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Zhang X, Shi F, Zhang S, Hosen MI, Zhao C. The Diversity and Taxonomy of Thelephoraceae (Basidiomycota) with Descriptions of Four Species from Southwestern China. J Fungi (Basel) 2024; 10:775. [PMID: 39590694 PMCID: PMC11595788 DOI: 10.3390/jof10110775] [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: 09/26/2024] [Revised: 11/03/2024] [Accepted: 11/06/2024] [Indexed: 11/28/2024] Open
Abstract
Taxonomy plays a central role in understanding the diversity of life, translating the products of biological exploration and discovery specimens and observations into systems of names that settle a "classification home" to taxa. The ectomycorrhizal basidiomycetes family Thelephoraceae has been understudied in subtropical ecosystems. Many species of Thelephoraceae are important edible and medicinal fungi, with substantial economic value. Four new species, Thelephora resupinata, T. subtropica, T. yunnanensis, and Tomentella tenuifarinacea, are proposed based on a combination of the morphological features and molecular evidence. Thelephora resupinata is characterized by the resupinate basidiomata having a tuberculate pileal surface hymenial, and the presence of the subglobose to globose basidiospores (9-12 × 7-9 µm). T. subtropica is solitary coriaceous infundibuliform gray-brown basidiomata with a presence of the subclavate basidia and subglobose to globose basidiospores (6-8 × 5-7 µm). T. yunnanensis is typical of the laterally stipitate basidiomata having a smooth, umber to coffee hymenial surface, a monomitic hyphal system with clamped generative hyphae, and the presence of the subglobose basidiospores (7-10 × 6-8 µm). Tomentella tenuifarinacea is typical of the arachnoid basidiomata having a smooth, gray, or dark gray hymenial surface, a monomitic hyphal system with clamped generative hyphae, and the presence of the subglobose to globose basidiospores (7-9 × 6-8 µm). Sequences of ITS+nLSU+mtSSU genes were used for the phylogentic analyses using maximum likelihood, maximum parsimony, and Bayesian inference methods. The three genes' (ITS+nLSU+mtSSU) phylogenetic analysis showed that the genera Thelephora and Tomentella grouped together within the family Thelephoraceae and three new species were nested into the genus Thelephora, and one new species was nested into the genus Tomentella.
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Affiliation(s)
- Xiaojie Zhang
- Yunnan Provincial Key Laboratory for Conservation and Utilization of In-Forest Resource, The Key Laboratory of Forest Resources Conservation and Utilization in the Southwest Mountains of China Ministry of Education, Southwest Forestry University, Kunming 650224, China; (X.Z.); (F.S.); (S.Z.); (M.I.H.)
- College of Forestry, Southwest Forestry University, Kunming 650224, China
| | - Fulei Shi
- Yunnan Provincial Key Laboratory for Conservation and Utilization of In-Forest Resource, The Key Laboratory of Forest Resources Conservation and Utilization in the Southwest Mountains of China Ministry of Education, Southwest Forestry University, Kunming 650224, China; (X.Z.); (F.S.); (S.Z.); (M.I.H.)
- College of Forestry, Southwest Forestry University, Kunming 650224, China
| | - Sicheng Zhang
- Yunnan Provincial Key Laboratory for Conservation and Utilization of In-Forest Resource, The Key Laboratory of Forest Resources Conservation and Utilization in the Southwest Mountains of China Ministry of Education, Southwest Forestry University, Kunming 650224, China; (X.Z.); (F.S.); (S.Z.); (M.I.H.)
- College of Forestry, Southwest Forestry University, Kunming 650224, China
| | - Md. Iqbal Hosen
- Yunnan Provincial Key Laboratory for Conservation and Utilization of In-Forest Resource, The Key Laboratory of Forest Resources Conservation and Utilization in the Southwest Mountains of China Ministry of Education, Southwest Forestry University, Kunming 650224, China; (X.Z.); (F.S.); (S.Z.); (M.I.H.)
- College of Forestry, Southwest Forestry University, Kunming 650224, China
| | - Changlin Zhao
- Yunnan Provincial Key Laboratory for Conservation and Utilization of In-Forest Resource, The Key Laboratory of Forest Resources Conservation and Utilization in the Southwest Mountains of China Ministry of Education, Southwest Forestry University, Kunming 650224, China; (X.Z.); (F.S.); (S.Z.); (M.I.H.)
- College of Forestry, Southwest Forestry University, Kunming 650224, China
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202
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Ouattara A, Kéré D, Hoareau M, Koïta K, Lefeuvre P, Lett JM. A new monopartite begomovirus infecting Melochia tomentosa in Burkina Faso. Arch Virol 2024; 169:240. [PMID: 39510996 DOI: 10.1007/s00705-024-06167-4] [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: 08/04/2024] [Accepted: 09/25/2024] [Indexed: 11/15/2024]
Abstract
This is the first description of the complete genome sequence of a newly characterized monopartite begomovirus isolated from an asymptomatic uncultivated plant, Melochia tomentosa, collected in Burkina Faso. The sequence was obtained through rolling-circle amplification, cloning, and Sanger sequencing. The provisional species name "Begomovirus melochiae" and common virus name "melochia associated virus" (MeAV) are proposed. The MeAV genome was found to share the most nucleotide sequence similarity with three African monopartite begomoviruses: tomato curly stunt virus (74%), pepper yellow vein Mali virus (73%), and tomato leaf curl Cameroon virus (73%). Phylogenetic analysis confirmed its relationship to Old World monopartite begomoviruses. The discovery of MeAV in an uncultivated and asymptomatic plant provides a further example of the high diversity of begomoviruses in sub-Saharan African ecosystems.
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Affiliation(s)
- Alassane Ouattara
- CIRAD, UMR PVBMT, 97410, Saint-Pierre, La Réunion, France.
- Laboratoire Biosciences, Université Joseph KI-ZERBO, 03 BP 7021 Ouagadougou 03, Ouagadougou, Burkina Faso.
| | - Dadjata Kéré
- Laboratoire Biosciences, Université Joseph KI-ZERBO, 03 BP 7021 Ouagadougou 03, Ouagadougou, Burkina Faso
| | | | - Kadidia Koïta
- Laboratoire Biosciences, Université Joseph KI-ZERBO, 03 BP 7021 Ouagadougou 03, Ouagadougou, Burkina Faso
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203
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Magpali L, Ramos E, Picorelli A, Freitas L, Nery MF. Molecular evolution of toothed whale genes reveals adaptations to echolocating in different environments. BMC Genomics 2024; 25:1049. [PMID: 39506652 PMCID: PMC11542384 DOI: 10.1186/s12864-024-10910-1] [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: 03/27/2024] [Accepted: 10/16/2024] [Indexed: 11/08/2024] Open
Abstract
BACKGROUND Echolocation was a key development in toothed whale evolution, enabling their adaptation and diversification across various environments. Previous bioacoustic and morphological studies suggest that environmental pressures have influenced the evolution of echolocation in toothed whales. This hypothesis demands further investigation, especially regarding the molecular mechanisms involved in the adaptive radiation of toothed whales across multiple habitats. Here we show that the coding sequences of four hearing genes involved in echolocation (CDH23, prestin, TMC1, and CLDN14) have different signatures of molecular evolution among riverine, coastal, and oceanic dolphins, suggesting that the evolutionary constraints of these habitats shaped the underlying genetic diversity of the toothed whale sonar. RESULTS Our comparative analysis across 37 odontocete species revealed patterns of accelerated evolution within coastal and riverine lineages, supporting the hypothesis that shallow habitats pose specific selective pressures to sonar propagation, which are not found in the deep ocean. All toothed whales with genes evolving under positive selection are shallow coastal species, including three species that have recently diverged from freshwater lineages (Cephalorhynchus commersonii, Sotalia guianensis, and Orcaella heinsohni - CDH23), and three species that operate specialized Narrow Band High Frequency (NBHF) Sonars (Phocoena sinus - prestin, Neophocaena phocaenoides - TMC1 and Cephalorhynchus commersonii - CDH23). For river dolphins and deep-diving toothed whales, we found signatures of positive selection and molecular convergence affecting specific sites on CDH23, TMC1, and prestin. Positively selected sites (PSS) were different in number, identity, and substitution rates (dN/dS) across riverine, coastal, and oceanic toothed whales. CONCLUSION Here we shed light on potential molecular mechanisms underlying the diversification of toothed whale echolocation. Our results suggest that toothed whale hearing genes changed under different selective pressures in coastal, riverine, and oceanic environments.
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Affiliation(s)
- L Magpali
- Laboratório de Genômica Evolutiva, Departamento de Genética, Microbiologia e Imunologia, Universidade Estadual de Campinas (Unicamp), Evolução, Campinas, São Paulo, Brasil
- Department of Biology, Dalhousie University, Halifax, NS, Canada
| | - E Ramos
- Laboratório de Genômica Evolutiva, Departamento de Genética, Microbiologia e Imunologia, Universidade Estadual de Campinas (Unicamp), Evolução, Campinas, São Paulo, Brasil
- Zoological Institute, Department of Environmental Science, University of Basel, Basel, Switzerland
- Natural History Museum Basel, Basel, Switzerland
| | - A Picorelli
- Laboratório de Genômica Evolutiva, Departamento de Genética, Microbiologia e Imunologia, Universidade Estadual de Campinas (Unicamp), Evolução, Campinas, São Paulo, Brasil
| | - L Freitas
- Laboratório de Genômica Evolutiva, Departamento de Genética, Microbiologia e Imunologia, Universidade Estadual de Campinas (Unicamp), Evolução, Campinas, São Paulo, Brasil
| | - M F Nery
- Laboratório de Genômica Evolutiva, Departamento de Genética, Microbiologia e Imunologia, Universidade Estadual de Campinas (Unicamp), Evolução, Campinas, São Paulo, Brasil.
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204
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Xia J, Qiu YY, Zhen Y, Chen Z, Li H, Chen B, Zou J, Jiang F. Mercury Immobilization without Methylation in Sulfidogenic Systems Dominated by Sulfur Disproportionating Bacteria. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:19714-19724. [PMID: 39360610 DOI: 10.1021/acs.est.4c03973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/04/2024]
Abstract
The sulfidogenic process mediated by sulfate-reducing bacteria (SRB) is not ideal for treating mercury (Hg)-bearing wastewater due to the risk of methylmercury (MeHg) production. Addressing this challenge, our study demonstrated that, under S0-rich conditions and without organic additives, sulfidogenic communities dominated by sulfur-disproportionating bacteria (SDB) can effectively remove Hg(II) and prevent MeHg production. Using various inocula, we successfully established biological sulfidogenic systems driven separately by SDB and SRB. Batch experiments revealed that SDB cultures completely removed Hg(II) from the solution as HgS. Remarkably, no MeHg production was observed in the SDB cultures, while an average concentration of 0.32 μg/L of MeHg was detected in the SRB cultures. The absence of MeHg production in the SDB cultures could be mainly attributed to the cultivation conditions that reshaped the microbial community, resulting in a rapid decline of SRB-dominated Hg-methylating microorganisms. Consequently, the average abundance of the hgcA gene was 28 times lower than the levels before cultivation. Additionally, we found that the enriched Dissulfurimicrobium sp. bin121 can produce biogenic sulfide through sulfur disproportionation but lacks the hgcA gene, rendering it incapable of methylating Hg. Overall, we propose a novel biotechnology driven by SDB that can safely and sustainably treat Hg-bearing wastewater.
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Affiliation(s)
- Juntao Xia
- Guangdong Provincial Key Lab of Environmental Pollution Control and Remediation Technology, School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, China
| | - Yan-Ying Qiu
- Guangdong Provincial Key Lab of Environmental Pollution Control and Remediation Technology, School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, China
| | - Yuming Zhen
- Guangdong Provincial Key Lab of Environmental Pollution Control and Remediation Technology, School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, China
| | - Zhe Chen
- Guangdong Provincial Key Lab of Environmental Pollution Control and Remediation Technology, School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, China
| | - Hao Li
- Guangdong Provincial Key Lab of Environmental Pollution Control and Remediation Technology, School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, China
| | - Boyu Chen
- Guangdong Provincial Key Lab of Environmental Pollution Control and Remediation Technology, School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, China
| | - Jiahui Zou
- Guangdong Provincial Key Lab of Environmental Pollution Control and Remediation Technology, School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, China
| | - Feng Jiang
- Guangdong Provincial Key Lab of Environmental Pollution Control and Remediation Technology, School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, China
- Guangdong Provincial Engineering Research Center of Low-Carbon Technology for Water Pollution Control, Sun Yat-sen University, Guangzhou 510275, China
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205
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Tolman ER, Beatty CD, Kohli MK, Abbott J, Bybee SM, Frandsen PB, Stephen Gosnell J, Guralnick R, Kalkman VJ, Newton LG, Suvorov A, Ware JL. A molecular phylogeny of the Petaluridae (Odonata: Anisoptera): A 160-Million-Year-Old story of drift and extinction. Mol Phylogenet Evol 2024; 200:108185. [PMID: 39209047 DOI: 10.1016/j.ympev.2024.108185] [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: 04/10/2024] [Revised: 08/12/2024] [Accepted: 08/26/2024] [Indexed: 09/04/2024]
Abstract
Petaluridae (Odonata: Anisoptera) is a relict dragonfly family, having diverged from its sister family in the Jurassic, of eleven species that are notable among odonates (dragonflies and damselflies) for their exclusive use of fen and bog habitats, their burrowing behavior as nymphs, large body size as adults, and extended lifespans. To date, several nodes within this family remain unresolved, limiting the study of the evolution of this peculiar family. Using an anchored hybrid enrichment dataset of over 900 loci we reconstructed the species tree of Petaluridae. To estimate the temporal origin of the genera within this family, we used a set of well-vetted fossils and a relaxed molecular clock model in a divergence time estimation analysis. We estimate that Petaluridae originated in the early Cretaceous and confirm the existence of monophyletic Gondwanan and Laurasian clades within the family. Our relaxed molecular clock analysis estimated that these clades diverged from their MRCA approximately 160 mya. Extant lineages within this family were identified to have persisted from 6 (Uropetala) to 120 million years (Phenes). Our biogeographical analyses focusing on a set of key regions suggest that divergence within Petaluridae is largely correlated with continental drift, the exposure of land bridges, and the development of mountain ranges. Our results support the hypothesis that species within Petaluridae have persisted for tens of millions of years, with little fossil evidence to suggest widespread extinction in the family, despite optimal conditions for the fossilization of nymphs. Petaluridae appear to be a rare example of habitat specialists that have persisted for tens of millions of years.
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Affiliation(s)
- Ethan R Tolman
- American Museum of Natural History, Department of Invertebrate Zoology, New York, 10024; Department of Biological Sciences, Virginia Tech, Blacksburg, VA; Conservation Connection Foundation, Boise, ID.
| | - Christopher D Beatty
- American Museum of Natural History, Department of Invertebrate Zoology, New York, 10024; Program for Conservation Genomics, Department of Biology, Stanford University
| | - Manpreet K Kohli
- American Museum of Natural History, Department of Invertebrate Zoology, New York, 10024; Conservation Connection Foundation, Boise, ID; Department of Natural Sciences, Baruch College, New York
| | - John Abbott
- Alabama Museum of Natural History and Department of Research and Collections, The University of Alabama
| | - Seth M Bybee
- Department of Biology and Monte L. Bean Museum, Brigham Young University, Provo, UT
| | - Paul B Frandsen
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT
| | - J Stephen Gosnell
- Department of Natural Sciences, Baruch College, New York; PhD Program in Biology, The Graduate Center of the City University of New York, 365 Fifth Avenue, Room 4315, New York, 10016
| | - Robert Guralnick
- Florida Museum of Natural History, University of Florida, Gainesville, FL
| | - V J Kalkman
- Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA Leiden
| | - Lacie G Newton
- American Museum of Natural History, Department of Invertebrate Zoology, New York, 10024
| | - Anton Suvorov
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA
| | - Jessica L Ware
- American Museum of Natural History, Department of Invertebrate Zoology, New York, 10024
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206
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Thaler M, Labarre A, Lovejoy C. Environmental selection and advective transport shape the distribution of two cyst-forming Acantharia clades in the Canadian Arctic. JOURNAL OF PLANKTON RESEARCH 2024; 46:542-554. [PMID: 39664261 PMCID: PMC11629782 DOI: 10.1093/plankt/fbae051] [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: 03/27/2024] [Accepted: 08/29/2024] [Indexed: 12/13/2024]
Abstract
Anthropogenic induced climate perturbations are seen in changes in oceanic circulation patterns, and Arctic water masses defined by salinity are vulnerable to change. Biogeography of marine microbial eukaryotes is expected to be impacted by changes in local environmental conditions and advective processes, but tracking the extent of plankton distribution requires understanding routes for both active and passive tracers. To identify such tracers, we focused on samples collected in the western (Canada Basin) and eastern (Nares Strait); extremes of the Canadian High Arctic that are connected by an east flowing current north of Canada. Sequencing of the V4 region of 18S rRNA revealed that Acantharia, a taxonomically and functionally diverse group of large planktonic protists, were particularly common. Arctic acantharians in our study were dominated by two clades belonging to cyst-forming groups. The distribution of one clade suggested successful advective transport from the Pacific sourced water in the Beaufort Gyre to southern Nares Strait, with cells transported along the northern shelf of the Canadian Arctic. A second clade appeared to be a resident taxon of the Canada Basin whose distribution correlated to local environmental conditions, and detection in deeper samples would be consistent with swarmer formation enabling reestablishment the following year.
