
Abstract
Recently, high-throughput sequencing of influenza A viruses has become a routine test. It should be noted that the extremely high diversity of the influenza A virus complicates the task of determining the sequences of all eight genome segments. For a fast and accurate analysis, it is necessary to select the most suitable reference for each segment. At the same time, there is no standardized method in the field of decoding sequencing results that allows the user to update the sequence databases to which the reads obtained by virus sequencing are compared. The IAVCP (influenza A virus consensus and phylogeny) was developed with the goal of automatically analyzing high-throughput sequencing data of influenza A viruses. Its goals include the extraction of a consensus genome directly from paired raw reads. In addition, the pipeline enables the identification of potential reassortment events in the evolutionary history of the virus of interest by analyzing the topological structure of phylogenetic trees that are automatically reconstructed.
Collapse
Affiliation(s)
- Anastasiia Iu. Paremskaia
- Federal Research Center for Innovator and Emerging Biomedical and Pharmaceutical Technologies, 125315 Moscow, Russia;
| | - Pavel Yu. Volchkov
- Federal Research Center for Innovator and Emerging Biomedical and Pharmaceutical Technologies, 125315 Moscow, Russia;
- Department of Fundamental Medicine, Lomonosov Moscow State University, 119992 Moscow, Russia
- The MCSC Named after A. S. Loginov, 111123 Moscow, Russia
| | - Andrei A. Deviatkin
- Federal Research Center for Innovator and Emerging Biomedical and Pharmaceutical Technologies, 125315 Moscow, Russia;
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119992 Moscow, Russia
| |
Collapse
|
30
|
Thompson A, Liebeskind BJ, Scully EJ, Landis MJ. Deep Learning and Likelihood Approaches for Viral Phylogeography Converge on the Same Answers Whether the Inference Model Is Right or Wrong. Syst Biol 2024; 73:183-206. [PMID: 38189575 PMCID: PMC11249978 DOI: 10.1093/sysbio/syad074] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 11/22/2023] [Accepted: 01/05/2024] [Indexed: 01/09/2024] Open
Abstract
Analysis of phylogenetic trees has become an essential tool in epidemiology. Likelihood-based methods fit models to phylogenies to draw inferences about the phylodynamics and history of viral transmission. However, these methods are often computationally expensive, which limits the complexity and realism of phylodynamic models and makes them ill-suited for informing policy decisions in real-time during rapidly developing outbreaks. Likelihood-free methods using deep learning are pushing the boundaries of inference beyond these constraints. In this paper, we extend, compare, and contrast a recently developed deep learning method for likelihood-free inference from trees. We trained multiple deep neural networks using phylogenies from simulated outbreaks that spread among 5 locations and found they achieve close to the same levels of accuracy as Bayesian inference under the true simulation model. We compared robustness to model misspecification of a trained neural network to that of a Bayesian method. We found that both models had comparable performance, converging on similar biases. We also implemented a method of uncertainty quantification called conformalized quantile regression that we demonstrate has similar patterns of sensitivity to model misspecification as Bayesian highest posterior density (HPD) and greatly overlap with HPDs, but have lower precision (more conservative). Finally, we trained and tested a neural network against phylogeographic data from a recent study of the SARS-Cov-2 pandemic in Europe and obtained similar estimates of region-specific epidemiological parameters and the location of the common ancestor in Europe. Along with being as accurate and robust as likelihood-based methods, our trained neural networks are on average over 3 orders of magnitude faster after training. Our results support the notion that neural networks can be trained with simulated data to accurately mimic the good and bad statistical properties of the likelihood functions of generative phylogenetic models.
Collapse
Affiliation(s)
- Ammon Thompson
- Participant in an Education Program Sponsored by U.S. Department of Defense (DOD) at the National Geospatial-Intelligence Agency, Springfield, VA 22150, USA
| | | | - Erik J Scully
- National Geospatial-Intelligence Agency, Springfield, VA 22150, USA
| | - Michael J Landis
- Department of Biology, Washington University in St. Louis, Rebstock Hall, St. Louis, MO 63130, USA
| |
Collapse
|
31
|
Rey Redondo E, Xu Y, Yung CCM. Genomic characterisation and ecological distribution of Mantoniella tinhauana: a novel Mamiellophycean green alga from the Western Pacific. Front Microbiol 2024; 15:1358574. [PMID: 38774501 PMCID: PMC11106453 DOI: 10.3389/fmicb.2024.1358574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 04/12/2024] [Indexed: 05/24/2024] Open
Abstract
Mamiellophyceae are dominant marine algae in much of the ocean, the most prevalent genera belonging to the order Mamiellales: Micromonas, Ostreococcus and Bathycoccus, whose genetics and global distributions have been extensively studied. Conversely, the genus Mantoniella, despite its potential ecological importance, remains relatively under-characterised. In this study, we isolated and characterised a novel species of Mamiellophyceae, Mantoniella tinhauana, from subtropical coastal waters in the South China Sea. Morphologically, it resembles other Mantoniella species; however, a comparative analysis of the 18S and ITS2 marker genes revealed its genetic distinctiveness. Furthermore, we sequenced and assembled the first genome of Mantoniella tinhauana, uncovering significant differences from previously studied Mamiellophyceae species. Notably, the genome lacked any detectable outlier chromosomes and exhibited numerous unique orthogroups. We explored gene groups associated with meiosis, scale and flagella formation, shedding light on species divergence, yet further investigation is warranted. To elucidate the biogeography of Mantoniella tinhauana, we conducted a comprehensive analysis using global metagenomic read mapping to the newly sequenced genome. Our findings indicate this species exhibits a cosmopolitan distribution with a low-level prevalence worldwide. Understanding the intricate dynamics between Mamiellophyceae and the environment is crucial for comprehending their impact on the ocean ecosystem and accurately predicting their response to forthcoming environmental changes.
Collapse
Affiliation(s)
| | | | - Charmaine Cheuk Man Yung
- Department of Ocean Science, The Hong Kong University of Science and Technology, Kowloon, Hong Kong SAR, China
| |
Collapse
|
32
|
Tominaga K, Ozaki S, Sato S, Katayama T, Nishimura Y, Omae K, Iwasaki W. Frequent nonhomologous replacement of replicative helicase loaders by viruses in Vibrionaceae. Proc Natl Acad Sci U S A 2024; 121:e2317954121. [PMID: 38683976 PMCID: PMC11087808 DOI: 10.1073/pnas.2317954121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 03/14/2024] [Indexed: 05/02/2024] Open
Abstract
Several microbial genomes lack textbook-defined essential genes. If an essential gene is absent from a genome, then an evolutionarily independent gene of unknown function complements its function. Here, we identified frequent nonhomologous replacement of an essential component of DNA replication initiation, a replicative helicase loader gene, in Vibrionaceae. Our analysis of Vibrionaceae genomes revealed two genes with unknown function, named vdhL1 and vdhL2, that were substantially enriched in genomes without the known helicase-loader genes. These genes showed no sequence similarities to genes with known function but encoded proteins structurally similar with a viral helicase loader. Analyses of genomic syntenies and coevolution with helicase genes suggested that vdhL1/2 encodes a helicase loader. The in vitro assay showed that Vibrio harveyi VdhL1 and Vibrio ezurae VdhL2 promote the helicase activity of DnaB. Furthermore, molecular phylogenetics suggested that vdhL1/2 were derived from phages and replaced an intrinsic helicase loader gene of Vibrionaceae over 20 times. This high replacement frequency implies the host's advantage in acquiring a viral helicase loader gene.
Collapse
Affiliation(s)
- Kento Tominaga
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba277-0882, Japan
| | - Shogo Ozaki
- Department of Molecular Biology, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka812-8582, Japan
| | - Shohei Sato
- Department of Molecular Biology, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka812-8582, Japan
| | - Tsutomu Katayama
- Department of Molecular Biology, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka812-8582, Japan
| | - Yuki Nishimura
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba277-0882, Japan
| | - Kimiho Omae
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba277-0882, Japan
| | - Wataru Iwasaki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba277-0882, Japan
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo113-0032, Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba277-0882, Japan
- Atmosphere and Ocean Research Institute, The University of Tokyo, Chiba277-8564, Japan
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo113-0032, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo113-8657, Japan
| |
Collapse
|
33
|
Morel-Letelier I, Yuen B, Kück AC, Camacho-García YE, Petersen JM, Lara M, Leray M, Eisen JA, Osvatic JT, Gros O, Wilkins LGE. Adaptations to nitrogen availability drive ecological divergence of chemosynthetic symbionts. PLoS Genet 2024; 20:e1011295. [PMID: 38820540 PMCID: PMC11168628 DOI: 10.1371/journal.pgen.1011295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 06/12/2024] [Accepted: 05/08/2024] [Indexed: 06/02/2024] Open
Abstract
Bacterial symbionts, with their shorter generation times and capacity for horizontal gene transfer (HGT), play a critical role in allowing marine organisms to cope with environmental change. The closure of the Isthmus of Panama created distinct environmental conditions in the Tropical Eastern Pacific (TEP) and Caribbean, offering a "natural experiment" for studying how closely related animals evolve and adapt under environmental change. However, the role of bacterial symbionts in this process is often overlooked. We sequenced the genomes of endosymbiotic bacteria in two sets of sister species of chemosymbiotic bivalves from the genera Codakia and Ctena (family Lucinidae) collected on either side of the Isthmus, to investigate how differing environmental conditions have influenced the selection of symbionts and their metabolic capabilities. The lucinid sister species hosted different Candidatus Thiodiazotropha symbionts and only those from the Caribbean had the genetic potential for nitrogen fixation, while those from the TEP did not. Interestingly, this nitrogen-fixing ability did not correspond to symbiont phylogeny, suggesting convergent evolution of nitrogen fixation potential under nutrient-poor conditions. Reconstructing the evolutionary history of the nifHDKT operon by including other lucinid symbiont genomes from around the world further revealed that the last common ancestor (LCA) of Ca. Thiodiazotropha lacked nif genes, and populations in oligotrophic habitats later re-acquired the nif operon through HGT from the Sedimenticola symbiont lineage. Our study suggests that HGT of the nif operon has facilitated niche diversification of the globally distributed Ca. Thiodiazotropha endolucinida species clade. It highlights the importance of nitrogen availability in driving the ecological diversification of chemosynthetic symbiont species and the role that bacterial symbionts may play in the adaptation of marine organisms to changing environmental conditions.
Collapse
Affiliation(s)
- Isidora Morel-Letelier
- Eco-Evolutionary Interactions Group, Max Planck Institute for Marine Microbiology (MPIMM), Bremen, Germany
| | - Benedict Yuen
- Eco-Evolutionary Interactions Group, Max Planck Institute for Marine Microbiology (MPIMM), Bremen, Germany
| | - A. Carlotta Kück
- Eco-Evolutionary Interactions Group, Max Planck Institute for Marine Microbiology (MPIMM), Bremen, Germany
| | - Yolanda E. Camacho-García
- Centro de Investigación en Ciencias del Mar y Limnología (CIMAR), Universidad de Costa Rica, San Pedro, San José, Costa Rica
- Centro de Investigación en Biodiversidad y Ecología Tropical (CIBET), Universidad de Costa Rica, San Pedro, San José, Costa Rica
- Escuela de Biología, Universidad de Costa Rica, San Pedro, San José, Costa Rica
| | - Jillian M. Petersen
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Minor Lara
- Diving Center Cuajiniquil, Provincia de Guanacaste, Cuajiniquil, Costa Rica
| | - Matthieu Leray
- Smithsonian Tropical Research Institute, Balboa, Ancon, Republic of Panamá
| | - Jonathan A. Eisen
- Department of Evolution and Ecology, University of California, Davis, Davis, California, United States of America
- Department of Medical Microbiology and Immunology, University of California, Davis, Davis, California, United States of America
| | - Jay T. Osvatic
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Vienna, Austria
- Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | - Olivier Gros
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d’Histoire Naturelle, CNRS, Sorbonne Université, Université des Antilles, Pointe-à-Pitre, France
| | - Laetitia G. E. Wilkins
- Eco-Evolutionary Interactions Group, Max Planck Institute for Marine Microbiology (MPIMM), Bremen, Germany
| |
Collapse
|
34
|
Morel M, Zhukova A, Lemoine F, Gascuel O. Accurate Detection of Convergent Mutations in Large Protein Alignments With ConDor. Genome Biol Evol 2024; 16:evae040. [PMID: 38451738 PMCID: PMC10986858 DOI: 10.1093/gbe/evae040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 01/30/2024] [Accepted: 02/22/2024] [Indexed: 03/09/2024] Open
Abstract
Evolutionary convergences are observed at all levels, from phenotype to DNA and protein sequences, and changes at these different levels tend to be correlated. Notably, convergent mutations can lead to convergent changes in phenotype, such as changes in metabolism, drug resistance, and other adaptations to changing environments. We propose a two-component approach to detect mutations subject to convergent evolution in protein alignments. The "Emergence" component selects mutations that emerge more often than expected, while the "Correlation" component selects mutations that correlate with the convergent phenotype under study. With regard to Emergence, a phylogeny deduced from the alignment is provided by the user and is used to simulate the evolution of each alignment position. These simulations allow us to estimate the expected number of mutations in a neutral model, which is compared to the observed number of mutations in the data studied. In Correlation, a comparative phylogenetic approach, is used to measure whether the presence of each of the observed mutations is correlated with the convergent phenotype. Each component can be used on its own, for example Emergence when no phenotype is available. Our method is implemented in a standalone workflow and a webserver, called ConDor. We evaluate the properties of ConDor using simulated data, and we apply it to three real datasets: sedge PEPC proteins, HIV reverse transcriptase, and fish rhodopsin. The results show that the two components of ConDor complement each other, with an overall accuracy that compares favorably to other available tools, especially on large datasets.
Collapse
Affiliation(s)
- Marie Morel
- Institut Pasteur, Université Paris Cité, Unité Bioinformatique Evolutive, Paris, France
- Université Claude Bernard Lyon 1, LBBE, UMR 5558, CNRS, VAS, Villeurbanne, 69100, France
| | - Anna Zhukova
- Institut Pasteur, Université Paris Cité, Unité Bioinformatique Evolutive, Paris, France
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, Paris, France
| | - Frédéric Lemoine
- Institut Pasteur, Université Paris Cité, Unité Bioinformatique Evolutive, Paris, France
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, Paris, France
- Institut Pasteur, Université Paris Cité, CNR Virus Des Infections Respiratoires, Paris, France
| | - Olivier Gascuel
- Institut Pasteur, Université Paris Cité, Unité Bioinformatique Evolutive, Paris, France
- Institut de Systématique, Evolution, Biodiversité (UMR 7205—CNRS, Muséum National d’Histoire Naturelle, SU, EPHE, UA), Paris, France
| |
Collapse
|
35
|
Ngou BPM, Wyler M, Schmid MW, Kadota Y, Shirasu K. Evolutionary trajectory of pattern recognition receptors in plants. Nat Commun 2024; 15:308. [PMID: 38302456 PMCID: PMC10834447 DOI: 10.1038/s41467-023-44408-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 12/12/2023] [Indexed: 02/03/2024] Open
Abstract
Cell-surface receptors play pivotal roles in many biological processes, including immunity, development, and reproduction, across diverse organisms. How cell-surface receptors evolve to become specialised in different biological processes remains elusive. To shed light on the immune-specificity of cell-surface receptors, we analyzed more than 200,000 genes encoding cell-surface receptors from 350 genomes and traced the evolutionary origin of immune-specific leucine-rich repeat receptor-like proteins (LRR-RLPs) in plants. Surprisingly, we discovered that the motifs crucial for co-receptor interaction in LRR-RLPs are closely related to those of the LRR-receptor-like kinase (RLK) subgroup Xb, which perceives phytohormones and primarily governs growth and development. Functional characterisation further reveals that LRR-RLPs initiate immune responses through their juxtamembrane and transmembrane regions, while LRR-RLK-Xb members regulate development through their cytosolic kinase domains. Our data suggest that the cell-surface receptors involved in immunity and development share a common origin. After diversification, their ectodomains, juxtamembrane, transmembrane, and cytosolic regions have either diversified or stabilised to recognise diverse ligands and activate differential downstream responses. Our work reveals a mechanism by which plants evolve to perceive diverse signals to activate the appropriate responses in a rapidly changing environment.