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Affiliation(s)
- Mary Thaler
- Département de Biologie and Institut de Biologie Intégrative et des Systèmes (IBIS), 1045 Avenue de la Medicine, Université Laval, Québec City, Québec, G1V OA6, Canada
| | - Aurélie Labarre
- Département de Biologie and Institut de Biologie Intégrative et des Systèmes (IBIS), 1045 Avenue de la Medicine, Université Laval, Québec City, Québec, G1V OA6, Canada
| | - Connie Lovejoy
- Département de Biologie and Institut de Biologie Intégrative et des Systèmes (IBIS), 1045 Avenue de la Medicine, Université Laval, Québec City, Québec, G1V OA6, Canada
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207
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Fletcher J, Smith A, Honan A, Leary W, Dabney T, Branco S. Inter- and intra-specific metal tolerance variation in ectomycorrhizal fungal Suillus species. MYCORRHIZA 2024; 34:417-427. [PMID: 39037611 DOI: 10.1007/s00572-024-01162-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Accepted: 07/04/2024] [Indexed: 07/23/2024]
Abstract
Soil metal contamination can affect growth, metabolism, and reproduction of organisms, and can lead to death. However, some fungi have evolved metal tolerance and are able to live in contaminated soils. Species in the ectomycorrhizal genus Suillus from Europe and Asia display variation in metal tolerance, yet it is unknown whether this is a widespread trait in the genus and whether it occurs in North America. Here we investigate cadmium (Cd) and zinc (Zn) tolerance in S. brevipes and S. tomentosus isolates collected from sites in the Rocky Mountains of Colorado displaying different metal content. In line with previous findings for other Suillus species, we hypothesized (1) S. brevipes and S. tomentosus to display intra-specific metal tolerance variation, (2) Zn and Cd tolerance to be correlated to soil metal content, and (3) tolerant isolates to show lower metal tissue content compared to sensitive isolates (due to increased metal exclusion). We found ample intra- and inter-specific Zn and Cd tolerance variation in both S. brevipes and S. tomentosus, but no correlation between soil metal content and tolerance. There was a negative correlation between tolerance level and Zn uptake, indicating an exclusion-based Zn tolerance strategy. Sensitive and tolerant isolates showed no difference in Cd accumulation, indicating that Cd tolerance in these species is likely not dependent on exclusion. Our study sets the groundwork for further investigation into the genetic basis of Suillus metal tolerance and whether and how it impacts pine mycorrhizal partners.
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Affiliation(s)
- Jessica Fletcher
- Department of Integrative Biology, University of Colorado Denver, Denver, CO, USA.
| | - Alexander Smith
- Department of Integrative Biology, University of Colorado Denver, Denver, CO, USA
| | - Amy Honan
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, US
| | - William Leary
- Department of Integrative Biology, University of Colorado Denver, Denver, CO, USA
| | - Treya Dabney
- Department of Integrative Biology, University of Colorado Denver, Denver, CO, USA
| | - Sara Branco
- Department of Integrative Biology, University of Colorado Denver, Denver, CO, USA
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208
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Suissa JS, De La Cerda GY, Graber LC, Jelley C, Wickell D, Phillips HR, Grinage AD, Moreau CS, Specht CD, Doyle JJ, Landis JB. Data-driven guidelines for phylogenomic analyses using SNP data. APPLICATIONS IN PLANT SCIENCES 2024; 12:e11611. [PMID: 39628540 PMCID: PMC11610416 DOI: 10.1002/aps3.11611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 05/01/2024] [Accepted: 05/03/2024] [Indexed: 12/06/2024]
Abstract
Premise There is a general lack of consensus on the best practices for filtering of single-nucleotide polymorphisms (SNPs) and whether it is better to use SNPs or include flanking regions (full "locus") in phylogenomic analyses and subsequent comparative methods. Methods Using genotyping-by-sequencing data from 22 Glycine species, we assessed the effects of SNP vs. locus usage and SNP retention stringency. We compared branch length, node support, and divergence time estimation across 16 datasets with varying amounts of missing data and total size. Results Our results revealed five aspects of phylogenomic data usage that may be generally applicable: (1) tree topology is largely congruent across analyses; (2) filtering strictly for SNP retention (e.g., 90-100%) reduces support and can alter some inferred relationships; (3) absolute branch lengths vary by two orders of magnitude between SNP and locus datasets; (4) data type and branch length variation have little effect on divergence time estimation; and (5) phylograms alter the estimation of ancestral states and rates of morphological evolution. Discussion Using SNP or locus datasets does not alter phylogenetic inference significantly, unless researchers want or need to use absolute branch lengths. We recommend against using excessive filtering thresholds for SNP retention to reduce the risk of producing inconsistent topologies and generating low support.
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Affiliation(s)
- Jacob S. Suissa
- Department of Ecology and Evolutionary BiologyUniversity of Tennessee at KnoxvilleKnoxvilleTennesseeUSA
| | - Gisel Y. De La Cerda
- School of Integrative Plant Science, Section of Plant Biology and the L. H. Bailey HortoriumCornell UniversityIthacaNew YorkUSA
| | | | - Chloe Jelley
- Department of EntomologyCornell UniversityIthacaNew YorkUSA
| | - David Wickell
- School of Integrative Plant Science, Section of Plant Biology and the L. H. Bailey HortoriumCornell UniversityIthacaNew YorkUSA
- Boyce Thompson InstituteIthacaNew YorkUSA
| | - Heather R. Phillips
- School of Integrative Plant Science, Section of Plant Biology and the L. H. Bailey HortoriumCornell UniversityIthacaNew YorkUSA
| | - Ayress D. Grinage
- School of Integrative Plant Science, Section of Plant Biology and the L. H. Bailey HortoriumCornell UniversityIthacaNew YorkUSA
- Department of Ecology and Evolutionary BiologyCornell UniversityIthacaNew YorkUSA
| | - Corrie S. Moreau
- Department of EntomologyCornell UniversityIthacaNew YorkUSA
- Department of Ecology and Evolutionary BiologyCornell UniversityIthacaNew YorkUSA
| | - Chelsea D. Specht
- School of Integrative Plant Science, Section of Plant Biology and the L. H. Bailey HortoriumCornell UniversityIthacaNew YorkUSA
| | - Jeff J. Doyle
- School of Integrative Plant Science, Section of Plant Biology and the L. H. Bailey HortoriumCornell UniversityIthacaNew YorkUSA
| | - Jacob B. Landis
- School of Integrative Plant Science, Section of Plant Biology and the L. H. Bailey HortoriumCornell UniversityIthacaNew YorkUSA
- BTI Computational Biology Center, Boyce Thompson InstituteIthacaNew YorkUSA
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209
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Bandeira AC, Pereira FM, Leal A, Santos SPO, Barbosa AC, Souza MSPL, de Souza DR, Guimaraes N, Fonseca V, Giovanetti M, Alcantara LCJ, Lessa AAA, Saavedra RC, Tomé LMR, Iani FCM, Barros RM, Purificação SMO, de Jesus JP, Fonseca RR, Araújo MLV. Fatal Oropouche Virus Infections in Nonendemic Region, Brazil, 2024. Emerg Infect Dis 2024; 30:2370-2374. [PMID: 39269651 PMCID: PMC11521185 DOI: 10.3201/eid3011.241132] [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] [Indexed: 09/15/2024] Open
Abstract
We report acute Oropouche virus infections in 2 previously healthy women from a nonendemic region of Brazil outside the Amazon Basin. Infections rapidly progressed to hemorrhagic manifestations and fatal outcomes in 4-5 days. These cases highlight the critical need for enhanced surveillance to clarify epidemiology of this neglected disease.
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210
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Lebeau E, Dunn JC. The prevalence and immune response to coinfection by avian haemosporidians in wild Eurasian blackbirds Turdus merula. Parasitology 2024; 151:1406-1415. [PMID: 39851095 PMCID: PMC12052428 DOI: 10.1017/s0031182024000829] [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: 01/25/2024] [Revised: 07/01/2024] [Accepted: 07/02/2024] [Indexed: 01/26/2025]
Abstract
Coinfection of a host by more than 1 parasite is more common than single infection in wild environments and can have differing impacts, although coinfections have relatively rarely been quantified. Host immune responses to coinfection can contribute to infection costs but are often harder to predict than those associated with single infection, due to the influence of within-host parasite–parasite interactions on infection virulence. To first quantify coinfection in a common bird species, and then to test for immune-related impacts of coinfection, we investigated the prevalence and immune response to avian haemosporidian (genera: Plasmodium, Haemoproteus and Leucocytozoon) coinfection in wild blackbirds. Coinfection status was diagnosed using a 1-step multiplex polymerase chain reaction, immune response was quantified through white blood cell counts and heterophil: lymphocyte ratios, and parasitaemia was quantified for each infected sample. We detected high rates of haemosporidian infection and coinfection, although neither impacted immune activity, despite a significantly higher parasitaemia in individuals experiencing double vs single infection. This suggests that immune-related costs of haemosporidian single and coinfection are low in this system. This could be due to long-term host–parasite coevolution, which has decreased infection virulence, or a consequence of reduced costs associated with chronic infections compared to acute infections. Alternatively, our results may obscure immune-related costs associated with specific combinations of coinfecting haemosporidian genera, species or lineages. Future research should investigate interactions that occur between haemosporidian parasites within hosts, as well as the ways in which these interactions and resulting impacts may vary depending on parasite identity.
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Affiliation(s)
- Ellie Lebeau
- Joseph Banks Laboratories, School of Life and Environmental Sciences, University of Lincoln, Lincoln, UK
| | - Jenny C. Dunn
- Joseph Banks Laboratories, School of Life and Environmental Sciences, University of Lincoln, Lincoln, UK
- School of Biology, University of Leeds, Leeds, UK
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Tegally H, Dellicour S, Poongavanan J, Mavian C, Dor G, Fonseca V, Tagliamonte MS, Dunaiski M, Moir M, Wilkinson E, de Albuquerque CFC, Frutuoso LCV, CLIMADE Consortium, Holmes EC, Baxter C, Lessells R, Kraemer MU, Lourenço J, Alcantara LCJ, de Oliveira T, Giovanetti M. Dynamics and ecology of a multi-stage expansion of Oropouche virus in Brazil. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.10.29.24316328. [PMID: 39574858 PMCID: PMC11581102 DOI: 10.1101/2024.10.29.24316328] [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] [Indexed: 12/01/2024]
Abstract
In March 2024, the Pan American Health Organization (PAHO) issued an alert in response to a rapid increase in Oropouche fever cases across South America. Brazil has been particularly affected, reporting a novel reassortant lineage of the Oropouche virus (OROV) and expansion to previously non-endemic areas beyond the Amazon Basin. Utilising phylogeographic approaches, we reveal a multi-scale expansion process with both short and long-distance dispersal events, and diffusion velocities in line with human-mediated jumps. We identify forest cover, banana and cocoa cultivation, temperature, and human population density as key environmental factors associated with OROV range expansion. Using ecological niche modelling, we show that OROV circulated in areas of enhanced ecological suitability immediately preceding its explosive epidemic expansion in the Amazon. This likely resulted from the virus being introduced into simultaneously densely populated and environmentally favourable regions in the Amazon, such as Manaus, leading to an amplified epidemic and spread beyond the Amazon. Our study provides valuable insights into the dispersal and ecological dynamics of OROV, highlighting the role of human mobility in colonisation of new areas, and raising concern over high viral suitability along the Brazilian coast.
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Affiliation(s)
- Houriiyah Tegally
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch 7600, South Africa
| | - Simon Dellicour
- Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, Brussels, Belgium
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
- Interuniversity Institute of Bioinformatics in Brussels, Université Libre de Bruxelles, Vrije Universiteit Brussel, Brussels, Belgium
| | - Jenicca Poongavanan
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch 7600, South Africa
| | - Carla Mavian
- Emerging Pathogens Institute, Department of Pathology, College of Medicine, University of Florida, Gainesville, Florida, USA
- Global Health Program Smithsonian’s National Zoo & Conservation Biology Institute, DC, USA
- Global Health Institute, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Graeme Dor
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch 7600, South Africa
| | - Vagner Fonseca
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch 7600, South Africa
- Department of Exact and Earth Science, University of the State of Bahia, Salvador 41192-010, Brazil
- Instituto René Rachou, Fundação Oswaldo Cruz, Minas Gerais, Brazil
| | | | - Marcel Dunaiski
- Computer Science Division, Department of Mathematical Sciences, Stellenbosch University, Stellenbosch, South Africa
| | - Monika Moir
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch 7600, South Africa
| | - Eduan Wilkinson
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch 7600, South Africa
| | | | - Livia C. V. Frutuoso
- Coordenadora-Geral de Vigilância de Arboviroses, Brazilian Ministry of Health, Brazil
| | | | - Edward C. Holmes
- School of Medical Sciences, University of Sydney, Sydney, NSW, Australia
| | - Cheryl Baxter
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch 7600, South Africa
| | - Richard Lessells
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban 4001, South Africa
| | - Moritz U.G. Kraemer
- Pandemic Sciences Institute, University of Oxford, UK
- Department of Biology, University of Oxford, Oxford,UK
| | - José Lourenço
- BioISI (Biosystems and Integrative Sciences Institute), University of Lisbon, Lisbon, Portugal
- Universidade Católica Portuguesa, Católica Medical School, Católica Biomedical Research Center, Lisboa, Portugal
| | | | - Tulio de Oliveira
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch 7600, South Africa
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban 4001, South Africa
| | - Marta Giovanetti
- Department of Sciences and Technologies for Sustainable Development and One Health, Università Campus Bio-Medico di Roma, Rome, Italy
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212
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Yuan Q, Li Y, Dai Y, Wang K, Wang Y, Zhao C. Morphological and molecular identification for four new wood-inhabiting species of Lyomyces (Basidiomycota) from China. MycoKeys 2024; 110:67-92. [PMID: 39512912 PMCID: PMC11541102 DOI: 10.3897/mycokeys.110.133108] [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: 07/25/2024] [Accepted: 10/15/2024] [Indexed: 11/15/2024] Open
Abstract
Fungi are one of the most diverse groups of organisms on Earth, in which the wood-inhabiting fungi play an important role in forest ecosystem processes and functions. Four new wood-inhabiting fungi, Lyomyceshengduanensis, L.niveomarginatus, L.wumengshanensis and L.zhaotongensis, are proposed, based on morphological features and molecular evidence. Lyomyceshengduanensis differs in the brittle basidiomata with pruinose hymenial surface, a monomitic hyphal system and ellipsoid basidiospores (3.5-6 × 3-4.5 µm). Lyomycesniveomarginatus is distinguished by the subceraceous basidiomata with crackled hymenial surface, a monomitic hyphal system and ellipsoid basidiospores (4.5-7 × 3-4 µm). Lyomyceswumengshanensis is distinguished by the grandinioid hymenial surface, a monomitic hyphal system and ellipsoid to broad ellipsoid basidiospores (4-6 × 3-5 µm). Lyomyceszhaotongensis is unique in the grandinioid hymenial surface, a monomitic hyphal system and broadly ellipsoid basidiospores measuring as 2.6-3.5 × 2.5-3 µm. Sequences of ITS and nLSU rRNA markers of the studied samples were generated and phylogenetic analyses were performed using the Maximum Likelihood, Maximum Parsimony and Bayesian Inference methods. The phylogram, based on the ITS+nLSU rDNA gene regions, included three genera within the Schizoporaceae viz. Fasciodontia, Lyomyces and Xylodon, in which the four new species were grouped into Lyomyces. The phylogenetic tree inferred from the ITS sequences highlighted that L.hengduanensis group with L.zhaotongensis and then closely grouped with L.crustosus, L.ochraceoalbus, and L.vietnamensis. The new taxon L.niveomarginatus was retrieved as a sister to L.juniperi. The new species L.wumengshanensis was sister to L.macrosporus. The new taxon L.zhaotongensis grouped with L.hengduanensis and then closely grouped with L.crustosus, L.ochraceoalbus and L.vietnamensis.