Collapse
Affiliation(s)
| | | | | | - Yasuhiro Kadota
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan.
| | - Ken Shirasu
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan.
| |
Collapse
|
36
|
Rosani U, De Felice S, Frizzo R, Kawato S, Wegner KM. FicD genes in invertebrates: A tale of transposons, pathogenic and integrated viruses. Gene 2024; 893:147895. [PMID: 37832807 DOI: 10.1016/j.gene.2023.147895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Revised: 10/05/2023] [Accepted: 10/10/2023] [Indexed: 10/15/2023]
Abstract
Many gene families are shared across the tree of life between distantly related species because of horizontal gene transfers (HGTs). However, the frequency of HGTs varies strongly between gene families and biotic realms suggesting differential selection pressures and functional bias. One gene family with a wide distribution are FIC-domain containing enzymes (FicDs). FicDs catalyze AMPylation, a post-translational protein modification consisting in the addition of adenosine monophosphate to accessible residues of target proteins. Beside the well-known conservation of FicDs in deuterostomes, we report the presence of a conserved FicD gene ortholog in a large number of protostomes and microbial eukaryotes. We also reported additional FicD gene copies in the genomes of some rotifers, parasitic worms and bivalves. A few dsDNA viruses of these invertebrates, including White spot syndrome virus, Cherax quadricarinatus iridovirus, Ostreid herpesvirus-1 and the beetle nudivirus, carry copies of FicDs, with phylogenetic analysis suggesting a common origin of these FicD copies and the duplicated FicDs of their invertebrate hosts. HGTs and gene duplications possibly mediated by endogenous viruses or genetic mobile elements seem to have contributed to the transfer of AMPylation ability from bacteria and eukaryotes to pathogenic viruses, where this pathway could have been hijacked to promote viral infection.
Collapse
Affiliation(s)
- Umberto Rosani
- Department of Biology, University of Padova, 35121 Padova, Italy.
| | - Sofia De Felice
- Department of Biology, University of Padova, 35121 Padova, Italy
| | - Riccardo Frizzo
- Department of Biology, University of Padova, 35121 Padova, Italy
| | - Satoshi Kawato
- Laboratory of Genome Science, Tokyo University of Marine Science and Technology, 108-8477 Tokyo, Japan
| | - K Mathias Wegner
- Alfred Wegener Institute - Helmholtz Centre for Polar and Marine Research, Waddensea Station Sylt, 25992 List, Germany
| |
Collapse
|
37
|
Thomy J, Sanchez F, Prioux C, Yau S, Xu Y, Mak J, Sun R, Piganeau G, Yung CCM. Unveiling Prasinovirus diversity and host specificity through targeted enrichment in the South China Sea. ISME COMMUNICATIONS 2024; 4:ycae109. [PMID: 39296779 PMCID: PMC11408933 DOI: 10.1093/ismeco/ycae109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2024] [Revised: 07/16/2024] [Accepted: 08/27/2024] [Indexed: 09/21/2024]
Abstract
Unicellular green picophytoplankton from the Mamiellales order are pervasive in marine ecosystems and susceptible to infections by prasinoviruses, large double-stranded DNA viruses within the Nucleocytoviricota phylum. We developed a double-stranded DNA virus enrichment and shotgun sequencing method, and successfully assembled 80 prasinovirus genomes from 43 samples in the South China Sea. Our research delivered the first direct estimation of 94% accuracy in correlating genome similarity to host range. Stirkingly, our analyses uncovered unexpected host-switching across diverse algal lineages, challenging the existing paradigms of host-virus co-speciation and revealing the dynamic nature of viral evolution. We also detected six instances of horizontal gene transfer between prasinoviruses and their hosts, including a novel alternative oxidase. Additionally, diversifying selection on a major capsid protein suggests an ongoing co-evolutionary arms race. These insights not only expand our understanding of prasinovirus genomic diversity but also highlight the intricate evolutionary mechanisms driving their ecological success and shaping broader virus-host interactions in marine environments.
Collapse
Affiliation(s)
- Julie Thomy
- Sorbonne Université, CNRS, Laboratoire de Biodiversité et Biotechnologies Microbiennes (LBBM), Observatoire Océanologique, F-66650 Banyuls/Mer, France
- Department of Oceanography, School of Ocean and Earth Science and Technology (SOEST), University of Hawai'i at Mānoa, Honolulu, HI 96822, United States
| | - Frederic Sanchez
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins (BIOM), UMR 7232, Observatoire Océanologique, F-66650 Banyuls/Mer, France
| | - Camille Prioux
- Sorbonne Université, CNRS, Laboratoire de Biodiversité et Biotechnologies Microbiennes (LBBM), Observatoire Océanologique, F-66650 Banyuls/Mer, France
- Centre Scientifique de Monaco, 8 Quai Antoine 1er, Monaco, MC 98000, Principality of Monaco
| | - Sheree Yau
- Sorbonne Université, CNRS, Laboratoire de Biodiversité et Biotechnologies Microbiennes (LBBM), Observatoire Océanologique, F-66650 Banyuls/Mer, France
| | - Yangbing Xu
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Julian Mak
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Ruixian Sun
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Gwenael Piganeau
- Sorbonne Université, CNRS, Laboratoire de Biodiversité et Biotechnologies Microbiennes (LBBM), Observatoire Océanologique, F-66650 Banyuls/Mer, France
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Charmaine C M Yung
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong SAR, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Hong Kong SAR, China
| |
Collapse
|
38
|
Zaharias P, Lemoine F, Gascuel O. Robustness of Felsenstein's Versus Transfer Bootstrap Supports With Respect to Taxon Sampling. Syst Biol 2023; 72:1280-1295. [PMID: 37756489 PMCID: PMC10939309 DOI: 10.1093/sysbio/syad052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 06/26/2023] [Accepted: 08/09/2023] [Indexed: 09/29/2023] Open
Abstract
The bootstrap method is based on resampling sequence alignments and re-estimating trees. Felsenstein's bootstrap proportions (FBP) are the most common approach to assess the reliability and robustness of sequence-based phylogenies. However, when increasing taxon sampling (i.e., the number of sequences) to hundreds or thousands of taxa, FBP tend to return low support for deep branches. The transfer bootstrap expectation (TBE) has been recently suggested as an alternative to FBP. TBE is measured using a continuous transfer index in [0,1] for each bootstrap tree, instead of the binary {0,1} index used in FBP to measure the presence/absence of the branch of interest. TBE has been shown to yield higher and more informative supports while inducing a very low number of falsely supported branches. Nonetheless, it has been argued that TBE must be used with care due to sampling issues, especially in datasets with a high number of closely related taxa. In this study, we conduct multiple experiments by varying taxon sampling and comparing FBP and TBE support values on different phylogenetic depths, using empirical datasets. Our results show that the main critique of TBE stands in extreme cases with shallow branches and highly unbalanced sampling among clades, but that TBE is still robust in most cases, while FBP is inescapably negatively impacted by high taxon sampling. We suggest guidelines and good practices in TBE (and FBP) computing and interpretation.
Collapse
Affiliation(s)
- Paul Zaharias
- Institut de Systématique, Evolution, Biodiversité (ISYEB UMR7205–CNRS, Muséum National d’Histoire Naturelle, SU, EPHE, UA), 75005 Paris, France
| | - Frédéric Lemoine
- Institut Pasteur, Université Paris Cité, G5 Evolutionary Genomics of RNA Viruses, 75015, Paris, France
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, 75015, Paris, France
| | - Olivier Gascuel
- Institut de Systématique, Evolution, Biodiversité (ISYEB UMR7205–CNRS, Muséum National d’Histoire Naturelle, SU, EPHE, UA), 75005 Paris, France
| |
Collapse
|
39
|
Matteson NL, Hassler GW, Kurzban E, Schwab MA, Perkins SA, Gangavarapu K, Levy JI, Parker E, Pride D, Hakim A, De Hoff P, Cheung W, Castro-Martinez A, Rivera A, Veder A, Rivera A, Wauer C, Holmes J, Wilson J, Ngo SN, Plascencia A, Lawrence ES, Smoot EW, Eisner ER, Tsai R, Chacón M, Baer NA, Seaver P, Salido RA, Aigner S, Ngo TT, Barber T, Ostrander T, Fielding-Miller R, Simmons EH, Zazueta OE, Serafin-Higuera I, Sanchez-Alavez M, Moreno-Camacho JL, García-Gil A, Murphy Schafer AR, McDonald E, Corrigan J, Malone JD, Stous S, Shah S, Moshiri N, Weiss A, Anderson C, Aceves CM, Spencer EG, Hufbauer EC, Lee JJ, King AJ, Ramesh KS, Nguyen KN, Saucedo K, Robles-Sikisaka R, Fisch KM, Gonias SL, Birmingham A, McDonald D, Karthikeyan S, Martin NK, Schooley RT, Negrete AJ, Reyna HJ, Chavez JR, Garcia ML, Cornejo-Bravo JM, Becker D, Isaksson M, Washington NL, Lee W, Garfein RS, Luna-Ruiz Esparza MA, Alcántar-Fernández J, Henson B, Jepsen K, Olivares-Flores B, Barrera-Badillo G, Lopez-Martínez I, Ramírez-González JE, Flores-León R, Kingsmore SF, Sanders A, Pradenas A, White B, Matthews G, Hale M, McLawhon RW, Reed SL, Winbush T, McHardy IH, Fielding RA, Nicholson L, Quigley MM, Harding A, Mendoza A, Bakhtar O, et alMatteson NL, Hassler GW, Kurzban E, Schwab MA, Perkins SA, Gangavarapu K, Levy JI, Parker E, Pride D, Hakim A, De Hoff P, Cheung W, Castro-Martinez A, Rivera A, Veder A, Rivera A, Wauer C, Holmes J, Wilson J, Ngo SN, Plascencia A, Lawrence ES, Smoot EW, Eisner ER, Tsai R, Chacón M, Baer NA, Seaver P, Salido RA, Aigner S, Ngo TT, Barber T, Ostrander T, Fielding-Miller R, Simmons EH, Zazueta OE, Serafin-Higuera I, Sanchez-Alavez M, Moreno-Camacho JL, García-Gil A, Murphy Schafer AR, McDonald E, Corrigan J, Malone JD, Stous S, Shah S, Moshiri N, Weiss A, Anderson C, Aceves CM, Spencer EG, Hufbauer EC, Lee JJ, King AJ, Ramesh KS, Nguyen KN, Saucedo K, Robles-Sikisaka R, Fisch KM, Gonias SL, Birmingham A, McDonald D, Karthikeyan S, Martin NK, Schooley RT, Negrete AJ, Reyna HJ, Chavez JR, Garcia ML, Cornejo-Bravo JM, Becker D, Isaksson M, Washington NL, Lee W, Garfein RS, Luna-Ruiz Esparza MA, Alcántar-Fernández J, Henson B, Jepsen K, Olivares-Flores B, Barrera-Badillo G, Lopez-Martínez I, Ramírez-González JE, Flores-León R, Kingsmore SF, Sanders A, Pradenas A, White B, Matthews G, Hale M, McLawhon RW, Reed SL, Winbush T, McHardy IH, Fielding RA, Nicholson L, Quigley MM, Harding A, Mendoza A, Bakhtar O, Browne SH, Olivas Flores J, Rincon Rodríguez DG, Gonzalez Ibarra M, Robles Ibarra LC, Arellano Vera BJ, Gonzalez Garcia J, Harvey-Vera A, Knight R, Laurent LC, Yeo GW, Wertheim JO, Ji X, Worobey M, Suchard MA, Andersen KG, Campos-Romero A, Wohl S, Zeller M. Genomic surveillance reveals dynamic shifts in the connectivity of COVID-19 epidemics. Cell 2023; 186:5690-5704.e20. [PMID: 38101407 PMCID: PMC10795731 DOI: 10.1016/j.cell.2023.11.024] [Show More Authors] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 08/21/2023] [Accepted: 11/21/2023] [Indexed: 12/17/2023]
Abstract
The maturation of genomic surveillance in the past decade has enabled tracking of the emergence and spread of epidemics at an unprecedented level. During the COVID-19 pandemic, for example, genomic data revealed that local epidemics varied considerably in the frequency of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) lineage importation and persistence, likely due to a combination of COVID-19 restrictions and changing connectivity. Here, we show that local COVID-19 epidemics are driven by regional transmission, including across international boundaries, but can become increasingly connected to distant locations following the relaxation of public health interventions. By integrating genomic, mobility, and epidemiological data, we find abundant transmission occurring between both adjacent and distant locations, supported by dynamic mobility patterns. We find that changing connectivity significantly influences local COVID-19 incidence. Our findings demonstrate a complex meaning of "local" when investigating connected epidemics and emphasize the importance of collaborative interventions for pandemic prevention and mitigation.
Collapse
Affiliation(s)
| | - Gabriel W Hassler
- Department of Computational Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Ezra Kurzban
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | - Madison A Schwab
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | - Sarah A Perkins
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | - Karthik Gangavarapu
- Department of Biomathematics, David Geffen School of Medicine at UCLA, University of California, Los Angeles, Los Angeles, CA, USA; Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | - Joshua I Levy
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | - Edyth Parker
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | - David Pride
- Department of Pathology, University of California, San Diego, La Jolla, CA, USA; Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Abbas Hakim
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA; Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, La Jolla, CA, USA; COVID-19 Detection, Investigation, Surveillance, Clinical, and Outbreak Response, California Department of Public Health, Richmond, CA, USA
| | - Peter De Hoff
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA; Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, La Jolla, CA, USA; COVID-19 Detection, Investigation, Surveillance, Clinical, and Outbreak Response, California Department of Public Health, Richmond, CA, USA
| | - Willi Cheung
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA; Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, La Jolla, CA, USA; COVID-19 Detection, Investigation, Surveillance, Clinical, and Outbreak Response, California Department of Public Health, Richmond, CA, USA
| | - Anelizze Castro-Martinez
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA; Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, La Jolla, CA, USA; Sanford Consortium of Regenerative Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Andrea Rivera
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Anthony Veder
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Ariana Rivera
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Cassandra Wauer
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Jacqueline Holmes
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Jedediah Wilson
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Shayla N Ngo
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Ashley Plascencia
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Elijah S Lawrence
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Elizabeth W Smoot
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Emily R Eisner
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Rebecca Tsai
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Marisol Chacón
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Nathan A Baer
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Phoebe Seaver
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Rodolfo A Salido
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Stefan Aigner
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Toan T Ngo
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Tom Barber
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Tyler Ostrander
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Rebecca Fielding-Miller
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California, San Diego, La Jolla, CA, USA; Division of Infectious Disease and Global Public Health, University of California, San Diego, La Jolla, CA, USA
| | | | - Oscar E Zazueta
- Department of Epidemiology, Secretaria de Salud de Baja California, Tijuana, Baja California, Mexico
| | | | - Manuel Sanchez-Alavez
- Centro de Diagnostico COVID-19 UABC, Tijuana, Baja California, Mexico; Department of Molecular Medicine, Scripps Research, La Jolla, CA, USA
| | | | - Abraham García-Gil
- Clinical Laboratory Department, Salud Digna, A.C, Tijuana, Baja California, Mexico
| | | | - Eric McDonald
- County of San Diego Health and Human Services Agency, San Diego, CA, USA
| | - Jeremy Corrigan
- County of San Diego Health and Human Services Agency, San Diego, CA, USA
| | - John D Malone
- County of San Diego Health and Human Services Agency, San Diego, CA, USA
| | - Sarah Stous
- County of San Diego Health and Human Services Agency, San Diego, CA, USA
| | - Seema Shah
- County of San Diego Health and Human Services Agency, San Diego, CA, USA
| | - Niema Moshiri
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA
| | - Alana Weiss
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | - Catelyn Anderson
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | - Christine M Aceves
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | - Emily G Spencer
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | - Emory C Hufbauer
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | - Justin J Lee
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | - Alison J King
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | - Karthik S Ramesh
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | - Kelly N Nguyen
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | - Kieran Saucedo
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | | | - Kathleen M Fisch
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, La Jolla, CA, USA; Center for Computational Biology and Bioinformatics, University of California San Diego, La Jolla, CA, USA
| | - Steven L Gonias
- Department of Pathology, University of California, San Diego, La Jolla, CA, USA
| | - Amanda Birmingham
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Daniel McDonald
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Smruthi Karthikeyan
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Natasha K Martin
- Division of Infectious Disease and Global Public Health, University of California, San Diego, La Jolla, CA, USA
| | - Robert T Schooley
- Division of Infectious Disease and Global Public Health, University of California, San Diego, La Jolla, CA, USA
| | - Agustin J Negrete
- Facultad de Ciencias de la Salud Universidad Autonoma de Baja California Valle de Las Palmas, Tijuana, Baja California, Mexico
| | - Horacio J Reyna
- Facultad de Ciencias de la Salud Universidad Autonoma de Baja California Valle de Las Palmas, Tijuana, Baja California, Mexico
| | - Jose R Chavez
- Facultad de Ciencias de la Salud Universidad Autonoma de Baja California Valle de Las Palmas, Tijuana, Baja California, Mexico
| | - Maria L Garcia