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Affiliation(s)
- Qi Yuan
- The Key Laboratory of Forest Resources Conservation and Utilization in the Southwest Mountains of China Ministry of Education, Key Laboratory of National Forestry and Grassland Administration on Biodiversity Conservation in Southwest China, Yunnan Provincial Key Laboratory for Conservation and Utilization of In-forest Resource, Southwest Forestry University, Kunming 650224, China
| | - Yunchao Li
- The Key Laboratory of Forest Resources Conservation and Utilization in the Southwest Mountains of China Ministry of Education, Key Laboratory of National Forestry and Grassland Administration on Biodiversity Conservation in Southwest China, Yunnan Provincial Key Laboratory for Conservation and Utilization of In-forest Resource, Southwest Forestry University, Kunming 650224, China
| | - Yunfei Dai
- The Key Laboratory of Forest Resources Conservation and Utilization in the Southwest Mountains of China Ministry of Education, Key Laboratory of National Forestry and Grassland Administration on Biodiversity Conservation in Southwest China, Yunnan Provincial Key Laboratory for Conservation and Utilization of In-forest Resource, Southwest Forestry University, Kunming 650224, China
| | - Kunyan Wang
- The Key Laboratory of Forest Resources Conservation and Utilization in the Southwest Mountains of China Ministry of Education, Key Laboratory of National Forestry and Grassland Administration on Biodiversity Conservation in Southwest China, Yunnan Provincial Key Laboratory for Conservation and Utilization of In-forest Resource, Southwest Forestry University, Kunming 650224, China
| | - Yixuan Wang
- College of Forestry, Southwest Forestry University, Kunming 650224, China
| | - Changlin Zhao
- The Key Laboratory of Forest Resources Conservation and Utilization in the Southwest Mountains of China Ministry of Education, Key Laboratory of National Forestry and Grassland Administration on Biodiversity Conservation in Southwest China, Yunnan Provincial Key Laboratory for Conservation and Utilization of In-forest Resource, Southwest Forestry University, Kunming 650224, China
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213
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Chrysostomou AC, The COMESSAR Network, Kostrikis LG. Into the Cauldron of the Variant Soup: Insights into the Molecular Epidemiology and Transition to Endemicity of SARS-CoV-2 in Cyprus (November 2022-February 2024). Viruses 2024; 16:1686. [PMID: 39599801 PMCID: PMC11599100 DOI: 10.3390/v16111686] [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: 09/24/2024] [Revised: 10/23/2024] [Accepted: 10/24/2024] [Indexed: 11/29/2024] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic, driven by the emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has been characterized by the virus's ongoing evolution, leading to the appearance of more transmissible variants that have often triggered infection surges. In this study, we analyzed the SARS-CoV-2 epidemic in Cyprus, utilizing 1627 viral sequences from infected individuals between November 2022 and February 2024. Over this period, 251 distinct lineages and sublineages were identified, predominantly categorized into three groups: Omicron 5, XBB, and JN.1 (parental lineage BA.2.86), all of which harbor S protein mutations linked to enhanced transmissibility and immune escape. Despite the relatively low numbers of new infections during this period, and the lack of any major waves, unlike earlier phases of the pandemic, these lineages demonstrated varying periods of dominance, with Omicron 5 prevailing from November 2022 to February 2023, XBB variants leading from March to November 2023, and JN.1 generating a wavelet from December 2023 to February 2024. These findings suggest that the SARS-CoV-2 epidemic in Cyprus has reached endemicity, with new variants gradually replacing previously circulating variants irrespective of seasonal patterns. This study highlights the critical importance of ongoing surveillance of SARS-CoV-2 evolution in Cyprus and emphasizes the role of preventive measures in limiting virus transmission, providing valuable insights for safeguarding public health.
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Affiliation(s)
| | | | - Leondios G. Kostrikis
- Department of Biological Sciences, University of Cyprus, Aglantzia, 2109 Nicosia, Cyprus
- Cyprus Academy of Sciences, Letters, and Arts, 60-68 Phaneromenis Street, 1011 Nicosia, Cyprus
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214
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Smith CH, Mejia-Trujillo R, Havird JC. Mitonuclear compatibility is maintained despite relaxed selection on male mitochondrial DNA in bivalves with doubly uniparental inheritance. Evolution 2024; 78:1790-1803. [PMID: 38995057 PMCID: PMC11519007 DOI: 10.1093/evolut/qpae108] [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: 11/17/2023] [Revised: 06/03/2024] [Accepted: 07/11/2024] [Indexed: 07/13/2024]
Abstract
Mitonuclear coevolution is common in eukaryotes, but bivalve lineages that have doubly uniparental inheritance (DUI) of mitochondria may be an interesting example. In this system, females transmit mtDNA (F mtDNA) to all offspring, while males transmit a different mtDNA (M mtDNA) solely to their sons. Molecular evolution and functional data suggest oxidative phosphorylation (OXPHOS) genes encoded in M mtDNA evolve under relaxed selection due to their function being limited to sperm only (vs. all other tissues for F mtDNA). This has led to the hypothesis that mitonuclear coevolution is less important for M mtDNA. Here, we use comparative phylogenetics, transcriptomics, and proteomics to understand mitonuclear interactions in DUI bivalves. We found nuclear OXPHOS proteins coevolve and maintain compatibility similarly with both F and M mtDNA OXPHOS proteins. Mitochondrial recombination did not influence mitonuclear compatibility and nuclear-encoded OXPHOS genes were not upregulated in tissues with M mtDNA to offset dysfunction. Our results support that selection maintains mitonuclear compatibility with F and M mtDNA despite relaxed selection on M mtDNA. Strict sperm transmission, lower effective population size, and higher mutation rates may explain the evolution of M mtDNA. Our study highlights that mitonuclear coevolution and compatibility may be broad features of eukaryotes.
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Affiliation(s)
- Chase H Smith
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, United States
| | - Raquel Mejia-Trujillo
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, United States
| | - Justin C Havird
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, United States
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215
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Ramaekers K, Keyaerts E, Houspie L, Beuselinck K, Reynders M, Lagrou K, Van Ranst M, Rector A. Epidemiology and genetic diversity of human respiratory syncytial virus in Belgium between 2011 and 2019. Virol J 2024; 21:270. [PMID: 39468663 PMCID: PMC11520483 DOI: 10.1186/s12985-024-02542-4] [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: 07/07/2024] [Accepted: 10/15/2024] [Indexed: 10/30/2024] Open
Abstract
BACKGROUND Human respiratory syncytial virus (HRSV) is worldwide one of the leading causes of acute respiratory tract infections in young children and the elderly population. Two distinct subtypes of HRSV (A and B) and a multitude of genotypes have been described. The laboratory of Clinical and Epidemiological Virology (KU Leuven/University Hospitals Leuven) has a long-standing history of HRSV surveillance in Belgium. METHODS In this study, the seasonal circulation of HRSV in Belgium was monitored during 8 consecutive seasons prior to the SARS-CoV-2 pandemic (2011-2012 until 2018-2019). By use of a multiplex quantitative real time PCR panel, 27,386 respiratory samples were tested for HRSV. Further subtyping and sequencing of the HRSV positive samples was performed by PCR and Sanger sequencing. The prevalence and positivity rate were estimated in 4 distinct age groups and the circulating strains of each subtype were situated in a global context and in reference to the described genotypes in literature. RESULTS HRSV circulated in Belgium in a yearly re-occurring pattern during the winter months and both HRSV subtypes co-circulated simultaneously. All HRSV-B strains contained the 60 nt duplication in the HVR2 region of the G gene. Strains of subtype HRSV-A with a 72 nt duplication in the HVR2 region were first observed during the 2011-2012 season and replaced all other circulating strains from 2014 to 2015 onwards.
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Affiliation(s)
- Kaat Ramaekers
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Herestraat 49 Box 1040, 3000, Leuven, Belgium.
| | - Els Keyaerts
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Herestraat 49 Box 1040, 3000, Leuven, Belgium
- Department of Laboratory Medicine, National Reference Centre for Respiratory Pathogens, University Hospitals Leuven, Herestraat 49, 3000, Louvain, Belgium
| | - Lieselot Houspie
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Herestraat 49 Box 1040, 3000, Leuven, Belgium
- QbD Clinical, Groeneborgerlaan 16, 2810, Wilrijk, Belgium
| | - Kurt Beuselinck
- Department of Laboratory Medicine, National Reference Centre for Respiratory Pathogens, University Hospitals Leuven, Herestraat 49, 3000, Louvain, Belgium
| | - Marijke Reynders
- Unit of Molecular Microbiology, Medical Microbiology, Department of Laboratory Medicine, Algemeen Ziekenhuis Sint-Jan, 3000, Brugge, Belgium
| | - Katrien Lagrou
- Department of Laboratory Medicine, National Reference Centre for Respiratory Pathogens, University Hospitals Leuven, Herestraat 49, 3000, Louvain, Belgium
| | - Marc Van Ranst
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Herestraat 49 Box 1040, 3000, Leuven, Belgium
- Department of Laboratory Medicine, National Reference Centre for Respiratory Pathogens, University Hospitals Leuven, Herestraat 49, 3000, Louvain, Belgium
| | - Annabel Rector
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Herestraat 49 Box 1040, 3000, Leuven, Belgium
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216
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Xia J, Yuan Z, Jiang F. Global metagenomic survey identifies sewage-derived hgcAB + microorganisms as key contributors to riverine methylmercury production. Nat Commun 2024; 15:9262. [PMID: 39461941 PMCID: PMC11513008 DOI: 10.1038/s41467-024-53479-9] [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: 04/08/2024] [Accepted: 10/14/2024] [Indexed: 10/28/2024] Open
Abstract
Methylmercury (MeHg) in aquatic systems poses a serious public health risk through bioaccumulation in the aquatic food web. In recent years, MeHg has been observed to increase to concerning levels globally in rivers near cities; however, the causes of this increase are not well understood. Here, we demonstrate the significant role of sewage contamination by analyzing over 1,300 publicly available metagenomes in urban rivers worldwide, and conducting experiments with water samples across China. We find that sewage contamination significantly increases the abundance of mercury (Hg)-methylating microorganisms in urban rivers globally. This increase is primarily attributed to the high abundance of active Hg-methylating microorganisms in sewage, which migrate to rivers via direct discharge or combined sewer overflows (CSOs), becoming key contributors to elevated riverine MeHg levels. Our findings underscore the importance of effectively eliminating Hg-methylating microorganisms from sewage to mitigate the public health risks associated with MeHg in urban rivers.
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Affiliation(s)
- Juntao Xia
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, China
| | - Zhiguo Yuan
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
- State Key Laboratory of Marine Pollution, City University of Hong Kong, Hong Kong SAR, China
| | - Feng Jiang
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, China.
- Guangdong Provincial Engineering Research Center of Low-Carbon Technology for Water Pollution Control, Sun Yat-sen University, Guangzhou, China.
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217
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Egan JP, Simons AM, Alavi-Yeganeh MS, Hammer MP, Tongnunui P, Arcila D, Betancur-R R, Bloom DD. Phylogenomics, Lineage Diversification Rates, and the Evolution of Diadromy in Clupeiformes (Anchovies, Herrings, Sardines, and Relatives). Syst Biol 2024; 73:683-703. [PMID: 38756097 DOI: 10.1093/sysbio/syae022] [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: 08/16/2021] [Revised: 05/01/2024] [Accepted: 05/15/2024] [Indexed: 05/18/2024] Open
Abstract
Migration independently evolved numerous times in animals, with a myriad of ecological and evolutionary implications. In fishes, perhaps the most extreme form of migration is diadromy, the migration between marine and freshwater environments. Key and long-standing questions are: how many times has diadromy evolved in fishes, how frequently do diadromous clades give rise to non-diadromous species, and does diadromy influence lineage diversification rates? Many diadromous fishes have large geographic ranges with constituent populations that use isolated freshwater habitats. This may limit gene flow between some populations, increasing the likelihood of speciation in diadromous lineages relative to nondiadromous lineages. Alternatively, diadromy may reduce lineage diversification rates if migration is associated with enhanced dispersal capacity that facilitates gene flow within and between populations. Clupeiformes (herrings, sardines, shads, and anchovies) is a model clade for testing hypotheses about the evolution of diadromy because it includes an exceptionally high proportion of diadromous species and several independent evolutionary origins of diadromy. However, relationships among major clupeiform lineages remain unresolved, and existing phylogenies sparsely sampled diadromous species, limiting the resolution of phylogenetically informed statistical analyses. We assembled a phylogenomic dataset and used multi-species coalescent and concatenation-based approaches to generate the most comprehensive, highly resolved clupeiform phylogeny to date, clarifying associations among several major clades and identifying recalcitrant relationships needing further examination. We determined that variation in rates of sequence evolution (heterotachy) and base-composition (nonstationarity) had little impact on our results. Using this phylogeny, we characterized evolutionary patterns of diadromy and tested for differences in lineage diversification rates between diadromous, marine, and freshwater lineages. We identified 13 transitions to diadromy, all during the Cenozoic Era (10 origins of anadromy, 2 origins of catadromy, and 1 origin of amphidromy), and 7 losses of diadromy. Two diadromous lineages rapidly generated nondiadromous species, demonstrating that diadromy is not an evolutionary dead end. We discovered considerably faster transition rates out of diadromy than to diadromy. The largest lineage diversification rate increase in Clupeiformes was associated with a transition to diadromy, but we uncovered little statistical support for categorically faster lineage diversification rates in diadromous versus nondiadromous fishes. We propose that diadromy may increase the potential for accelerated lineage diversification, particularly in species that migrate long distances. However, this potential may only be realized in certain biogeographic contexts, such as when diadromy allows access to ecosystems in which there is limited competition from incumbent species.
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Affiliation(s)
- Joshua P Egan
- Department of Biological Sciences, Western Michigan University, 1903 W Michigan Ave., Kalamazoo, MI 49008, USA
- Bell Museum of Natural History, University of Minnesota, 100 Ecology, 1987 Upper Buford Circle, Saint Paul, MN 55108, USA
| | - Andrew M Simons
- Bell Museum of Natural History, University of Minnesota, 100 Ecology, 1987 Upper Buford Circle, Saint Paul, MN 55108, USA
- Department of Fisheries, Wildlife and Conservation Biology, University of Minnesota, 2003 Upper Buford Circle, Saint Paul, MN 55108, USA
| | | | - Michael P Hammer
- Museum and Art Gallery of the Northern Territory, GPO Box 4646, Darwin, NT 0801, Australia
| | - Prasert Tongnunui
- Department of Marine Science and Environment, Faculty of Science and Fisheries Technology, Rajamangala University of Technology Srivijaya, Sikao, Trang 92150, Thailand
| | - Dahiana Arcila
- Scripps Institution of Oceanography, University of California - San Diego, La Jolla, CA 92093, USA
| | - Ricardo Betancur-R
- Scripps Institution of Oceanography, University of California - San Diego, La Jolla, CA 92093, USA
| | - Devin D Bloom
- Department of Biological Sciences, Western Michigan University, 1903 W Michigan Ave., Kalamazoo, MI 49008, USA
- School of the Environment, Geography, and Sustainability, Western Michigan University, 1903 W Michigan Ave, Kalamazoo, MI 49008, USA
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218
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Napit R, Elong Ngono A, Mihindukulasuriya KA, Pradhan A, Khadka B, Shrestha S, Droit L, Paredes A, Karki L, Khatiwada R, Tamang M, Chalise BS, Rawal M, Jha BK, Wang D, Handley SA, Shresta S, Manandhar KD. Dengue virus surveillance in Nepal yields the first on-site whole genome sequences of isolates from the 2022 outbreak. BMC Genomics 2024; 25:998. [PMID: 39449117 PMCID: PMC11515306 DOI: 10.1186/s12864-024-10879-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Accepted: 10/08/2024] [Indexed: 10/26/2024] Open
Abstract
BACKGROUND The 4 serotypes of dengue virus (DENV1-4) can each cause potentially deadly dengue disease, and are spreading globally from tropical and subtropical areas to more temperate ones. Nepal provides a microcosm of this global phenomenon, having met each of these grim benchmarks. To better understand DENV transmission dynamics and spread into new areas, we chose to study dengue in Nepal and, in so doing, to build the onsite infrastructure needed to manage future, larger studies. METHODS AND RESULTS During the 2022 dengue season, we enrolled 384 patients presenting at a hospital in Kathmandu with dengue-like symptoms; 79% of the study participants had active or recent DENV infection (NS1 antigen and IgM). To identify circulating serotypes, we screened serum from 50 of the NS1+ participants by RT-PCR and identified DENV1, 2, and 3 - with DENV1 and 3 codominant. We also performed whole-genome sequencing of DENV, for the first time in Nepal, using our new on-site capacity. Sequencing analysis demonstrated the DENV1 and 3 genomes clustered with sequences reported from India in 2019, and the DENV2 genome clustered with a sequence reported from China in 2018. CONCLUSION These findings highlight DENV's geographic expansion from neighboring countries, identify China and India as the likely origin of the 2022 DENV cases in Nepal, and demonstrate the feasibility of building onsite capacity for more rapid genomic surveillance of circulating DENV. These ongoing efforts promise to protect populations in Nepal and beyond by informing the development and deployment of DENV drugs and vaccines in real time.
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Affiliation(s)
- Rajindra Napit
- Central Department of Biotechnology, Tribhuvan University, Kirtipur, Kathmandu, Nepal
| | - Annie Elong Ngono
- Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Kathie A Mihindukulasuriya
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Aunji Pradhan
- Central Department of Biotechnology, Tribhuvan University, Kirtipur, Kathmandu, Nepal
| | - Binod Khadka
- Central Department of Biotechnology, Tribhuvan University, Kirtipur, Kathmandu, Nepal
| | - Smita Shrestha
- Central Department of Biotechnology, Tribhuvan University, Kirtipur, Kathmandu, Nepal
| | - Lindsay Droit
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Anne Paredes
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Lata Karki
- Central Department of Biotechnology, Tribhuvan University, Kirtipur, Kathmandu, Nepal
| | - Rabindra Khatiwada
- Central Department of Biotechnology, Tribhuvan University, Kirtipur, Kathmandu, Nepal
| | - Mamata Tamang
- Central Department of Biotechnology, Tribhuvan University, Kirtipur, Kathmandu, Nepal
| | - Bimal Sharma Chalise
- Department of Tropical and Infectious Disease, Sukraraj Tropical and Infectious Disease Hospital, Teku, Kathmandu, Nepal
| | - Manisha Rawal
- Department of Tropical and Infectious Disease, Sukraraj Tropical and Infectious Disease Hospital, Teku, Kathmandu, Nepal
| | | | - David Wang
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Scott A Handley
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Sujan Shresta
- Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, CA, USA.
- Division of Host-Microbe Systems and Therapeutics, Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, USA.
| | - Krishna Das Manandhar
- Central Department of Biotechnology, Tribhuvan University, Kirtipur, Kathmandu, Nepal.
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Brigleb PH, Sharp B, Roubidoux EK, Meliopoulos V, Tan S, Livingston B, Morris D, Ripperger T, Lazure L, Balaraman V, Thompson AC, Kleinhenz K, Dimitrov K, Thomas PG, Schultz-Cherry S. Immune History Modifies Disease Severity to HPAI H5N1 Clade 2.3.4.4b Viral Challenge. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.10.23.619695. [PMID: 39484458 PMCID: PMC11526876 DOI: 10.1101/2024.10.23.619695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2024]
Abstract
The most recent outbreak of highly pathogenic avian H5 influenza (HPAI) virus in cattle is now widespread across the U.S. with spillover events happening to other mammals, including humans. Several human cases have been reported with clinical signs ranging from conjunctivitis to respiratory illness. However, most of those infected report mild to moderate symptoms, while previously reported HPAI H5Nx infections in humans have had mortality rates upwards of 50%. We recently reported that mice with pre-existing immunity to A/Puerto Rico/08/1934 H1N1 virus were protected from lethal challenge from highly pathogenic clade 2.3.4.4b H5N1 influenza virus. Here, we demonstrate that mice infected with the 2009 pandemic H1N1 virus strain A/California/04/2009 (Cal09) or vaccinated with a live-attenuated influenza vaccine (LAIV) were moderately-to-highly protected against a lethal A/bovine/Ohio/B24OSU-439/2024 H5N1 virus challenge. We also observed that ferrets with mixed pre-existing immunity-either from LAIV vaccination and/or from Cal09 infection-showed protection against a HPAI H5N1 clade 2.3.4.4b virus isolated from a cat. Notably, this protection occurred independently of any detectable hemagglutination inhibition titers (HAIs) against the H5N1 virus. To explore factors that may contribute to protection, we conducted detailed T cell epitope mapping using previously published sequences from H1N1 strains. This analysis revealed a high conservation of amino acid sequences within the internal proteins of our bovine HPAI H5N1 virus strain. These data highlight the necessity to explore additional factors that contribute to protection against HPAI H5N1 viruses, such as memory T cell responses, in addition to HA-inhibition or neutralizing antibodies.
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Du HZ, Lu YH, Cheewangkoon R, Liu JK. Morpho-phylogenetic evidence reveals novel species and new records of Nigrograna (Nigrogranaceae) associated with medicinal plants in Southwestern China. MycoKeys 2024; 110:1-33. [PMID: 39493641 PMCID: PMC11525206 DOI: 10.3897/mycokeys.110.132628] [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: 07/20/2024] [Accepted: 09/23/2024] [Indexed: 11/05/2024] Open
Abstract
During a survey of saprobic fungal niches in Southwestern China, eighteen ascomycetous collections of Nigrograna (Nigrogranaceae, Pleosporales, Dothideomycetes) were found on dead branches of medicinal plants. These taxa were characterized and identified based on morphological and culture characteristics, and phylogenetic analyses of a combined the internal transcribed spacer region of rDNA (ITS), nuclear large subunit rDNA (28S, LSU), RNA polymerase second-largest subunit (rpb2), nuclear small subunit rDNA (18S, SSU), and translation elongation factor 1-alpha (tef1-α) sequence dataset also confirmed their placement. As a result, four novel species, namely Nigrogranacamelliae, N.guttulata, N.longiorostiolata and N.neriicola were described. Additionally, four new host records of N.acericola, N.magnoliae, N.oleae and N.thymi were introduced. Furthermore, this study addresses the taxonomic status of N.trachycarpi, proposing its synonymy under N.oleae. Detailed illustrations, descriptions and informative notes for each newly identified taxon and novel host record are provided in this study.
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Affiliation(s)
- Hong-Zhi Du
- School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 611731, Sichuan Province, China
- School of Pharmacy, Guizhou University of Traditional Chinese Medicine, Guiyang 550025, Guizhou Province, China
- Department of Entomology and Plant Pathology, Faculty of Agriculture, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Yu-Hang Lu
- School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 611731, Sichuan Province, China
- Department of Entomology and Plant Pathology, Faculty of Agriculture, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Ratchadawan Cheewangkoon
- Department of Entomology and Plant Pathology, Faculty of Agriculture, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Jian-Kui Liu
- School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 611731, Sichuan Province, China
- Department of Entomology and Plant Pathology, Faculty of Agriculture, Chiang Mai University, Chiang Mai 50200, Thailand
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Nardi F, Funari R, Carapelli A, Badano D, Frati F, Cucini C. The complete mitochondrial genome of the shining leaf chafer Mimela junii (Duftschmidt, 1805) (Coleoptera: Scarabaeidae). Mitochondrial DNA B Resour 2024; 9:1439-1444. [PMID: 39450202 PMCID: PMC11500510 DOI: 10.1080/23802359.2024.2417936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2024] [Accepted: 10/11/2024] [Indexed: 10/26/2024] Open
Abstract
The complete mitochondrial genome of the shining leaf chafer Mimela junii was sequenced and is herein described. The mitogenome consists of a circular molecule of 16,805 bp, with an overall AT content of 75.7%. It encodes for 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs) and contains a non-coding Control Region (CR) characterized by the presence of tandem repeats. The gene order corresponds to the ancestral Pancrustacea model and mitogenome characteristics are congruous with those of hexapods. In the phylogenetic analysis, M. junii is nested within a paraphyletic Anomala with high support, and is herein associated with Anomala corpulenta with medium/low support.
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Affiliation(s)
- Francesco Nardi
- Department of Life Sciences, University of Siena, Siena, Italy
- National Biodiversity Future Center (NBFC), Palermo, Italy
| | - Rebecca Funari
- Department of Life Sciences, University of Siena, Siena, Italy
| | - Antonio Carapelli
- Department of Life Sciences, University of Siena, Siena, Italy
- National Biodiversity Future Center (NBFC), Palermo, Italy
| | - Davide Badano
- Department of Life Sciences, University of Siena, Siena, Italy
- National Biodiversity Future Center (NBFC), Palermo, Italy
| | - Francesco Frati
- Department of Life Sciences, University of Siena, Siena, Italy
- National Biodiversity Future Center (NBFC), Palermo, Italy
| | - Claudio Cucini
- Department of Life Sciences, University of Siena, Siena, Italy
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222
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Seshadri L, Atickem A, Zinner D, Roos C, Zhang L. Whole Genome Analysis Reveals Evolutionary History and Introgression Events in Bale Monkeys. Genes (Basel) 2024; 15:1359. [PMID: 39596559 PMCID: PMC11593718 DOI: 10.3390/genes15111359] [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: 09/20/2024] [Revised: 10/16/2024] [Accepted: 10/19/2024] [Indexed: 11/28/2024] Open
Abstract
Background/Objective: The Bale monkey (Chlorocebus djamdjamensis) is a threatened primate species endemic to Ethiopia and, in contrast to other members of the genus Chlorocebus, lives at high altitudes and feeds mainly on bamboo. Two populations of the species are present, one in continuous bamboo forest (CF) in the eastern part of the species' range, and the other in fragmented forest (FF) in the western part. Based on mitochondrial DNA and phenotypic characteristics, previous studies have suggested introgression by parapatric congeners into the FF population but not into the CF population. The objective of this study was to gain insights into the evolutionary history of Bale monkeys and their potential genetic adaptations to high altitudes and for bamboo consumption. Methods: We sequenced the whole genomes of individuals from both populations and compared their genomes with those of the other five Chlorocebus species. We applied phylogenetic methods and conducted population demographic simulations to elucidate their evolutionary history. A genome-wide analysis was conducted to assess gene flow and identify mutations potentially associated with adaptations to high altitudes and for bamboo metabolism. Results: Our analyses revealed Bale monkeys as the sister clade to Chlorocebus aethiops and showed that gene flow occurred between C. aethiops and FF but not between C. aethiops and CF. In addition, we detected non-synonymous mutations in genes potentially associated with the adaptation to high altitudes (EPAS1) in both populations and with the adaptation for bamboo metabolism (TAS2R16, MPST, and TST) mainly in the CF population. Conclusions: Our study provides insights into the evolutionary history of a threatened primate species and reveals the genetic basis for its adaptions to unique environments and for diet specialization.
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Affiliation(s)
- Lakshmi Seshadri
- Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, 37077 Göttingen, Germany;
- International Max Planck Research School for Genome Science (IMPRS-GS), Georg-August-Universität Göttingen, 37077 Göttingen, Germany
| | - Anagaw Atickem
- Department of Zoological Sciences, Addis Ababa University, Addis Ababa 999047, Ethiopia;
| | - Dietmar Zinner
- Cognitive Ethology Laboratory, German Primate Center, Leibniz Institute for Primate Research, 37077 Göttingen, Germany;
- Department of Primate Cognition, Georg-August-Universität Göttingen, 37077 Göttingen, Germany
- Leibniz ScienceCampus Primate Cognition, 37077 Göttingen, Germany
| | - Christian Roos
- Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, 37077 Göttingen, Germany;
- Gene Bank of Primates, German Primate Center, Leibniz Institute for Primate Research, 37077 Göttingen, Germany
| | - Liye Zhang
- Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, 37077 Göttingen, Germany;
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Adelino TÉR, Pedroso SHSP, Lima M, Tomé LMR, Guimarães NR, Fonseca V, da Silva PEDS, Moreno KMF, Silva ACAE, Pinheiro NR, de Souza CSA, Alcantara LCJ, Giovanetti M, Iani FCDM. Exploring Dengue Infection in a Vaccinated Individual: Preliminary Molecular Diagnosis and Sequencing Insights. Viruses 2024; 16:1603. [PMID: 39459936 PMCID: PMC11512295 DOI: 10.3390/v16101603] [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: 09/03/2024] [Revised: 10/04/2024] [Accepted: 10/10/2024] [Indexed: 10/28/2024] Open
Abstract
This study examines a case involving a 7-year-old child who developed dengue symptoms following Qdenga vaccination. Despite initial negative diagnostic results, molecular analysis confirmed an infection with DENV4. Next-generation sequencing detected viral RNA from both DENV2 and DENV4 serotypes, which were identified as vaccine-derived strains using specific primers. Phylogenetic analysis further confirmed that these sequences belonged to the Qdenga vaccine rather than circulating wild-type viruses. This case underscores the critical need for precise diagnostic interpretation in vaccinated individuals to avoid misdiagnosis and to strengthen public health surveillance. A comprehensive understanding of vaccine-induced viremia is essential for refining dengue surveillance, improving diagnostic accuracy, and informing public health strategies in endemic regions.
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Affiliation(s)
- Talita Émile Ribeiro Adelino
- Fundação Ezequiel Dias, Belo Horizonte 30510-010, Brazil; (S.H.S.P.P.); (M.L.); (L.M.R.T.); (N.R.G.); (P.E.d.S.d.S.); (K.M.F.M.)
- Instituto René Rachou, Fundação Oswaldo Cruz, Belo Horizonte 30190-009, Brazil;
| | | | - Maurício Lima
- Fundação Ezequiel Dias, Belo Horizonte 30510-010, Brazil; (S.H.S.P.P.); (M.L.); (L.M.R.T.); (N.R.G.); (P.E.d.S.d.S.); (K.M.F.M.)
| | - Luiz Marcelo Ribeiro Tomé
- Fundação Ezequiel Dias, Belo Horizonte 30510-010, Brazil; (S.H.S.P.P.); (M.L.); (L.M.R.T.); (N.R.G.); (P.E.d.S.d.S.); (K.M.F.M.)
- Instituto René Rachou, Fundação Oswaldo Cruz, Belo Horizonte 30190-009, Brazil;
| | - Natália Rocha Guimarães
- Fundação Ezequiel Dias, Belo Horizonte 30510-010, Brazil; (S.H.S.P.P.); (M.L.); (L.M.R.T.); (N.R.G.); (P.E.d.S.d.S.); (K.M.F.M.)
- Instituto René Rachou, Fundação Oswaldo Cruz, Belo Horizonte 30190-009, Brazil;
| | - Vagner Fonseca
- Department of Exact and Earth Science, University of the State of Bahia, Salvador 41192-010, Brazil;
- Climate Amplified Diseases and Epidemics (CLIMADE), Brasília 70070-130, Brazil
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch 7600, South Africa
| | - Paulo Eduardo de Souza da Silva
- Fundação Ezequiel Dias, Belo Horizonte 30510-010, Brazil; (S.H.S.P.P.); (M.L.); (L.M.R.T.); (N.R.G.); (P.E.d.S.d.S.); (K.M.F.M.)
| | - Keldenn Melo Farias Moreno
- Fundação Ezequiel Dias, Belo Horizonte 30510-010, Brazil; (S.H.S.P.P.); (M.L.); (L.M.R.T.); (N.R.G.); (P.E.d.S.d.S.); (K.M.F.M.)
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - Ana Cândida Araújo e Silva
- Comitê Técnico Científico Multidisciplinar, Universidade Federal dos Vales do Jequitinhonha e Mucuri, Teófilo Otoni 39800-091, Brazil; (A.C.A.e.S.); (N.R.P.)
| | - Náthale Rodrigues Pinheiro
- Comitê Técnico Científico Multidisciplinar, Universidade Federal dos Vales do Jequitinhonha e Mucuri, Teófilo Otoni 39800-091, Brazil; (A.C.A.e.S.); (N.R.P.)
| | | | - Luiz Carlos Junior Alcantara
- Instituto René Rachou, Fundação Oswaldo Cruz, Belo Horizonte 30190-009, Brazil;
- Climate Amplified Diseases and Epidemics (CLIMADE), Brasília 70070-130, Brazil
| | - Marta Giovanetti
- Instituto René Rachou, Fundação Oswaldo Cruz, Belo Horizonte 30190-009, Brazil;
- Climate Amplified Diseases and Epidemics (CLIMADE), Brasília 70070-130, Brazil
- Sciences and Technologies for Sustainable Development and One Health, Università Campus Bio-Medico di Roma, 00128 Roma, Italy
| | - Felipe Campos de Melo Iani
- Fundação Ezequiel Dias, Belo Horizonte 30510-010, Brazil; (S.H.S.P.P.); (M.L.); (L.M.R.T.); (N.R.G.); (P.E.d.S.d.S.); (K.M.F.M.)