- Facultad de Ciencias de la Salud Universidad Autonoma de Baja California Valle de Las Palmas, Tijuana, Baja California, Mexico
| | - Jose M Cornejo-Bravo
- Facultad de Ciencias Quimicas e Ingenieria, Universidad Autonoma de Baja California, Tijuana, Baja California, Mexico
| | | | | | | | | | - Richard S Garfein
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California, San Diego, La Jolla, CA, USA
| | | | | | - Benjamin Henson
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Kristen Jepsen
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Beatriz Olivares-Flores
- Instituto de Diagnóstico y Referencia Epidemiológicos (InDRE), Ciudad de México, CDMX, Mexico
| | - Gisela Barrera-Badillo
- Instituto de Diagnóstico y Referencia Epidemiológicos (InDRE), Ciudad de México, CDMX, Mexico
| | - Irma Lopez-Martínez
- Instituto de Diagnóstico y Referencia Epidemiológicos (InDRE), Ciudad de México, CDMX, Mexico
| | - José E Ramírez-González
- Instituto de Diagnóstico y Referencia Epidemiológicos (InDRE), Ciudad de México, CDMX, Mexico
| | - Rita Flores-León
- Instituto de Diagnóstico y Referencia Epidemiológicos (InDRE), Ciudad de México, CDMX, Mexico
| | | | - Alison Sanders
- Return to Learn, University of California, San Diego, La Jolla, CA, USA
| | - Allorah Pradenas
- Return to Learn, University of California, San Diego, La Jolla, CA, USA
| | - Benjamin White
- Return to Learn, University of California, San Diego, La Jolla, CA, USA
| | - Gary Matthews
- Return to Learn, University of California, San Diego, La Jolla, CA, USA
| | - Matt Hale
- Return to Learn, University of California, San Diego, La Jolla, CA, USA
| | - Ronald W McLawhon
- Return to Learn, University of California, San Diego, La Jolla, CA, USA
| | - Sharon L Reed
- Return to Learn, University of California, San Diego, La Jolla, CA, USA
| | - Terri Winbush
- Return to Learn, University of California, San Diego, La Jolla, CA, USA
| | | | | | | | | | | | | | | | - Sara H Browne
- Division of Infectious Disease and Global Public Health, University of California, San Diego, La Jolla, CA, USA; Specialist in Global Health, Encinitas, CA, USA
| | - Jocelyn Olivas Flores
- Facultad de Ciencias Quimicas e Ingenieria, Universidad Autonoma de Baja California, Tijuana, Baja California, Mexico; University of HealthMx, Tijuana, Baja California, Mexico
| | - Diana G Rincon Rodríguez
- University of HealthMx, Tijuana, Baja California, Mexico; Facultad de Medicina, Universidad Xochicalco, Tijuana, Baja California, Mexico
| | - Martin Gonzalez Ibarra
- University of HealthMx, Tijuana, Baja California, Mexico; Facultad de Medicina, Universidad Xochicalco, Tijuana, Baja California, Mexico
| | - Luis C Robles Ibarra
- University of HealthMx, Tijuana, Baja California, Mexico; Instituto de Seguridad y Servicios Sociales de los Trabajadores del Estado, Tijuana, Baja California, Mexico
| | - Betsy J Arellano Vera
- University of HealthMx, Tijuana, Baja California, Mexico; Instituto Mexicano del Seguro Social, Tijuana, Baja California, Mexico
| | - Jonathan Gonzalez Garcia
- University of HealthMx, Tijuana, Baja California, Mexico; SIMNSA, Tijuana, Baja California, Mexico
| | | | - Rob Knight
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA; Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA; Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Louise C Laurent
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA; Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, La Jolla, CA, USA; Sanford Consortium of Regenerative Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Gene W Yeo
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA; Sanford Consortium of Regenerative Medicine, University of California, San Diego, La Jolla, CA, USA; Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Joel O Wertheim
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Xiang Ji
- Department of Mathematics, School of Science and Engineering, Tulane University, New Orleans, LA, USA
| | - Michael Worobey
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
| | - Marc A Suchard
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Kristian G Andersen
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA.
| | - Abraham Campos-Romero
- Innovation and Research Department, Salud Digna, A.C, Tijuana, Baja California, Mexico
| | - Shirlee Wohl
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | - Mark Zeller
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA.
| |
Collapse
|
40
|
Suspène R, Raymond KA, Boutin L, Guillier S, Lemoine F, Ferraris O, Tournier JN, Iseni F, Simon-Lorière E, Vartanian JP. APOBEC3F Is a Mutational Driver of the Human Monkeypox Virus Identified in the 2022 Outbreak. J Infect Dis 2023; 228:1421-1429. [PMID: 37224627 PMCID: PMC11009509 DOI: 10.1093/infdis/jiad165] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 04/24/2023] [Accepted: 05/12/2023] [Indexed: 05/26/2023] Open
Abstract
BACKGROUND On May 6, 2022, a powerful outbreak of monkeypox virus (MPXV) had been reported outside of Africa, with many continuing new cases being reported around the world. Analysis of mutations among the 2 different lineages present in the 2021 and 2022 outbreaks revealed the presence of G->A mutations occurring in the 5'GpA context, indicative of APOBEC3 cytidine deaminase activity. METHODS By using a sensitive polymerase chain reaction (differential DNA denaturation PCR) method allowing differential amplification of AT-rich DNA, we analyzed the level of APOBEC3-induced MPXV editing in infected cells and in patients. RESULTS We demonstrate that G->A hypermutated MPXV genomes can be recovered experimentally from APOBEC3 transfection followed by MPXV infection. Here, among the 7 human APOBEC3 cytidine deaminases (A3A-A3C, A3DE, A3F-A3H), only APOBEC3F was capable of extensively deaminating cytidine residues in MPXV genomes. Hyperedited genomes were also recovered in ∼42% of analyzed patients. Moreover, we demonstrate that substantial repair of these mutations occurs. Upon selection, corrected G->A mutations escaping drift loss contribute to the MPXV evolution observed in the current epidemic. CONCLUSIONS Stochastic or transient overexpression of the APOBEC3F gene exposes the MPXV genome to a broad spectrum of mutations that may be modeling the mutational landscape after multiple cycles of viral replication.
Collapse
Affiliation(s)
- Rodolphe Suspène
- Virus and Cellular Stress Unit, Department of Virology, Institut Pasteur, Université de Paris Cité, Paris, France
| | - Kyle A Raymond
- Virus and Cellular Stress Unit, Department of Virology, Institut Pasteur, Université de Paris Cité, Paris, France
- Sorbonne Université, Complexité du Vivant, Paris, France
| | - Laetitia Boutin
- Microbiology and Infectious Diseases Department, Institut de Recherche Biomédicale des Armées, Brétigny-sur-Orge, France
- Institut de Recherche Biomédicale des Armées, National Reference Center for Orthopoxviruses, (CNR-LE Orthopoxvirus), Brétigny-sur-Orge, France
| | - Sophie Guillier
- Microbiology and Infectious Diseases Department, Institut de Recherche Biomédicale des Armées, Brétigny-sur-Orge, France
| | - Frédéric Lemoine
- Institut Pasteur, Université Paris Cité, G5 Evolutionary Genomics of RNA Viruses, Paris, France
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, Paris, France
| | - Olivier Ferraris
- Microbiology and Infectious Diseases Department, Institut de Recherche Biomédicale des Armées, Brétigny-sur-Orge, France
- Institut de Recherche Biomédicale des Armées, National Reference Center for Orthopoxviruses, (CNR-LE Orthopoxvirus), Brétigny-sur-Orge, France
| | - Jean-Nicolas Tournier
- Microbiology and Infectious Diseases Department, Institut de Recherche Biomédicale des Armées, Brétigny-sur-Orge, France
- Ecole du Val-de-Grâce, Paris, France
| | - Frédéric Iseni
- Microbiology and Infectious Diseases Department, Institut de Recherche Biomédicale des Armées, Brétigny-sur-Orge, France
| | - Etienne Simon-Lorière
- Institut Pasteur, Université Paris Cité, G5 Evolutionary Genomics of RNA Viruses, Paris, France
| | - Jean-Pierre Vartanian
- Virus and Cellular Stress Unit, Department of Virology, Institut Pasteur, Université de Paris Cité, Paris, France
| |
Collapse
|
41
|
Zufan SE, Lau KA, Donald A, Hoang T, Foster CSP, Sikazwe C, Theis T, Rawlinson WD, Ballard SA, Stinear TP, Howden BP, Jennison AV, Seemann T. Bioinformatic investigation of discordant sequence data for SARS-CoV-2: insights for robust genomic analysis during pandemic surveillance. Microb Genom 2023; 9. [PMID: 38019123 DOI: 10.1099/mgen.0.001146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2023] Open
Abstract
The COVID-19 pandemic has necessitated the rapid development and implementation of whole-genome sequencing (WGS) and bioinformatic methods for managing the pandemic. However, variability in methods and capabilities between laboratories has posed challenges in ensuring data accuracy. A national working group comprising 18 laboratory scientists and bioinformaticians from Australia and New Zealand was formed to improve data concordance across public health laboratories (PHLs). One effort, presented in this study, sought to understand the impact of the methodology on consensus genome concordance and interpretation. SARS-CoV-2 WGS proficiency testing programme (PTP) data were retrospectively obtained from the 2021 Royal College of Pathologists of Australasia Quality Assurance Programmes (RCPAQAP), which included 11 participating Australian laboratories. The submitted consensus genomes and reads from eight contrived specimens were investigated, focusing on discordant sequence data and findings were presented to the working group to inform best practices. Despite using a variety of laboratory and bioinformatic methods for SARS-CoV-2 WGS, participants largely produced concordant genomes. Two participants returned five discordant sites in a high-Cτ replicate, which could be resolved with reasonable bioinformatic quality thresholds. We noted ten discrepancies in genome assessment that arose from nucleotide heterogeneity at three different sites in three cell-culture-derived control specimens. While these sites were ultimately accurate after considering the participants' bioinformatic parameters, it presented an interesting challenge for developing standards to account for intrahost single nucleotide variation (iSNV). Observed differences had little to no impact on key surveillance metrics, lineage assignment and phylogenetic clustering, while genome coverage <90 % affected both. We recommend PHLs bioinformatically generate two consensus genomes with and without ambiguity thresholds for quality control and downstream analysis, respectively, and adhere to a minimum 90 % genome coverage threshold for inclusion in surveillance interpretations. We also suggest additional PTP assessment criteria, including primer efficiency, detection of iSNVs and minimum genome coverage of 90 %. This study underscores the importance of multidisciplinary national working groups in informing guidelines in real time for bioinformatic quality acceptance criteria. It demonstrates the potential for enhancing public health responses through improved data concordance and quality control in SARS-CoV-2 genomic analysis during pandemic surveillance.