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Zou M, Al-Otibi F, Hyde KD, Wang Y, Pan XJ. New Helminthosporium (Massarinaceae, Dothideomycetes) and Nigrospora (Incertae sedis, Sordariomycetes) species associated with walnut ( Juglansregia L.) in China. MycoKeys 2024; 109:265-284. [PMID: 39430416 PMCID: PMC11489710 DOI: 10.3897/mycokeys.109.133431] [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: 07/30/2024] [Accepted: 09/22/2024] [Indexed: 10/22/2024] Open
Abstract
Six collections of ascomycetes were obtained from samples collected from dead branches and leaves of Juglansregia in Guizhou and Yunnan provinces, China. By incorporating multigene phylogenetic analysis (ITS, LSU, rpb2, SSU, tef1-α, tub2) supplemented by morphological data, we establish two novel species, namely Helminthosporiumguizhouense and Nigrosporayunnanensis. In morphology, H.guizhouense can be distinguished from H.caespitosum by its narrower conidia (13-16 µm vs. 27.3-35.5 µm), and N.yunnanensis is characterized by black, globose conidia (16.2 × 14.4 µm). The phylogenetic results further substantiated them as novel taxa. The present study contributes to our comprehension of the range of fungi found in Juglansregia, thereby expanding our knowledge of the diversity of fungi within this host.
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Affiliation(s)
- Mengting Zou
- Department of Plant Pathology, Agricultural College, Guizhou University, Guiyang, 550025, China
| | - Fatimah Al-Otibi
- Institute of Plant Health and Medicine, College of Agriculture, Guizhou University, Guiyang Guizhou 550025, China
| | - Kevin David Hyde
- Institute of Plant Health and Medicine, College of Agriculture, Guizhou University, Guiyang Guizhou 550025, China
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 22452, Riyadh 11495, Saudi Arabia
| | - Yong Wang
- Department of Plant Pathology, Agricultural College, Guizhou University, Guiyang, 550025, China
| | - Xue-Jun Pan
- Department of Plant Pathology, Agricultural College, Guizhou University, Guiyang, 550025, China
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de Oliveira FS, Azambuja M, Schemberger MO, Nascimento VD, Oliveira JIN, Wolf IR, Nogaroto V, Martins C, Vicari MR. Characterization of hAT DNA transposon superfamily in the genome of Neotropical fish Apareiodon sp. Mol Genet Genomics 2024; 299:96. [PMID: 39382723 DOI: 10.1007/s00438-024-02190-x] [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: 12/06/2023] [Accepted: 09/28/2024] [Indexed: 10/10/2024]
Abstract
DNA transposons are diverse in fish genomes and have been described to generate genomic evolutionary novelties. hAT transposable element data are scarce in Teleostei genomes, making it challenging to conduct comparative genomic studies to understand their neutrality or function. This study aimed to perform a genomic and molecular characterization of hAT copies to assess the diversity of these elements and associate changes in these sequences to genomic and karyotypic novelties in Apareiodon sp. The data revealed that hAT TEs are highly abundant in the Apareiodon sp. genome, with few possibly autonomous copies. Highly conserved sequences with likely functional transposases were observed in nine hAT elements. A great diversity of hAT subgroups was observed, especially from Ac, Charlie, Blackjack, Tip100, hAT6, and hAT5, and a similar wave of hAT genomic invasion was identified in the genome for these six groups of hAT sequences. The data also revealed a distinct number of microsatellites within degenerated hAT copies. hAT sites were demonstrated to be dispersed in the Apareiodon sp. chromosomes and not involved in W chromosome-specific region differentiation. In conclusion, the genomic analysis revealed a great diversity of hAT elements, possible autonomous copies, and differentiation of degenerated transposable elements into tandem sequences.
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Affiliation(s)
- Fernanda Souza de Oliveira
- Programa de Pós-Graduação em Genética, Universidade Federal do Paraná, Centro Politécnico, Avenida Coronel Francisco H. Dos Santos, 100, Curitiba, Paraná, 81531-990, Brazil
| | - Matheus Azambuja
- Programa de Pós-Graduação em Genética, Universidade Federal do Paraná, Centro Politécnico, Avenida Coronel Francisco H. Dos Santos, 100, Curitiba, Paraná, 81531-990, Brazil
| | - Michelle Orane Schemberger
- Programa de Pós-Graduação em Genética, Universidade Federal do Paraná, Centro Politécnico, Avenida Coronel Francisco H. Dos Santos, 100, Curitiba, Paraná, 81531-990, Brazil
| | - Viviane Demetrio Nascimento
- Programa de Pós-Graduação em Genética, Universidade Federal do Paraná, Centro Politécnico, Avenida Coronel Francisco H. Dos Santos, 100, Curitiba, Paraná, 81531-990, Brazil
| | - Jordana Inácio Nascimento Oliveira
- Departamento de Morfologia, Instituto de Biociências de Botucatu, Universidade Estadual Paulista, Distrito de Rubião Júnior, S/N, Botucatu, São Paulo, 18618-689, Brazil
| | - Ivan Rodrigo Wolf
- Departamento de Morfologia, Instituto de Biociências de Botucatu, Universidade Estadual Paulista, Distrito de Rubião Júnior, S/N, Botucatu, São Paulo, 18618-689, Brazil
| | - Viviane Nogaroto
- Departamento de Biologia Estrutural, Molecular e Genética, Universidade Estadual de Ponta Grossa, Av. Carlos Cavalcanti, 4748, Ponta Grossa, Paraná, 84030-900, Brazil
| | - Cesar Martins
- Departamento de Morfologia, Instituto de Biociências de Botucatu, Universidade Estadual Paulista, Distrito de Rubião Júnior, S/N, Botucatu, São Paulo, 18618-689, Brazil
| | - Marcelo Ricardo Vicari
- Programa de Pós-Graduação em Genética, Universidade Federal do Paraná, Centro Politécnico, Avenida Coronel Francisco H. Dos Santos, 100, Curitiba, Paraná, 81531-990, Brazil.
- Departamento de Biologia Estrutural, Molecular e Genética, Universidade Estadual de Ponta Grossa, Av. Carlos Cavalcanti, 4748, Ponta Grossa, Paraná, 84030-900, Brazil.
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Ortiz-Morazán AS, Moncada MM, Escobar D, Cabrera-Moreno LA, Fontecha G. Coevolutionary Analysis of the Pfs47-P47Rec Complex: A Bioinformatics Approach. Bioinform Biol Insights 2024; 18:11779322241284223. [PMID: 39386977 PMCID: PMC11462556 DOI: 10.1177/11779322241284223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 08/28/2024] [Indexed: 10/12/2024] Open
Abstract
Background The ability to predict and comprehend molecular interactions offers significant insights into the biological functions of proteins. The interaction between surface protein 47 of Plasmodium falciparum (Pfs47) and receptor of the protein 47 (P47Rec) has attracted increased attention due to their role in parasite evasion of the mosquito immune system and the concept of geographical coevolution between species. The aims of this study were as follows: to apply a bioinformatics approach to investigate the interaction between Pfs47 and P47Rec proteins and to identify the potential binding sites, protein orientations and receptor specificity sites concerning the geographical origins of the vectors and the parasite. Methods Public sequences of the pfs47 and p47rec genes were downloaded and subsequently filtered to predict functional and structural annotations of the Pfs47-P47Rec complex. Phylogenetic analyses of both proteins were carried out. In addition, the p47Rec gene was subjected to sequencing and subsequent analysis in 2 distinct Anopheles species collected in Honduras. Results The examination of motifs reveals a significant degree of conservation in pfs47, suggesting that Pfs47 might have undergone recent evolutionary development and adaptation. Structural models and docking analyses supported the theory of selectivity of Plasmodium falciparum strains towards their vectors in diverse geographical regions. A detailed description of the putative interaction between the Pfs47-P47Rec complex is shown. Conclusions The study identifies coevolutionary patterns between P47Rec and Pfs47 related to the speciation and geographic dispersion of Anopheles species and Plasmodium falciparum, with Pfs47 evolving more recently than P47Rec. This suggests a link between the parasite's adaptability and existing anopheline species across different regions. P47Rec likely has a cytoplasmic localization due to its lack of membrane attachment elements. However, these findings are based on simulations and require validation through methods like cryo-electron microscopy. A significant limitation is the scarcity of sequences in global databases, which restricts precise interaction modelling. Further research with diverse parasite isolates and anopheline species is recommended to enhance understanding of these proteins' structure and interaction.
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Affiliation(s)
- Andrés S Ortiz-Morazán
- Instituto de Investigaciones en Microbiología, Facultad de Ciencias, Universidad Nacional Autónoma de Honduras, Tegucigalpa, Honduras
| | - Marcela María Moncada
- Instituto de Investigaciones en Microbiología, Facultad de Ciencias, Universidad Nacional Autónoma de Honduras, Tegucigalpa, Honduras
| | - Denis Escobar
- Instituto de Investigaciones en Microbiología, Facultad de Ciencias, Universidad Nacional Autónoma de Honduras, Tegucigalpa, Honduras
| | - Leonardo A Cabrera-Moreno
- Instituto de Investigaciones en Microbiología, Facultad de Ciencias, Universidad Nacional Autónoma de Honduras, Tegucigalpa, Honduras
| | - Gustavo Fontecha
- Instituto de Investigaciones en Microbiología, Facultad de Ciencias, Universidad Nacional Autónoma de Honduras, Tegucigalpa, Honduras
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Huang JH, Lei CY, Shen YL, Tian EJ. Two new species of Pholiota (Agaricales, Strophariaceae) from the southwest of China. MycoKeys 2024; 109:171-185. [PMID: 39416397 PMCID: PMC11480669 DOI: 10.3897/mycokeys.109.133879] [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: 08/04/2024] [Accepted: 09/05/2024] [Indexed: 10/19/2024] Open
Abstract
Two new mushroom species from Southwest China, Pholiotacylindrospora and P.subterrestris, are described in this study. Pholiotacylindrospora is characterized by its dry pileus with slightly recurved and triangular scales, cylindrical basidiospores, and two types of pleurocystidia-leptocystidia and chrysocystidia-as well as its growth on soil. Pholiotasubterrestris is identified by a brownish-orange pileus with numerous brown fibrillose scales; pale brown lamellae with even edges; a stipe covered with recurved fibrillose scales; elliptical spores with a distinct but small germ pore; and pleurocystidia containing typical amorphous refractive inclusions of chrysocystidia. Both species are described and illustrated, and a phylogenetic analysis of a multigene dataset (ITS + 28S) is presented. Morphological and phylogenetic analyses confirm that P.cylindrospora and P.subterrestris are distinct from the other Pholiota species, and both belong to the subgenus Pholiota. A key to the species of subgenus Pholiota from China is provided.
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Affiliation(s)
- Jia-hui Huang
- Engineering Research Center of Edible and Medicinal Fungi, Ministry of Education, Jilin Agricultural University, Changchun, 130118, ChinaJilin Agricultural UniversityChangchunChina
| | - Chun-yu Lei
- Engineering Research Center of Edible and Medicinal Fungi, Ministry of Education, Jilin Agricultural University, Changchun, 130118, ChinaJilin Agricultural UniversityChangchunChina
| | - Ya-lun Shen
- Engineering Research Center of Edible and Medicinal Fungi, Ministry of Education, Jilin Agricultural University, Changchun, 130118, ChinaJilin Agricultural UniversityChangchunChina
| | - En-jing Tian
- Engineering Research Center of Edible and Medicinal Fungi, Ministry of Education, Jilin Agricultural University, Changchun, 130118, ChinaJilin Agricultural UniversityChangchunChina
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Owuor DC, Ngoi JM, Nyasimi FM, Murunga N, Nyiro JU, Chaves SS, Nokes DJ, Agoti CN. Local patterns of spread of influenza A H3N2 virus in coastal Kenya over a 1-year period revealed through virus sequence data. Sci Rep 2024; 14:23426. [PMID: 39379445 PMCID: PMC11461663 DOI: 10.1038/s41598-024-74218-6] [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: 02/28/2024] [Accepted: 09/24/2024] [Indexed: 10/10/2024] Open
Abstract
The patterns of spread of influenza A viruses in local populations in tropical and sub-tropical regions are unclear due to sparsity of representative spatiotemporal sequence data. We sequenced and analyzed 58 influenza A(H3N2) virus genomes sampled between December 2015 and December 2016 from nine health facilities within the Kilifi Health and Demographic Surveillance System (KHDSS), a predominantly rural region, covering approximately 891 km2 along the Kenyan coastline. The genomes were compared with 1571 contemporaneous global sequences from 75 countries. We observed at least five independent introductions of A(H3N2) viruses into the region during the one-year period, with the importations originating from Africa, Europe, and North America. We also inferred 23 virus location transition events between the nine facilities included in the study. International virus imports into the study area were captured at the facilities of Chasimba, Matsangoni, Mtondia, and Mavueni, while all four exports from the region were captured from the Chasimba facility, all occurring to Africa destinations. A strong spatial clustering of virus strains at all locations was observed associated with local evolution. Our study shows that influenza A(H3N2) virus epidemics in local populations appear to be characterized by limited introductions followed by significant local spread and evolution. Knowledge of the viral lineages that circulate within specific populations in understudied tropical and subtropical regions is required to understand the full diversity and global ecology of influenza viruses and to inform vaccination strategies within these populations.
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Affiliation(s)
- D Collins Owuor
- Epidemiology and Demography Department, Kenya Medical Research Institute (KEMRI) - Wellcome Trust Research Programme, Kilifi, Kenya.
| | - Joyce M Ngoi
- Epidemiology and Demography Department, Kenya Medical Research Institute (KEMRI) - Wellcome Trust Research Programme, Kilifi, Kenya
| | - Festus M Nyasimi
- Epidemiology and Demography Department, Kenya Medical Research Institute (KEMRI) - Wellcome Trust Research Programme, Kilifi, Kenya
| | - Nickson Murunga
- Epidemiology and Demography Department, Kenya Medical Research Institute (KEMRI) - Wellcome Trust Research Programme, Kilifi, Kenya
| | - Joyce U Nyiro
- Epidemiology and Demography Department, Kenya Medical Research Institute (KEMRI) - Wellcome Trust Research Programme, Kilifi, Kenya
| | - Sandra S Chaves
- Influenza Division, National Center for Immunization and Respiratory Diseases (NCIRD), CDC, Atlanta, GA, USA
- Influenza Division, Centres for Disease Control and Prevention (CDC), Nairobi, Kenya
| | - D James Nokes
- Epidemiology and Demography Department, Kenya Medical Research Institute (KEMRI) - Wellcome Trust Research Programme, Kilifi, Kenya
- School of Life Sciences and Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research (SBIDER), University of Warwick, Coventry, UK
| | - Charles N Agoti
- Epidemiology and Demography Department, Kenya Medical Research Institute (KEMRI) - Wellcome Trust Research Programme, Kilifi, Kenya
- School of Public Health and Human Sciences, Pwani University, Kilifi, Kenya
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229
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Bourke BP, de Oliveira J, Ergunay K, Linton YM. Leveraging transcriptome sequence read archives for virus detection in wild and colony populations of triatomines (Hemiptera: Reduviidae: Triatominae). Arch Virol 2024; 169:215. [PMID: 39365450 PMCID: PMC11452441 DOI: 10.1007/s00705-024-06130-3] [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: 08/06/2024] [Accepted: 08/29/2024] [Indexed: 10/05/2024]
Abstract
Triatomines are infamous as vectors of the parasite Trypanosoma cruzi, the causative agent of Chagas disease. However, climate-driven range expansion and urbanization adaptation of triatomine populations, coupled with their highly diverse feeding strategies (vertebrate haematophagy, kleptohaematophagy, and coprophagy), and has elevated interest in triatomines as potential arboviral vectors. Information on the triatomine virome is scant, with prior records including only eight insect-specific viruses: Triatoma virus (TrV) and Rhodnius prolixus viruses 1-7. Here, we leverage publicly available transcriptome datasets to assess viral diversity in 122 wild and colony kissing bugs representing eight species from six countries. In total, six viruses were detected (including Rhodnius prolixus viruses 4-6), and TrV was detected in almost half of all screened triatomines. This is the first report of TrV in Triatoma brasiliensis and in members of the genus Mepraia (M. gajardoi, M. spinolai, and M. parapatrica), and this effort has vastly expanded the publicly available genomic resources of TrV, adding 39 genome sequences to the single genome sequence currently available in the GenBank database. Furthermore, two additional viruses-Meccus longipennis virus 1 and Drosophila melanogaster Nora virus-are herein reported for the first time from kissing bugs. Meccus longipennis virus 1 was detected in Triatoma infestans from Argentina, Brazil, Chile, and Peru, and Drosophila melanogaster Nora virus was found in T. infestans from Argentina. Our results illustrate the advantage and utility of low-cost transcriptome data mining for the discovery of known and novel arboviruses in triatomines and other potential insect vectors.