Collapse
Affiliation(s)
- Sara E Zufan
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | | | - Angela Donald
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Tuyet Hoang
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Charles S P Foster
- Serology and Virology Division (SAViD) SEALS Microbiology, NSW Health Pathology, Sydney, NSW, Australia
- School of Biomedical Sciences, Faculty of Medicine and Health, University of New South Wales, Sydney, NSW, Australia
| | - Chisha Sikazwe
- Department of Microbiology, PathWest Laboratory Medicine Western Australia, Nedlands, WA, Australia
- School of Biomedical Sciences, The University of Western Australia, Nedlands, WA, Australia
| | | | - William D Rawlinson
- RCPAQAP Biosecurity, St. Leonards, NSW, Australia
- Serology and Virology Division (SAViD) SEALS Microbiology, NSW Health Pathology, Sydney, NSW, Australia
- School of Biomedical Sciences, Faculty of Medicine and Health, University of New South Wales, Sydney, NSW, Australia
- School of Women's and Children's Health, Faculty of Medicine and Health, University of New South Wales, Sydney, NSW, Australia
- School of Biotechnology and Biomolecular Sciences, Faculty of Science, University of New South Wales, Sydney, NSW, Australia
| | - Susan A Ballard
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Timothy P Stinear
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Benjamin P Howden
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Amy V Jennison
- Public Health Microbiology, Forensic and Scientific Services, Queensland Department of Health, Brisbane, Australia
| | - Torsten Seemann
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| |
Collapse
|
42
|
Caro H, Dollin S, Biton A, Brancotte B, Desvillechabrol D, Dufresne Y, Li B, Kornobis E, Lemoine F, Maillet N, Perrin A, Traut N, Néron B, Cokelaer T. BioConvert: a comprehensive format converter for life sciences. NAR Genom Bioinform 2023; 5:lqad074. [PMID: 37608802 PMCID: PMC10440784 DOI: 10.1093/nargab/lqad074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 07/18/2023] [Accepted: 08/15/2023] [Indexed: 08/24/2023] Open
Abstract
Bioinformatics is a field known for the numerous standards and formats that have been developed over the years. This plethora of formats, sometimes complementary, and often redundant, poses many challenges to bioinformatics data analysts. They constantly need to find the best tool to convert their data into the suitable format, which is often a complex, technical and time consuming task. Moreover, these small yet important tasks are often difficult to make reproducible. To overcome these difficulties, we initiated BioConvert, a collaborative project to facilitate the conversion of life science data from one format to another. BioConvert aggregates existing software within a single framework and complemented them with original code when needed. It provides a common interface to make the user experience more streamlined instead of having to learn tens of them. Currently, BioConvert supports about 50 formats and 100 direct conversions in areas such as alignment, sequencing, phylogeny, and variant calling. In addition to being useful for end-users, BioConvert can also be utilized by developers as a universal benchmarking framework for evaluating and comparing numerous conversion tools. Additionally, we provide a web server implementing an online user-friendly interface to BioConvert, hence allowing direct use for the community.
Collapse
Affiliation(s)
- Hugo Caro
- Institut Pasteur, Université Paris Cité, Plate-forme Technologique Biomics, F-75015 Paris, France
| | - Sulyvan Dollin
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, F-75015 Paris, France
| | - Anne Biton
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, F-75015 Paris, France
| | - Bryan Brancotte
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, F-75015 Paris, France
| | - Dimitri Desvillechabrol
- Institut Pasteur, Université Paris Cité, Plate-forme Technologique Biomics, F-75015 Paris, France
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, F-75015 Paris, France
| | - Yoann Dufresne
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, F-75015 Paris, France
- Institut Pasteur, Université Paris Cité, G5 Sequence Bioinformatics, Paris, France
| | - Blaise Li
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, F-75015 Paris, France
| | - Etienne Kornobis
- Institut Pasteur, Université Paris Cité, Plate-forme Technologique Biomics, F-75015 Paris, France
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, F-75015 Paris, France
| | - Frédéric Lemoine
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, F-75015 Paris, France
- Institut Pasteur, Université Paris Cité, G5 Evolutionary Genomics of RNA Viruses, Paris, France
| | - Nicolas Maillet
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, F-75015 Paris, France
| | - Amandine Perrin
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, F-75015 Paris, France
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Microbial Evolutionary Genomics, Paris, France
| | - Nicolas Traut
- Institut Pasteur, Université Paris Cité, Unité de Neuroanatomie Appliquée et Théorique, F-75015 Paris, France
| | - Bertrand Néron
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, F-75015 Paris, France
| | - Thomas Cokelaer
- Institut Pasteur, Université Paris Cité, Plate-forme Technologique Biomics, F-75015 Paris, France
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, F-75015 Paris, France
| |
Collapse
|
43
|
Stockdale JE, Susvitasari K, Tupper P, Sobkowiak B, Mulberry N, Gonçalves da Silva A, Watt AE, Sherry NL, Minko C, Howden BP, Lane CR, Colijn C. Genomic epidemiology offers high resolution estimates of serial intervals for COVID-19. Nat Commun 2023; 14:4830. [PMID: 37563113 PMCID: PMC10415581 DOI: 10.1038/s41467-023-40544-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 07/31/2023] [Indexed: 08/12/2023] Open
Abstract
Serial intervals - the time between symptom onset in infector and infectee - are a fundamental quantity in infectious disease control. However, their estimation requires knowledge of individuals' exposures, typically obtained through resource-intensive contact tracing efforts. We introduce an alternate framework using virus sequences to inform who infected whom and thereby estimate serial intervals. We apply our technique to SARS-CoV-2 sequences from case clusters in the first two COVID-19 waves in Victoria, Australia. We find that our approach offers high resolution, cluster-specific serial interval estimates that are comparable with those obtained from contact data, despite requiring no knowledge of who infected whom and relying on incompletely-sampled data. Compared to a published serial interval, cluster-specific serial intervals can vary estimates of the effective reproduction number by a factor of 2-3. We find that serial interval estimates in settings such as schools and meat processing/packing plants are shorter than those in healthcare facilities.