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Affiliation(s)
- Brian P Bourke
- Walter Reed Biosystematics Unit, Museum Support Center MRC-534, Smithsonian Institution, 4210 Silver Hill Rd., Suitland, MD, 20746, USA.
- One Health Branch, Walter Reed Army Institute of Research, 503 Robert Grant Ave, Silver Spring, MD, 20910, USA.
- Department of Entomology, Smithsonian Institution-National Museum of Natural History, 10th St NE & Constitution Ave NE, Washington, DC, 20002, USA.
| | - Jader de Oliveira
- Walter Reed Biosystematics Unit, Museum Support Center MRC-534, Smithsonian Institution, 4210 Silver Hill Rd., Suitland, MD, 20746, USA
- One Health Branch, Walter Reed Army Institute of Research, 503 Robert Grant Ave, Silver Spring, MD, 20910, USA
- Department of Entomology, Smithsonian Institution-National Museum of Natural History, 10th St NE & Constitution Ave NE, Washington, DC, 20002, USA
- Laboratory of Entomology in Public Health, Department of Epidemiology, Faculty of Public Health (FSP), University of São Paulo (USP), Avenue Dr. Arnaldo, 715, São Paulo, SP, 01246-904, Brazil
| | - Koray Ergunay
- Walter Reed Biosystematics Unit, Museum Support Center MRC-534, Smithsonian Institution, 4210 Silver Hill Rd., Suitland, MD, 20746, USA
- One Health Branch, Walter Reed Army Institute of Research, 503 Robert Grant Ave, Silver Spring, MD, 20910, USA
- Department of Entomology, Smithsonian Institution-National Museum of Natural History, 10th St NE & Constitution Ave NE, Washington, DC, 20002, USA
- Department of Medical Microbiology, Virology Unit, Faculty of Medicine, Hacettepe University, Ankara, 06800, Turkey
| | - Yvonne-Marie Linton
- Walter Reed Biosystematics Unit, Museum Support Center MRC-534, Smithsonian Institution, 4210 Silver Hill Rd., Suitland, MD, 20746, USA
- One Health Branch, Walter Reed Army Institute of Research, 503 Robert Grant Ave, Silver Spring, MD, 20910, USA
- Department of Entomology, Smithsonian Institution-National Museum of Natural History, 10th St NE & Constitution Ave NE, Washington, DC, 20002, USA
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230
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Zhu Z, Trenner J, Delker C, Quint M. Tracing the Evolutionary History of the Temperature-Sensing Prion-like Domain in EARLY FLOWERING 3 Highlights the Uniqueness of AtELF3. Mol Biol Evol 2024; 41:msae205. [PMID: 39391982 PMCID: PMC11523139 DOI: 10.1093/molbev/msae205] [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: 05/08/2024] [Revised: 09/03/2024] [Accepted: 09/17/2024] [Indexed: 10/12/2024] Open
Abstract
Plants have evolved mechanisms to anticipate and adjust their growth and development in response to environmental changes. Understanding the key regulators of plant performance is crucial to mitigate the negative influence of global climate change on crop production. EARLY FLOWERING 3 (ELF3) is one such regulator playing a critical role in the circadian clock and thermomorphogenesis. In Arabidopsis thaliana, ELF3 contains a prion-like domain (PrLD) that acts as a thermosensor, facilitating liquid-liquid phase separation at high ambient temperatures. To assess the conservation of this function across the plant kingdom, we traced the evolutionary emergence of ELF3, with a focus on the presence of PrLDs. We found that the PrLD, primarily influenced by the length of polyglutamine (polyQ) repeats, is most prominent in Brassicales. Analyzing 319 natural A. thaliana accessions, we confirmed the previously described wide range of polyQ length variation in AtELF3, but found it to be only weakly associated with geographic origin, climate conditions, and classic temperature-responsive phenotypes. Interestingly, similar polyQ length variation was not observed in several other investigated Bassicaceae species. Based on these findings, available prediction tools and limited experimental evidence, we conclude that the emergence of PrLD, and particularly polyQ length variation, is unlikely to be a key driver of environmental adaptation. Instead, it likely adds an additional layer to ELF3's role in thermomorphogenesis in A. thaliana, with its relevance in other species yet to be confirmed.
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Affiliation(s)
- Zihao Zhu
- Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Jana Trenner
- Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Carolin Delker
- Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Marcel Quint
- Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
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231
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Lescoat C, Perrotte D, Barry S, Oden É, Herbet V, Beaunée G, Tabouret M, Benoit F, Pitel PH, Duquesne V, Bailly X, Thézé J, Kouokam G. Spatio-temporal distribution and international context of bovine viral diarrhoea virus genetic diversity in France. Vet Res 2024; 55:129. [PMID: 39363368 PMCID: PMC11451180 DOI: 10.1186/s13567-024-01377-9] [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: 05/21/2024] [Accepted: 08/20/2024] [Indexed: 10/05/2024] Open
Abstract
Bovine viral diarrhoea (BVD) is one of the most economically damaging livestock enzootic diseases in the world. BVD aetiological agents are three pestiviruses (BVDV-1, -2 and HoBi-like pestivirus), which exhibit high genetic diversity and complex transmission cycles. This considerably hampers the management of the disease, which is why eradication plans have been implemented in several countries. In France, a national plan has been in place since 2019. Our understanding of its impact on the distribution of BVDV genotypes is limited by the availability of French genetic data. Here, we conducted a molecular epidemiology study to refine our knowledge of BVDV genetic diversity in France, characterise its international relationships, and analyse national spatio-temporal genotypic distribution. We collated 1037 BVDV-positive samples throughout France between 2011 and 2023, with a greater sampling effort in two major cattle production areas. We developed a high-throughput sequencing protocol which we used to complete the 5'UTR genotyping of this collection. We show that two main BVDV-1 genotypes, 1e and 1b, account for 88% of genotyped sequences. We also identified seven other BVDV-1 genotypes occurring at low frequencies and three BVDV-2 samples (genotype 2c). Phylogenetic analyses indicate different worldwide distribution patterns between the two main BVDV-1 genotypes. Their relative frequencies present no major changes in France since the 1990s and few variations at the national scale. We also found some degree of local spatial structuring in western France. Overall, our results demonstrate the potential of large-scale sequence-based surveillance to monitor changes in the epidemiological situation of enzootic diseases.
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Affiliation(s)
- Claire Lescoat
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR EPIA, Saint-Genès-Champanelle, France
| | | | - Séverine Barry
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR EPIA, Saint-Genès-Champanelle, France
| | | | - Valentin Herbet
- Ruminant Disease and Welfare Unit, National Reference Laboratory for BVD, ANSES, Ploufragan-Plouzané-Niort Laboratory, Niort, France
| | | | - Marc Tabouret
- Ruminant Disease and Welfare Unit, National Reference Laboratory for BVD, ANSES, Ploufragan-Plouzané-Niort Laboratory, Niort, France
| | | | | | | | - Xavier Bailly
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR EPIA, Saint-Genès-Champanelle, France
| | - Julien Thézé
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR EPIA, Saint-Genès-Champanelle, France.
| | - Guy Kouokam
- Ruminant Disease and Welfare Unit, National Reference Laboratory for BVD, ANSES, Ploufragan-Plouzané-Niort Laboratory, Niort, France
- French Federation of Animal Health Protection Groups (GDS France), Paris, France
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232
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Crespo-Bellido A, Hoyer JS, Burgos-Amengual Y, Duffy S. Phylogeographic analysis of Begomovirus coat and replication-associated proteins. J Gen Virol 2024; 105:002037. [PMID: 39446128 PMCID: PMC11500754 DOI: 10.1099/jgv.0.002037] [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: 11/20/2023] [Accepted: 10/04/2024] [Indexed: 10/25/2024] Open
Abstract
Begomoviruses are globally distributed plant pathogens that significantly limit crop production. These viruses are traditionally described according to phylogeographic distribution and categorized into two groups: begomoviruses from the Africa, Asia, Europe and Oceania (AAEO) region and begomoviruses from the Americas. Monopartite begomoviruses are more common in the AAEO region, while bipartite viruses predominate in the Americas, where the begomoviruses lack the V2/AV2 gene involved in inter-cellular movement and RNA silencing suppression found in AAEO begomoviruses. While these features are generally accepted as lineage-defining, the number of known species has doubled due to sequence-based discovery since 2010. To re-evaluate the geographic groupings after the rapid expansion of the genus, we conducted phylogenetic analyses for begomovirus species representatives of the two longest and most conserved begomovirus proteins: the coat and replication-associated proteins. Both proteins still largely support the broad AAEO and Americas begomovirus groupings, except for sweet potato-infecting begomoviruses that form an independent, well-supported clade for their coat protein regardless of the region they were isolated from. Our analyses do not support more fine-scaled phylogeographic groupings. Monopartite and bipartite genome organizations are broadly interchanged throughout the phylogenies, and the absence of the V2/AV2 gene is highly reflective of the split between Americas and AAEO begomoviruses. We observe significant evidence of recombination within the Americas and within the AAEO region but rarely between the regions. We speculate that increased globalization of agricultural trade, the invasion of polyphagous whitefly vector biotypes and recombination will blur begomovirus phylogeographic delineations in the future.
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Affiliation(s)
- Alvin Crespo-Bellido
- Department of Ecology, Evolution and Natural Resources, School of Environmental and Biological Sciences, Rutgers, the State University of New Jersey, New Brunswick, NJ, USA
| | - J. Steen Hoyer
- Department of Ecology, Evolution and Natural Resources, School of Environmental and Biological Sciences, Rutgers, the State University of New Jersey, New Brunswick, NJ, USA
| | - Yeissette Burgos-Amengual
- Department of Ecology, Evolution and Natural Resources, School of Environmental and Biological Sciences, Rutgers, the State University of New Jersey, New Brunswick, NJ, USA
- Department of Biology, University of Puerto Rico at Mayagüez, Mayagüez, Puerto Rico
| | - Siobain Duffy
- Department of Ecology, Evolution and Natural Resources, School of Environmental and Biological Sciences, Rutgers, the State University of New Jersey, New Brunswick, NJ, USA
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233
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Kryukov AP, Kryukov KA, Collier K, Fang B, Edwards SV. Mitogenomics clarifies the position of the Nearctic magpies ( Pica hudsonia and Pica nuttalli) within the Holarctic magpie radiation. Curr Zool 2024; 70:618-630. [PMID: 39463698 PMCID: PMC11502158 DOI: 10.1093/cz/zoad048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 10/27/2023] [Indexed: 10/29/2024] Open
Abstract
Partial separation of a peripheral population may lead to its divergence and, potentially, speciation due to genetic drift followed by selection and geographic isolation. This process may cause taxonomic uncertainty because reproductive isolation in allopatry cannot be verified directly. The two Nearctic allopatric species of magpies (Aves, Corvidae: Pica) serve as a good example of these problems. The Black-billed magpie Pica hudsonia is widely distributed in North America, whereas the Yellow-billed Magpie Pica nuttalli is endemic to a restricted range in California. Their relationships with Palearctic species have been little studied. We obtained complete mitochondrial genomes of both Nearctic magpie species, along with the Eurasian Magpie (Pica pica) and the Oriental Magpie (Pica serica), 20 mitogenomes in total. Phylogenetic analysis reveals a basal position of P. serica, and P. pica as a sister clade to the two Nearctic species. P. hudsonia and P. nuttalli form reciprocal monophyletic subclades, showing recent divergence between and within them. Our data show that the Nearctic magpie lineage diverged from the common ancestor with P. pica, with a single migration wave via the Beringia. Within the Nearctic, we hypothesize a peripatric mode of speciation among Pica taxa due to the divergence and separation of the small marginal population in California below the Sierra-Nevada mountains. Diversifying amino acid substitutions in ND4-ND5-ND6 genes along the branch leading to the New World clade may indicate selection for heat-tolerance. Considering the clear phenotypic differences between P. hudsonia and P. nuttalli, our data, showing their reciprocal monophylies and genetic distinctness, is consistent with the two-species taxonomy.
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Affiliation(s)
- Alexey P Kryukov
- Laboratory of Evolutionary Zoology and Genetics, Federal Scientific Center of the East Asia Terrestrial Biodiversity, Russian Academy of Sciences, Vladivostok 690022, Russia
| | - Kirill A Kryukov
- Center for Genome Informatics, Bioinformation and DDBJ Center, National Institute of Genetics, 1111 Yata, Mishima 411-8540, Japan
| | - Kathleen Collier
- University of Alaska Museum of the North, University of Alaska, Fairbanks, AK 99775, USA
| | - Bohao Fang
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, USA
| | - Scott V Edwards
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, USA
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234
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Gent V, Lu YJ, Lukhele S, Dhar N, Dangor Z, Hosken N, Malley R, Madhi SA, Kwatra G. Surface protein distribution in Group B Streptococcus isolates from South Africa and identifying vaccine targets through in silico analysis. Sci Rep 2024; 14:22665. [PMID: 39349584 PMCID: PMC11442663 DOI: 10.1038/s41598-024-73175-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Accepted: 09/16/2024] [Indexed: 10/04/2024] Open
Abstract
Group B Streptococcus (GBS) is a major cause of pneumonia, sepsis, and meningitis in infants younger than 3 months of age. Furthermore, GBS infection in pregnant women is associated with stillbirths and pre-term delivery. It also causes disease in immunocompromised adults and the elderly, but the highest incidence of the disease occurs in neonates and young infants. At this time, there are no licensed vaccines against GBS. Complete GBS genome sequencing has helped identify genetically conserved and immunogenic proteins, which could serve as vaccine immunogens. In this study, in silico reverse vaccinology method were used to evaluate the prevalence and conservation of GBS proteins in invasive and colonizing isolates from South African infants and women, respectively. Furthermore, this study aimed to predict potential GBS vaccine targets by evaluating metrics such as antigenicity, physico-chemical properties, subcellular localization, secondary and tertiary structures, and epitope prediction and conservation. A total of 648 invasive and 603 colonizing GBS isolate sequences were screened against a panel of 89 candidate GBS proteins. Ten of the 89 proteins were highly genetically conserved in invasive and colonizing GBS isolates, nine of which were computationally inferred proteins (gbs2106, SAN_1577, SAN_0356, SAN_1808, SAN_1685, SAN_0413, SAN_0990, SAN_1040, SAN_0226) and one was the surface Immunogenic Protein (SIP). Additionally, the nine proteins were predicted to be more antigenic than the SIP protein (antigenicity score of > 0.6498), highlighting their potential as GBS vaccine antigen targets.
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Affiliation(s)
- Vicky Gent
- South African Medical Research Council: Vaccines and Infectious Diseases Analytics Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Ying-Jie Lu
- Division of Infectious Diseases, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | - Sindiswa Lukhele
- South African Medical Research Council: Vaccines and Infectious Diseases Analytics Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Nisha Dhar
- South African Medical Research Council: Vaccines and Infectious Diseases Analytics Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Ziyaad Dangor
- South African Medical Research Council: Vaccines and Infectious Diseases Analytics Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Nancy Hosken
- Center for Vaccine Innovation and Access, PATH, Seattle, WA, USA
| | - Richard Malley
- Division of Infectious Diseases, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | - Shabir A Madhi
- South African Medical Research Council: Vaccines and Infectious Diseases Analytics Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Wits Infectious Diseases and Oncology Research Institute, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Gaurav Kwatra
- South African Medical Research Council: Vaccines and Infectious Diseases Analytics Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
- Department of Clinical Microbiology, Christian Medical College, Vellore, India.
- Division of Infectious Diseases, Department of Pediatrics, Cincinnati Children's Hospital Medical Center and University of Cincinnati College of Medicine, Cincinnati, OH, USA.