Collapse
Affiliation(s)
| | | | - Paul Tupper
- Department of Mathematics, Simon Fraser University, Burnaby, BC, Canada
| | | | - Nicola Mulberry
- Department of Mathematics, Simon Fraser University, Burnaby, BC, Canada
| | - Anders Gonçalves da Silva
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, VIC, Australia
| | - Anne E Watt
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, VIC, Australia
| | - Norelle L Sherry
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, VIC, Australia
| | - Corinna Minko
- Victorian Department of Health, Melbourne, VIC, Australia
| | - Benjamin P Howden
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, VIC, Australia
| | - Courtney R Lane
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, VIC, Australia
| | - Caroline Colijn
- Department of Mathematics, Simon Fraser University, Burnaby, BC, Canada
| |
Collapse
|
44
|
Liu B, Warnow T. Weighted ASTRID: fast and accurate species trees from weighted internode distances. Algorithms Mol Biol 2023; 18:6. [PMID: 37468904 PMCID: PMC10355063 DOI: 10.1186/s13015-023-00230-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 06/10/2023] [Indexed: 07/21/2023] Open
Abstract
BACKGROUND Species tree estimation is a basic step in many biological research projects, but is complicated by the fact that gene trees can differ from the species tree due to processes such as incomplete lineage sorting (ILS), gene duplication and loss (GDL), and horizontal gene transfer (HGT), which can cause different regions within the genome to have different evolutionary histories (i.e., "gene tree heterogeneity"). One approach to estimating species trees in the presence of gene tree heterogeneity resulting from ILS operates by computing trees on each genomic region (i.e., computing "gene trees") and then using these gene trees to define a matrix of average internode distances, where the internode distance in a tree T between two species x and y is the number of nodes in T between the leaves corresponding to x and y. Given such a matrix, a tree can then be computed using methods such as neighbor joining. Methods such as ASTRID and NJst (which use this basic approach) are provably statistically consistent, very fast (low degree polynomial time) and have had high accuracy under many conditions that makes them competitive with other popular species tree estimation methods. In this study, inspired by the very recent work of weighted ASTRAL, we present weighted ASTRID, a variant of ASTRID that takes the branch uncertainty on the gene trees into account in the internode distance. RESULTS Our experimental study evaluating weighted ASTRID typically shows improvements in accuracy compared to the original (unweighted) ASTRID, and shows competitive accuracy against weighted ASTRAL, the state of the art. Our re-implementation of ASTRID also improves the runtime, with marked improvements on large datasets. CONCLUSIONS Weighted ASTRID is a new and very fast method for species tree estimation that typically improves upon ASTRID and has comparable accuracy to weighted ASTRAL, while remaining much faster. Weighted ASTRID is available at https://github.com/RuneBlaze/internode .
Collapse
Affiliation(s)
- Baqiao Liu
- Department of Computer Science, University of Illinois Urbana-Champaign, Urbana, IL USA
| | - Tandy Warnow
- Department of Computer Science, University of Illinois Urbana-Champaign, Urbana, IL USA
| |
Collapse
|
45
|
Holtz A, Baele G, Bourhy H, Zhukova A. Integrating full and partial genome sequences to decipher the global spread of canine rabies virus. Nat Commun 2023; 14:4247. [PMID: 37460566 DOI: 10.1038/s41467-023-39847-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 06/30/2023] [Indexed: 07/20/2023] Open
Abstract
Despite the rapid growth in viral genome sequencing, statistical methods face challenges in handling historical viral endemic diseases with large amounts of underutilized partial sequence data. We propose a phylogenetic pipeline that harnesses both full and partial viral genome sequences to investigate historical pathogen spread between countries. Its application to rabies virus (RABV) yields precise dating and confident estimates of its geographic dispersal. By using full genomes and partial sequences, we reduce both geographic and genetic biases that often hinder studies that focus on specific genes. Our pipeline reveals an emergence of the present canine-mediated RABV between years 1301 and 1403 and reveals regional introductions over a 700-year period. This geographic reconstruction enables us to locate episodes of human-mediated introductions of RABV and examine the role that European colonization played in its spread. Our approach enables phylogeographic analysis of large and genetically diverse data sets for many viral pathogens.
Collapse
Affiliation(s)
- Andrew Holtz
- Institut Pasteur, Université Paris Cité, Lyssavirus Epidemiology and Neuropathology Unit, F-75015, Paris, France.
| | - Guy Baele
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Hervé Bourhy
- Institut Pasteur, Université Paris Cité, Lyssavirus Epidemiology and Neuropathology Unit, F-75015, Paris, France
- World Health Organization Collaborating Center for Reference and Research on Rabies, Institut Pasteur, Paris, France
| | - Anna Zhukova
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, F-75015, Paris, France.
| |
Collapse
|
46
|
Zhukova A, Dunn D, Gascuel O. Modeling Drug Resistance Emergence and Transmission in HIV-1 in the UK. Viruses 2023; 15:1244. [PMID: 37376544 DOI: 10.3390/v15061244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 05/15/2023] [Accepted: 05/19/2023] [Indexed: 06/29/2023] Open
Abstract
A deeper understanding of HIV-1 transmission and drug resistance mechanisms can lead to improvements in current treatment policies. However, the rates at which HIV-1 drug resistance mutations (DRMs) are acquired and which transmitted DRMs persist are multi-factorial and vary considerably between different mutations. We develop a method for the estimation of drug resistance acquisition and transmission patterns. The method uses maximum likelihood ancestral character reconstruction informed by treatment roll-out dates and allows for the analysis of very large datasets. We apply our method to transmission trees reconstructed on the data obtained from the UK HIV Drug Resistance Database to make predictions for known DRMs. Our results show important differences between DRMs, in particular between polymorphic and non-polymorphic DRMs and between the B and C subtypes. Our estimates of reversion times, based on a very large number of sequences, are compatible but more accurate than those already available in the literature, with narrower confidence intervals. We consistently find that large resistance clusters are associated with polymorphic DRMs and DRMs with long loss times, which require special surveillance. As in other high-income countries (e.g., Switzerland), the prevalence of sequences with DRMs is decreasing, but among these, the fraction of transmitted resistance is clearly increasing compared to the fraction of acquired resistance mutations. All this indicates that efforts to monitor these mutations and the emergence of resistance clusters in the population must be maintained in the long term.
Collapse
Affiliation(s)
- Anna Zhukova
- Bioinformatics and Biostatistics Hub, Institut Pasteur, Université Paris Cité, 75015 Paris, France
| | - David Dunn
- UK MRC Clinical Trials Unit, University College London, London WC1V 6LJ, UK
| | - Olivier Gascuel
- Institut de Systématique, Evolution, Biodiversité (ISYEB)-URM 7205 CNRS, Muséum National d'Histoire Naturelle, SU, EPHE & UA, 75005 Paris, France
| |
Collapse
|
47
|
Touret F, Giraud E, Bourret J, Donati F, Tran-Rajau J, Chiaravalli J, Lemoine F, Agou F, Simon-Lorière E, van der Werf S, de Lamballerie X. Enhanced neutralization escape to therapeutic monoclonal antibodies by SARS-CoV-2 omicron sub-lineages. iScience 2023; 26:106413. [PMID: 36968074 PMCID: PMC10015083 DOI: 10.1016/j.isci.2023.106413] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 02/20/2023] [Accepted: 03/10/2023] [Indexed: 03/17/2023] Open
Abstract
The landscape of SARS-CoV-2 variants dramatically diversified with the simultaneous appearance of multiple subvariants originating from BA.2, BA.4, and BA.5 Omicron sub-lineages. They harbor a specific set of mutations in the spike that can make them more evasive to therapeutic monoclonal antibodies. In this study, we compared the neutralizing potential of monoclonal antibodies against the Omicron BA.2.75.2, BQ.1, BQ.1.1, and XBB variants, with a pre-Omicron Delta variant as a reference. Sotrovimab retains some activity against BA.2.75.2, BQ.1, and XBB as it did against BA.2/BA.5, but is less active against BQ.1.1. Within the Evusheld/AZD7442 cocktail, Cilgavimab lost all activity against all subvariants studied, resulting in loss of Evusheld activity. Finally, Bebtelovimab, while still active against BA.2.75, also lost all neutralizing activity against BQ.1, BQ.1.1, and XBB variants.