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235
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Logsdon GA, Ebert P, Audano PA, Loftus M, Porubsky D, Ebler J, Yilmaz F, Hallast P, Prodanov T, Yoo D, Paisie CA, Harvey WT, Zhao X, Martino GV, Henglin M, Munson KM, Rabbani K, Chin CS, Gu B, Ashraf H, Austine-Orimoloye O, Balachandran P, Bonder MJ, Cheng H, Chong Z, Crabtree J, Gerstein M, Guethlein LA, Hasenfeld P, Hickey G, Hoekzema K, Hunt SE, Jensen M, Jiang Y, Koren S, Kwon Y, Li C, Li H, Li J, Norman PJ, Oshima KK, Paten B, Phillippy AM, Pollock NR, Rausch T, Rautiainen M, Scholz S, Song Y, Söylev A, Sulovari A, Surapaneni L, Tsapalou V, Zhou W, Zhou Y, Zhu Q, Zody MC, Mills RE, Devine SE, Shi X, Talkowski ME, Chaisson MJP, Dilthey AT, Konkel MK, Korbel JO, Lee C, Beck CR, Eichler EE, Marschall T. Complex genetic variation in nearly complete human genomes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.24.614721. [PMID: 39372794 PMCID: PMC11451754 DOI: 10.1101/2024.09.24.614721] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/08/2024]
Abstract
Diverse sets of complete human genomes are required to construct a pangenome reference and to understand the extent of complex structural variation. Here, we sequence 65 diverse human genomes and build 130 haplotype-resolved assemblies (130 Mbp median continuity), closing 92% of all previous assembly gaps1,2 and reaching telomere-to-telomere (T2T) status for 39% of the chromosomes. We highlight complete sequence continuity of complex loci, including the major histocompatibility complex (MHC), SMN1/SMN2, NBPF8, and AMY1/AMY2, and fully resolve 1,852 complex structural variants (SVs). In addition, we completely assemble and validate 1,246 human centromeres. We find up to 30-fold variation in α-satellite high-order repeat (HOR) array length and characterize the pattern of mobile element insertions into α-satellite HOR arrays. While most centromeres predict a single site of kinetochore attachment, epigenetic analysis suggests the presence of two hypomethylated regions for 7% of centromeres. Combining our data with the draft pangenome reference1 significantly enhances genotyping accuracy from short-read data, enabling whole-genome inference3 to a median quality value (QV) of 45. Using this approach, 26,115 SVs per sample are detected, substantially increasing the number of SVs now amenable to downstream disease association studies.
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Affiliation(s)
- Glennis A Logsdon
- Perelman School of Medicine, University of Pennsylvania, Department of Genetics, Epigenetics Institute, Philadelphia, PA, USA
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Peter Ebert
- Core Unit Bioinformatics, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University, Düsseldorf, Germany
- Center for Digital Medicine, Heinrich Heine University, Düsseldorf, Germany
| | - Peter A Audano
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Mark Loftus
- Clemson University, Department of Genetics & Biochemistry, Clemson, SC, USA
- Center for Human Genetics, Clemson University, Greenwood, SC, USA
| | - David Porubsky
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Jana Ebler
- Institute for Medical Biometry and Bioinformatics, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University, Düsseldorf, Germany
- Center for Digital Medicine, Heinrich Heine University, Düsseldorf, Germany
| | - Feyza Yilmaz
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Pille Hallast
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Timofey Prodanov
- Institute for Medical Biometry and Bioinformatics, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University, Düsseldorf, Germany
- Center for Digital Medicine, Heinrich Heine University, Düsseldorf, Germany
| | - DongAhn Yoo
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Carolyn A Paisie
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - William T Harvey
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Xuefang Zhao
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Gianni V Martino
- Clemson University, Department of Genetics & Biochemistry, Clemson, SC, USA
- Center for Human Genetics, Clemson University, Greenwood, SC, USA
- Medical University of South Carolina, College of Graduate Studies, Charleston, SC, USA
| | - Mir Henglin
- Institute for Medical Biometry and Bioinformatics, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University, Düsseldorf, Germany
- Center for Digital Medicine, Heinrich Heine University, Düsseldorf, Germany
| | - Katherine M Munson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Keon Rabbani
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA
| | - Chen-Shan Chin
- Foundation of Biological Data Sciences, Belmont, CA, USA
| | - Bida Gu
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA
| | - Hufsah Ashraf
- Institute for Medical Biometry and Bioinformatics, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University, Düsseldorf, Germany
- Center for Digital Medicine, Heinrich Heine University, Düsseldorf, Germany
| | - Olanrewaju Austine-Orimoloye
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | | | - Marc Jan Bonder
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands; Oncode Institute, Utrecht, The Netherlands
- Division of Computational Genomics and Systems Genetics, German Cancer Research Center, Heidelberg, Germany
| | - Haoyu Cheng
- Department of Biomedical Informatics and Data Science, Yale School of Medicine, New Haven, CT, USA
| | - Zechen Chong
- Department of Biomedical Informatics and Data Science, Heersink School of Medicine, University of Alabama, Birmingham, AL, USA
| | - Jonathan Crabtree
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Mark Gerstein
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
| | - Lisbeth A Guethlein
- Department of Structural Biology, School of Medicine, Stanford University, Stanford, CA, USA
| | - Patrick Hasenfeld
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - Glenn Hickey
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA
| | - Kendra Hoekzema
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Sarah E Hunt
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Matthew Jensen
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
| | - Yunzhe Jiang
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
| | - Sergey Koren
- Genome Informatics Section, Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Youngjun Kwon
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Chong Li
- Temple University, Department of Computer and Information Sciences, College of Science and Technology, Philadelphia, PA, USA
- Temple University, Institute for Genomics and Evolutionary Medicine, Philadelphia, PA, USA
| | - Heng Li
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Jiaqi Li
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
| | - Paul J Norman
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO, USA
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Keisuke K Oshima
- Perelman School of Medicine, University of Pennsylvania, Department of Genetics, Epigenetics Institute, Philadelphia, PA, USA
| | - Benedict Paten
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA
| | - Adam M Phillippy
- Genome Informatics Section, Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Nicholas R Pollock
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO, USA
| | - Tobias Rausch
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - Mikko Rautiainen
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Stephan Scholz
- Institute of Medical Microbiology and Hospital Hygiene, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
| | - Yuwei Song
- Department of Biomedical Informatics and Data Science, Heersink School of Medicine, University of Alabama, Birmingham, AL, USA
| | - Arda Söylev
- Institute for Medical Biometry and Bioinformatics, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University, Düsseldorf, Germany
- Center for Digital Medicine, Heinrich Heine University, Düsseldorf, Germany
| | - Arvis Sulovari
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Likhitha Surapaneni
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Vasiliki Tsapalou
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - Weichen Zhou
- Department of Computational Medicine & Bioinformatics, University of Michigan, MI, USA
| | - Ying Zhou
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Qihui Zhu
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
- Stanford Health Care, Palo Alto, CA, USA
| | | | - Ryan E Mills
- Department of Computational Medicine & Bioinformatics, University of Michigan, MI, USA
| | - Scott E Devine
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Xinghua Shi
- Temple University, Department of Computer and Information Sciences, College of Science and Technology, Philadelphia, PA, USA
- Temple University, Institute for Genomics and Evolutionary Medicine, Philadelphia, PA, USA
| | - Mike E Talkowski
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Neurology, Harvard Medical School, Boston, MA, USA
| | - Mark J P Chaisson
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA
| | - Alexander T Dilthey
- Center for Digital Medicine, Heinrich Heine University, Düsseldorf, Germany
- Institute of Medical Microbiology and Hospital Hygiene, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
| | - Miriam K Konkel
- Clemson University, Department of Genetics & Biochemistry, Clemson, SC, USA
- Center for Human Genetics, Clemson University, Greenwood, SC, USA
| | - Jan O Korbel
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - Charles Lee
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Christine R Beck
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
- The University of Connecticut Health Center, Farmington, CT, USA
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Tobias Marschall
- Institute for Medical Biometry and Bioinformatics, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University, Düsseldorf, Germany
- Center for Digital Medicine, Heinrich Heine University, Düsseldorf, Germany
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236
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Lu W, Nutaratat P, Kumla J, Tibpromma S, Elgorban AM, Karunarathna SC, Suwannarach N. Morphological and molecular identification of two new Marasmiellus species (Omphalotaceae, Agaricales) from Thailand. MycoKeys 2024; 109:31-48. [PMID: 39359355 PMCID: PMC11445607 DOI: 10.3897/mycokeys.109.129791] [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: 06/16/2024] [Accepted: 08/29/2024] [Indexed: 10/04/2024] Open
Abstract
Marasmiellus (Omphalotaceae, Agaricales) specimens collected in Thailand were investigated based on morphological characteristics and molecular phylogenetic analyses. In the present study, two species are introduced as new to science, namely Marasmiellusthailandicus and M.minutisporus. Phylogenetic analyses were carried out based on the internal transcribed spacer (nrITS) and nuclear ribosomal RNA large subunit (nrLSU) regions, and the results revealed that the two new taxa are distinct species within Marasmiellus. Another specimen was identified as M.scandens and is reported for the first time with morphology and molecular data from Thailand. Descriptions, illustrations, and phylogenetic results are provided. In addition, M.diaphanus and M.colocasiae are proposed as new combinations of Collybiopsisdiaphana and Paramarasmiuscolocasiae, respectively, based on the phylogenetic evidence.
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Affiliation(s)
- Wenhua Lu
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Pumin Nutaratat
- Center of Excellence in Microbial Diversity and Sustainable Utilization, Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Jaturong Kumla
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Saowaluck Tibpromma
- Department of Biology, Faculty of Science and Digital Innovation, Thaksin University, Pa Phayom, Phatthalung 93210, Thailand
| | - Abdallah M. Elgorban
- Microbial Technology for Agriculture, Food and Environment Research Center, Faculty of Science and Digital Innovation, Thaksin University, Pa Phayom, Phatthalung 93210, Thailand
| | - Samantha C. Karunarathna
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
- Department of Biology, Faculty of Science and Digital Innovation, Thaksin University, Pa Phayom, Phatthalung 93210, Thailand
| | - Nakarin Suwannarach
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
- Center of Excellence in Microbial Diversity and Sustainable Utilization, Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
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237
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Quiroga-Carmona M, Liphardt S, Bautista NM, Jayat P, Teta P, Malaney JL, McFarland T, Cook JA, Blumer LM, Herrera ND, Cheviron ZA, Good JM, D’Elía G, Storz JF. Species limits and hybridization in Andean leaf-eared mice ( Phyllotis). BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.31.610610. [PMID: 39282442 PMCID: PMC11398333 DOI: 10.1101/2024.08.31.610610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 09/21/2024]
Abstract
Leaf-eared mice (genus Phyllotis) are among the most widespread and abundant small mammals in the Andean Altiplano, but species boundaries and distributional limits are often poorly delineated due to sparse survey data from remote mountains and high-elevation deserts. Here we report a combined analysis of mitochondrial DNA variation and whole-genome sequence (WGS) variation in Phyllotis mice to delimit species boundaries, to assess the timescale of diversification of the group, and to examine evidence for interspecific hybridization. Estimates of divergence dates suggest that most diversification of Phyllotis occurred during the past 3 million years. Consistent with the Pleistocene Aridification hypothesis, our results suggest that diversification of Phyllotis largely coincided with climatically induced environmental changes in the mid- to late Pleistocene. Contrary to the Montane Uplift hypothesis, most diversification in the group occurred well after the major phase of uplift of the Central Andean Plateau. Species delimitation analyses revealed surprising patterns of cryptic diversity within several nominal forms, suggesting the presence of much undescribed alpha diversity in the genus. Results of genomic analyses revealed evidence of ongoing hybridization between the sister species Phyllotis limatus and P. vaccarum and suggest that the contemporary zone of range overlap between the two species represents an active hybrid zone.
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Affiliation(s)
- Marcial Quiroga-Carmona
- School of Biological Sciences, University of Nebraska, Lincoln, NE, United States
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
- Colección de Mamíferos, Facultad de Ciencias, Universidad Austral de Chile, Campus Isla Teja, Valdivia, Chile
| | - Schuyler Liphardt
- Division of Biological Sciences, University of Montana, Missoula, MT, United States
| | - Naim M. Bautista
- School of Biological Sciences, University of Nebraska, Lincoln, NE, United States
| | - Pablo Jayat
- Unidad Ejecutora Lillo (CONICET-Fundación Miguel Lillo), San Miguel de Tucumán, Argentina
- Departamento de Ciencias Básicas y Tecnológicas, Universidad Nacional de Chilecito (UNdeC), Argentina
| | - Pablo Teta
- División Mastozoología, Museo Argentino de Ciencias Naturales “Bernardino Rivadavia”, Ciudad Autónoma de Buenos Aires, Argentina
| | - Jason L. Malaney
- New Mexico Museum of Natural History and Science, Albuquerque, NM, United States
| | - Tabitha McFarland
- Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM, United States
- Department of Biology, University of New Mexico, Albuquerque, NM, United States
| | - Joseph A. Cook
- Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM, United States
- Department of Biology, University of New Mexico, Albuquerque, NM, United States
| | - L. Moritz Blumer
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Nathanael D. Herrera
- Division of Biological Sciences, University of Montana, Missoula, MT, United States
| | - Zachary A. Cheviron
- Division of Biological Sciences, University of Montana, Missoula, MT, United States
| | - Jeffrey M. Good
- Division of Biological Sciences, University of Montana, Missoula, MT, United States
| | - Guillermo D’Elía
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
- Colección de Mamíferos, Facultad de Ciencias, Universidad Austral de Chile, Campus Isla Teja, Valdivia, Chile
| | - Jay F. Storz
- School of Biological Sciences, University of Nebraska, Lincoln, NE, United States
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238
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Manzo E, Tomasello S. The first complete chloroplast genome for the species-rich genus Anthemis (Asteraceae). Mitochondrial DNA B Resour 2024; 9:1248-1253. [PMID: 39301046 PMCID: PMC11411556 DOI: 10.1080/23802359.2024.2405528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Accepted: 09/12/2024] [Indexed: 09/22/2024] Open
Abstract
Anthemis L. 1753 is a species-rich genus of Asteraceae. It includes species of economic value as ornamental, edible and medicinal plants. We report here the complete chloroplast genome of Anthemis cretica subsp. calabrica (Arcang.) R. Fern. 1975, the first chloroplast genome of any Anthemis species. For the scope, we have used long reads obtained with Oxford Nanopore technology. The assembled plastome is 149,509 bp long and is subdivided in a large single-copy region (LSC, 82,317 bp), a small single-copy region (SSC, 18,212 bp) and two inverted repeat regions (IR: 24,490 bp). It comprehends 136 predicted genes, of which 92 protein-coding genes, 35 tRNAs, and 8 rRNAs. The overall GC content is 37.54%. The position of A. cretica subsp. calabrica in the phylogenetic tree is congruent with those of previous analyses based on a few chloroplast or nuclear regions.
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Affiliation(s)
- Eleonora Manzo
- Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), University of Göttingen, Göttingen, Germany
| | - Salvatore Tomasello
- Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), University of Göttingen, Göttingen, Germany
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239
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Zhang X, Shi F, Yang K, Zhao C. The diversity and taxonomy of Tomentella (Thelephoraceae, Thelephorales) with descriptions of four new species from Southwestern China. MycoKeys 2024; 109:1-29. [PMID: 39328961 PMCID: PMC11422715 DOI: 10.3897/mycokeys.109.132941] [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: 07/24/2024] [Accepted: 08/28/2024] [Indexed: 09/28/2024] Open
Abstract
Taxonomy plays a central role in understanding the diversity of life, translating the products of biological exploration and discovery specimens and observations into systems of names that settle a "classification home" to taxa. Up to this point, studies on the taxonomy and phylogeny of the basidiomycetous genus Tomentella stemmed mainly from the temperate to boreal zones of the North Hemisphere, but were scarce in tropical Asia. In this study, four new species, viz. Tomentellaolivaceobasidiosa, T.velutina, T.wumenshanensis and T.yunnanensis from China, are described and illustrated based on the morphological characteristics and molecular phylogenetic analyses, in which the sequences of ITS+nLSU+mtSSU+RPB2 genes were used for the phylogenetic analyses using Maximum Likelihood, Maximum Parsimony and Bayesian Inference methods. All the new species can be well recognised by their macroscopical and anatomical characteristics. The four new species, closely related taxa in the phylogenetic tree and morphologically similar species are discussed.