Collapse
Affiliation(s)
- Franck Touret
- Unité des Virus Émergents (UVE: Aix-Marseille University - IRD 190 - Inserm 1207), Marseille, France
| | - Emilie Giraud
- Institut Pasteur, Université Paris Cité, CNRS UMR 3523, Chemogenomic and Biological Screening Core Facility, C2RT, Paris, France
| | - Jérôme Bourret
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Molecular Genetics of RNA Viruses, National Reference Center for Respiratory Viruses, Paris, France
| | - Flora Donati
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Molecular Genetics of RNA Viruses, National Reference Center for Respiratory Viruses, Paris, France
| | - Jaouen Tran-Rajau
- Institut Pasteur, Université Paris Cité, CNRS UMR 3523, Chemogenomic and Biological Screening Core Facility, C2RT, Paris, France
| | - Jeanne Chiaravalli
- Institut Pasteur, Université Paris Cité, CNRS UMR 3523, Chemogenomic and Biological Screening Core Facility, C2RT, Paris, France
| | - Frédéric Lemoine
- Institut Pasteur, Université Paris Cité, G5 Evolutionary Genomics of RNA Viruses, Paris, France
| | - Fabrice Agou
- Institut Pasteur, Université Paris Cité, CNRS UMR 3523, Chemogenomic and Biological Screening Core Facility, C2RT, Paris, France
| | - Etienne Simon-Lorière
- Institut Pasteur, Université Paris Cité, G5 Evolutionary Genomics of RNA Viruses, Paris, France
| | - Sylvie van der Werf
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Molecular Genetics of RNA Viruses, National Reference Center for Respiratory Viruses, Paris, France
| | - Xavier de Lamballerie
- Unité des Virus Émergents (UVE: Aix-Marseille University - IRD 190 - Inserm 1207), Marseille, France
| |
Collapse
|
48
|
In-Depth Characterization of Full-Length Archived Viral Genomes after Nine Years of Posttreatment HIV Control. Microbiol Spectr 2023; 11:e0326722. [PMID: 36692300 PMCID: PMC9927157 DOI: 10.1128/spectrum.03267-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
In the search for control of human immunodeficiency virus type 1 (HIV-1) infection without antiretroviral therapy, posttreatment controllers (PTCs) are models of HIV remission. To better understand their mechanisms of control, we characterized the HIV blood reservoirs of 8 PTCs (median of 9.4 years after treatment interruption) in comparison with those of 13 natural HIV infection controllers (HICs) (median of 18 years of infection) and with those of individuals receiving efficient antiretroviral therapy initiated during either primary HIV infection (PHIs; n = 8) or chronic HIV infection (CHIs; n = 6). This characterization was performed with single-genome amplification and deep sequencing. The proviral diversity, which reflects the history of past viral replication, was lower in the PTCs, PHIs, and aviremic HICs than in the blipper HICs and CHIs. The proportions of intact and defective proviruses among the proviral pool in PTCs were not significantly different from those of other groups. When looking at the quantities of proviruses per million peripheral blood mononuclear cells (PBMCs), they had similar amounts of intact proviruses as other groups but smaller amounts of defective proviruses than CHIs, suggesting a role of these forms in HIV pathogenesis. Two HICs but none of the PTCs harbored only proviruses with deletion in nef; these attenuated strains could contribute to viral control in these participants. We show, for the first time, the presence of intact proviruses and low viral diversity in PTCs long after treatment interruption, as well as the absence of evolution of the proviral quasispecies in subsequent samples. This reflects low residual replication over time. Further data are necessary to confirm these results. IMPORTANCE Most people living with HIV need antiretroviral therapy to control their infection and experience viral relapse in case of treatment interruption, because of viral reservoir (proviruses) persistence. Knowing that proviruses are very diverse and most of them are defective in treated individuals, we aimed to characterize the HIV blood reservoirs of posttreatment controllers (PTCs), rare models of drug-free remission, in comparison with spontaneous controllers and treated individuals. At a median time of 9 years after treatment interruption, which is unprecedented in the literature, we showed that the proportions and quantities of intact proviruses were similar between PTCs and other individuals. Unlike 2/7 spontaneous controllers who harbored only nef-deleted proviruses, which are attenuated strains, which could contribute to their control, no such case was observed in PTCs. Furthermore, PTCs displayed low viral genetic diversity and no evolution of their reservoirs, indicating very low residual replication, despite the presence of intact proviruses.
Collapse
|
49
|
Vakirlis N, Vance Z, Duggan KM, McLysaght A. De novo birth of functional microproteins in the human lineage. Cell Rep 2022; 41:111808. [PMID: 36543139 PMCID: PMC10073203 DOI: 10.1016/j.celrep.2022.111808] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 06/21/2022] [Accepted: 11/18/2022] [Indexed: 12/24/2022] Open
Abstract
Small open reading frames (sORFs) can encode functional "microproteins" that perform crucial biological tasks. However, their size makes them less amenable to genomic analysis, and their origins and conservation are poorly understood. Given their short length, it is plausible that some of these functional microproteins have recently originated entirely de novo from noncoding sequences. Here we sought to identify such cases in the human lineage by reconstructing the evolutionary origins of human microproteins previously found to have measurable, statistically significant fitness effects. By tracing the formation of each ORF and its transcriptional activation, we show that novel microproteins with significant phenotypic effects have emerged de novo throughout animal evolution, including two after the human-chimpanzee split. Notably, traditional methods for assessing coding potential would miss most of these cases. This evidence demonstrates that the functional potential intrinsic to sORFs can be relatively rapidly and frequently realized through de novo gene emergence.
Collapse
Affiliation(s)
- Nikolaos Vakirlis
- Institute for Fundamental Biomedical Research, Biomedical Sciences Research Center "Alexander Fleming", Vari, Greece.
| | - Zoe Vance
- Smurfit Institute of Genetics, Trinity College Dublin, University of Dublin, Dublin, Ireland
| | - Kate M Duggan
- Smurfit Institute of Genetics, Trinity College Dublin, University of Dublin, Dublin, Ireland
| | - Aoife McLysaght
- Smurfit Institute of Genetics, Trinity College Dublin, University of Dublin, Dublin, Ireland.
| |
Collapse
|
50
|
Díaz-Escandón D, Tagirdzhanova G, Vanderpool D, Allen CCG, Aptroot A, Češka O, Hawksworth DL, Huereca A, Knudsen K, Kocourková J, Lücking R, Resl P, Spribille T. Genome-level analyses resolve an ancient lineage of symbiotic ascomycetes. Curr Biol 2022; 32:5209-5218.e5. [PMID: 36423639 DOI: 10.1016/j.cub.2022.11.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 08/30/2022] [Accepted: 11/07/2022] [Indexed: 11/24/2022]
Abstract
Ascomycota account for about two-thirds of named fungal species.1 Over 98% of known Ascomycota belong to the Pezizomycotina, including many economically important species as well as diverse pathogens, decomposers, and mutualistic symbionts.2 Our understanding of Pezizomycotina evolution has until now been based on sampling traditionally well-defined taxonomic classes.3,4,5 However, considerable diversity exists in undersampled and uncultured, putatively early-diverging lineages, and the effect of these on evolutionary models has seldom been tested. We obtained genomes from 30 putative early-diverging lineages not included in recent phylogenomic analyses and analyzed these together with 451 genomes covering all available ascomycete genera. We show that 22 of these lineages, collectively representing over 600 species, trace back to a single origin that diverged from the common ancestor of Eurotiomycetes and Lecanoromycetes over 300 million years BP. The new clade, which we recognize as a more broadly defined Lichinomycetes, includes lichen and insect symbionts, endophytes, and putative mycorrhizae and encompasses a range of morphologies so disparate that they have recently been placed in six different taxonomic classes. To test for shared hidden features within this group, we analyzed genome content and compared gene repertoires to related groups in Ascomycota. Regardless of their lifestyle, Lichinomycetes have smaller genomes than most filamentous Ascomycota, with reduced arsenals of carbohydrate-degrading enzymes and secondary metabolite gene clusters. Our expanded genome sample resolves the relationships of numerous "orphan" ascomycetes and establishes the independent evolutionary origins of multiple mutualistic lifestyles within a single, morphologically hyperdiverse clade of fungi.
Collapse
Affiliation(s)
- David Díaz-Escandón
- Department of Biological Sciences CW405, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Gulnara Tagirdzhanova
- Department of Biological Sciences CW405, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Dan Vanderpool
- National Genomics Center for Wildlife and Fish Conservation, Rocky Mountain Research Station, 800 E Beckwith, Missoula, MT 59812, USA
| | - Carmen C G Allen
- Department of Biological Sciences CW405, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - André Aptroot
- Laboratório de Botânica / Liquenologia, Instituto de Biociências Universidade Federal de Mato Grosso do Sul, Avenida Costa e Silva s/n Bairro Universitário, Campo Grande, Mato Grosso do Sul CEP 79070-900, Brazil
| | | | - David L Hawksworth
- Comparative Fungal Biology, Royal Botanic Gardens, Kew, Surrey TW9 3DS, UK; Department of Life Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, UK; Jilin Agricultural University, Changchun, Jilin Province 130118, China
| | - Alejandro Huereca
- Department of Biological Sciences CW405, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Kerry Knudsen
- Czech University of Life Sciences, Faculty of Environmental Sciences, Department of Ecology, Kamýcká 129, Praha-Suchdol 165 00, Czech Republic
| | - Jana Kocourková
- Czech University of Life Sciences, Faculty of Environmental Sciences, Department of Ecology, Kamýcká 129, Praha-Suchdol 165 00, Czech Republic
| | - Robert Lücking
- Botanischer Garten, Freie Universität Berlin, Königin-Luise-Straße 6-8, 14195 Berlin, Germany
| | - Philipp Resl
- Institute of Biology, University of Graz, Universitätsplatz 2, 8010 Graz, Austria
| | - Toby Spribille
- Department of Biological Sciences CW405, University of Alberta, Edmonton, AB T6G 2R3, Canada.
| |
Collapse
|