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Affiliation(s)
- Xiaojie Zhang
- The Key Laboratory of Forest Resources Conservation and Utilization in the Southwest Mountains of China Ministry of Education, Key Laboratory of National Forestry and Grassland Administration on Biodiversity Conservation in Southwest China, Yunnan Provincial Key Laboratory for Conservation and Utilization of In-forest Resource, Southwest Forestry University, Kunming 650224, China
| | - Fulei Shi
- The Key Laboratory of Forest Resources Conservation and Utilization in the Southwest Mountains of China Ministry of Education, Key Laboratory of National Forestry and Grassland Administration on Biodiversity Conservation in Southwest China, Yunnan Provincial Key Laboratory for Conservation and Utilization of In-forest Resource, Southwest Forestry University, Kunming 650224, China
| | - Ke Yang
- College of Forestry, Southwest Forestry University, Kunming 650224, China
| | - Changlin Zhao
- The Key Laboratory of Forest Resources Conservation and Utilization in the Southwest Mountains of China Ministry of Education, Key Laboratory of National Forestry and Grassland Administration on Biodiversity Conservation in Southwest China, Yunnan Provincial Key Laboratory for Conservation and Utilization of In-forest Resource, Southwest Forestry University, Kunming 650224, China
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240
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Bunyat-Zada AR, Ducharme SE, Cleveland ME, Hoffman ER, Howe GW. Genome Mining Leads to the Identification of a Stable and Promiscuous Baeyer-Villiger Monooxygenase from a Thermophilic Microorganism. Chembiochem 2024; 25:e202400443. [PMID: 38991205 DOI: 10.1002/cbic.202400443] [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: 05/21/2024] [Revised: 07/05/2024] [Accepted: 07/11/2024] [Indexed: 07/13/2024]
Abstract
Baeyer-Villiger monooxygenases (BVMOs) are NAD(P)H-dependent flavoproteins that convert ketones to esters and lactones. While these enzymes offer an appealing alternative to traditional Baeyer-Villiger oxidations, these proteins tend to be either too unstable or exhibit too narrow of a substrate scope for implementation as industrial biocatalysts. Here, sequence similarity networks were used to search for novel BVMOs that are both stable and promiscuous. Our genome mining led to the identification of an enzyme from Chloroflexota bacterium (strain G233) dubbed ssnBVMO that exhibits i) the highest melting temperature of any naturally sourced BVMO (62.5 °C), ii) a remarkable kinetic stability across a wide range of conditions, similar to those of PAMO and PockeMO, iii) optimal catalysis at 50 °C, and iv) a broad substrate scope that includes linear aliphatic, aromatic, and sterically bulky ketones. Subsequent quantitative assays using propiophenone demonstrated >95 % conversion. Several fusions were also constructed that linked ssnBVMO to a thermostable phosphite dehydrogenase. These fusions can recycle NADPH and catalyze oxidations with sub-stoichiometric quantities of this expensive cofactor. Characterization of these fusions permitted identification of PTDH-L1-ssnBVMO as the most promising protein that could have utility as a seed sequence for enzyme engineering campaigns aiming to develop biocatalysts for Baeyer-Villiger oxidations.
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Affiliation(s)
- Amir R Bunyat-Zada
- Department of Chemistry, Queen's University, Kingston, Ontario, K7L 3N6, Canada
| | - Stephan E Ducharme
- Department of Chemistry, Queen's University, Kingston, Ontario, K7L 3N6, Canada
| | - Maria E Cleveland
- Department of Chemistry, Queen's University, Kingston, Ontario, K7L 3N6, Canada
| | - Esther R Hoffman
- Department of Chemistry, Queen's University, Kingston, Ontario, K7L 3N6, Canada
| | - Graeme W Howe
- Department of Chemistry, Queen's University, Kingston, Ontario, K7L 3N6, Canada
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241
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Bang WJ, Seol A, Shin S. Insights from multigene analysis: first report of a Southeast Asian Mosquito, Aedes (Mucidus) laniger (Diptera: Culicidae) on Jeju Island from Korea. Parasit Vectors 2024; 17:386. [PMID: 39267122 PMCID: PMC11395179 DOI: 10.1186/s13071-024-06373-8] [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: 02/21/2024] [Accepted: 06/24/2024] [Indexed: 09/14/2024] Open
Abstract
BACKGROUND Certain mosquitoes are known as dominant vectors worldwide, and transmit infectious diseases. The expansion of mosquito habitats due to climate change and increased human activities poses a significant health threat by facilitating the spread of various non-native infectious diseases. This study focused on the detection of the Southeast Asian mosquito species, Aedes (Mucidus) laniger (Wiedemann, 1820) on Jeju Island, the southernmost region of the Republic of Korea (ROK), highlighting the potential risks associated with the spread of vector-borne diseases, particularly emphasizing the elevated likelihood of invasion by Southeast Asian mosquitoes. METHODS Field surveys were conducted in August 2023 on Jeju Island. Adult mosquitoes were collected using BG-sentinel traps and identified to the species level using taxonomic keys. Morphological and molecular analyses were employed to confirm species designations. Molecular data, including mitochondrial and nuclear genes, were used for phylogenetic analysis, which was performed to compare and identify among recorded subgenera in ROK. Species distribution modeling for Ae. laniger was performed to predict potential habitats using R package 'BIOMOD2'. RESULTS The two specimens of Ae. laniger were collected for the first time on Jeju Island. Morphological and molecular analyses confirmed the identity of this species within the subgenus Mucidus and validated the first record of this species in the ROK. We employed a simple multigene phylogenetic analysis to confirm a new mosquito record at the genus and subgenus levels, finally validating the consistency between morphological identification and molecular phylogenetic outcomes. Furthermore, we have updated the taxonomic keys for the genus Aedes in the ROK, and revised mosquito lists for Jeju Island, incorporating the inclusion of Ae. laniger. On the basis of species distribution modeling, the area of suitable habitat for Ae. laniger is expected to expand due to climate change, but this change did not appear to be meaningful in East Asia. CONCLUSIONS This case offers the first report of the Southeast Asian mosquito, Ae. laniger, in the ROK. The detection of this species on Jeju Island suggests the potential establishment of a breeding population their habitat and raises concerns about further expansion into the Korean Peninsula. Considering the annual occurrence of mosquito-borne disease cases in the Southeast Asia, it is essential to conduct monitoring not only in Jeju Island, where Ae. laniger has been identified, but also across the entire Korean Peninsula.
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Affiliation(s)
- Woo Jun Bang
- School of Biological Sciences, Seoul National University, Seoul, 08826, Republic of Korea
- Comparative Medicine Disease Research Center, Seoul National University, Seoul, 08826, Republic of Korea
| | - Ara Seol
- Warm Temperate and Subtropical Forest Research Center, National Institute of Forest Science, Jeju, 63582, Republic of Korea
| | - Seunggwan Shin
- School of Biological Sciences, Seoul National University, Seoul, 08826, Republic of Korea.
- Comparative Medicine Disease Research Center, Seoul National University, Seoul, 08826, Republic of Korea.
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242
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Tomasello S, Manzo E, Karbstein K. Comparative plastome assembly of the yellow ironweed ( Verbesina alternifolia) using Nanopore and Illumina reads. FRONTIERS IN PLANT SCIENCE 2024; 15:1429494. [PMID: 39328796 PMCID: PMC11424524 DOI: 10.3389/fpls.2024.1429494] [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: 05/08/2024] [Accepted: 08/16/2024] [Indexed: 09/28/2024]
Abstract
Chloroplast genomes (plastomes) represent a very important source of valuable information for phylogenetic and biogeographic reconstructions. The use of short reads (as those produced from Illumina sequencing), along with de novo read assembly, has been considered the "gold standard" for plastome reconstruction. However, short reads often cannot reconstruct long repetitive regions in chloroplast genomes. Long Nanopore (ONT) reads can help bridging long repetitive regions but are by far more error-prone than those produced by Illumina sequencing. Verbesina is the largest genus of tribe Heliantheae (Asteraceae) and includes species of economic importance as ornamental or as invasive weeds. However, no complete chloroplast genomes have been published yet for the genus. We utilized Illumina and Nanopore sequencing data and different assembly strategies to reconstruct the plastome of Verbesina alternifolia and evaluated the usefulness of the Nanopore assemblies. The two plastome sequence assemblages, one obtained with the Nanopore sequencing and the other inferred with Illumina reads, were identical, except for missing bases in homonucleotide regions. The best-assembled plastome of V. alternifolia was 152,050 bp in length and contained 80, 29, and four unique protein-coding genes, tRNAs, and rRNAs, respectively. When used as reference for mapping Illumina reads, all plastomes performed similarly. In a phylogenetic analysis including 28 other plastomes from closely related taxa (from the Heliantheae alliance), the two Verbesina chloroplast genomes grouped together and were nested among the other members of the tribe Heliantheae s.str. Our study highlights the usefulness of the Nanopore technology for assembling rapidly and cost-effectively chloroplast genomes, especially in taxonomic groups with paucity of publicly available plastomes.
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Affiliation(s)
- Salvatore Tomasello
- Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), University of Göttingen, Göttingen, Germany
| | - Eleonora Manzo
- Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), University of Göttingen, Göttingen, Germany
| | - Kevin Karbstein
- Department of Biogeochemical Integration, Max Planck Institute for Biogeochemistry, Jena, Germany
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243
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Topcu C, Vrancken B, Rodosthenous JH, van de Vijver D, Siakallis G, Lemey P, Kostrikis LG. Mapping Transmission Dynamics and Drug Resistance Surveillance in the Cyprus HIV-1 Epidemic (2017-2021). Viruses 2024; 16:1449. [PMID: 39339925 PMCID: PMC11437465 DOI: 10.3390/v16091449] [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: 06/26/2024] [Revised: 09/05/2024] [Accepted: 09/05/2024] [Indexed: 09/30/2024] Open
Abstract
The human immunodeficiency virus type 1 (HIV-1) epidemic has been a major public health threat on a global scale since the early 1980s. Despite the introduction of combination antiretroviral therapy (cART), the incidence of new HIV-1 infections continues to rise in some regions around the world. Thus, with the continuous transmission of HIV-1 and the lack of a cure, it is imperative for molecular epidemiological studies to be performed, to monitor the infection and ultimately be able to control the spread of this virus. This work provides a comprehensive molecular epidemiological analysis of the HIV-1 infection in Cyprus, through examining 305 HIV-1 sequences collected between 9 March 2017 and 14 October 2021. Employing advanced statistical and bioinformatic techniques, the research delved deeply into understanding the transmission dynamics of the HIV-1 epidemic in Cyprus, as well as the monitoring of HIV-1's genetic diversity and the surveillance of transmitted drug resistance. The characterization of Cyprus's HIV-1 epidemic revealed a diverse landscape, comprising 21 HIV-1 group M pure subtypes and circulating recombinant forms (CRFs), alongside numerous uncharacterized recombinant strains. Subtypes A1 and B emerged as the most prevalent strains, followed by CRF02_AG. The findings of this study also revealed high levels of transmitted drug resistance (TDR) patterns, raising concerns for the efficacy of cART. The demographic profiles of individuals involved in HIV-1 transmission underscored the disproportionate burden borne by young to middle-aged Cypriot males, particularly those in the MSM community, who reported contracting the virus in Cyprus. An assessment of the spatiotemporal evolutionary dynamics illustrated the global interconnectedness of HIV-1 transmission networks, implicating five continents in the dissemination of strains within Cyprus: Europe, Africa, Asia, North America, and Oceania. Overall, this study advances the comprehension of the HIV-1 epidemic in Cyprus and highlights the importance of understanding HIV-1's transmission dynamics through continuous surveillance efforts. Furthermore, this work emphasizes the critical role of state-of-the-art bioinformatics analyses in addressing the challenges posed by HIV-1 transmission globally, laying the groundwork for public health interventions aimed at curbing its spread and improving patient outcomes.
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Affiliation(s)
- Cicek Topcu
- Laboratory of Biotechnology and Molecular Virology, Department of Biological Sciences, University of Cyprus, 2109 Nicosia, Cyprus
| | - Bram Vrancken
- Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, 1050 Bruxelles, Belgium
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000 Leuven, Belgium
| | - Johana Hezka Rodosthenous
- Laboratory of Biotechnology and Molecular Virology, Department of Biological Sciences, University of Cyprus, 2109 Nicosia, Cyprus
| | - David van de Vijver
- Department of Viroscience, Erasmus University Medical Centre, 3015 GD Rotterdam, The Netherlands
| | | | - Philippe Lemey
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000 Leuven, Belgium
| | - Leondios G. Kostrikis
- Laboratory of Biotechnology and Molecular Virology, Department of Biological Sciences, University of Cyprus, 2109 Nicosia, Cyprus
- Cyprus Academy of Sciences, Letters, and Arts, 1011 Nicosia, Cyprus
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244
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Rødsgaard-Jørgensen A, Leal-Dutra CA, de Santana SF, Jensen AR, Marques RE, Aguiar ERGR, Shik JZ. Two +ssRNA mycoviruses cohabiting the fungal cultivar of leafcutter ants. Virol J 2024; 21:211. [PMID: 39232804 PMCID: PMC11373429 DOI: 10.1186/s12985-024-02465-0] [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: 05/22/2024] [Accepted: 08/08/2024] [Indexed: 09/06/2024] Open
Abstract
Leafcutter ants are dominant herbivores in the Neotropics and rely on a fungus (Leucoagaricus gongylophorus) to transform freshly gathered leaves into a source of nourishment rather than consuming the vegetation directly. Here we report two virus-like particles that were isolated from L. gongylophorus and observed using transmission electron microscopy. RNA sequencing identified two +ssRNA mycovirus strains, Leucoagaricus gongylophorus tymo-like virus 1 (LgTlV1) and Leucoagaricus gongylophorus magoulivirus 1 (LgMV1). Genome annotation of LgTlV1 (7401 nt) showed conserved domains for methyltransferase, endopeptidase, viral RNA helicase, and RNA-dependent RNA polymerase (RdRp). The smaller genome of LgMV1 (2636 nt) contains one open reading frame encoding an RdRp. While we hypothesize these mycoviruses function as symbionts in leafcutter farming systems, further study will be needed to test whether they are mutualists, commensals, or parasites.
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Affiliation(s)
- Asta Rødsgaard-Jørgensen
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100, Copenhagen, Denmark
| | - Caio Ambrosio Leal-Dutra
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100, Copenhagen, Denmark.
| | - Sabrina Ferreira de Santana
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100, Copenhagen, Denmark
- Department of Biological Science, Center of Biotechnology and Genetics, Universidade Estadual de Santa Cruz, Ilhéus, Brazil
| | - Asger Roland Jensen
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100, Copenhagen, Denmark
| | - Rafael Elias Marques
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | | | - Jonathan Zvi Shik
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100, Copenhagen, Denmark
- Smithsonian Tropical Research Institute, Apartado Postal, 0843-03092, Balboa, Ancon, Panama
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245
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Banyard AC, Bennison A, Byrne AMP, Reid SM, Lynton-Jenkins JG, Mollett B, De Silva D, Peers-Dent J, Finlayson K, Hall R, Blockley F, Blyth M, Falchieri M, Fowler Z, Fitzcharles EM, Brown IH, James J. Detection and spread of high pathogenicity avian influenza virus H5N1 in the Antarctic Region. Nat Commun 2024; 15:7433. [PMID: 39227574 PMCID: PMC11372179 DOI: 10.1038/s41467-024-51490-8] [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: 11/23/2023] [Accepted: 08/08/2024] [Indexed: 09/05/2024] Open
Abstract
Until recent events, the Antarctic was the only major geographical region in which high pathogenicity avian influenza virus (HPAIV) had never previously been detected. Here we report on the detection of clade 2.3.4.4b H5N1 HPAIV in the Antarctic and sub-Antarctic regions of South Georgia and the Falkland Islands, respectively. We initially detected H5N1 HPAIV in samples collected from brown skuas at Bird Island, South Georgia on 8th October 2023. Since this detection, mortalities were observed in several avian and mammalian species at multiple sites across South Georgia. Subsequent testing confirmed H5N1 HPAIV across several sampling locations in multiple avian species and two seal species. Simultaneously, we also confirmed H5N1 HPAIV in southern fulmar and black-browed albatross in the Falkland Islands. Genetic assessment of the virus indicates spread from South America, likely through movement of migratory birds. Critically, genetic assessment of sequences from mammalian species demonstrates no increased risk to human populations above that observed in other instances of mammalian infections globally. Here we describe the detection, species impact and genetic composition of the virus and propose both introductory routes and potential long-term impact on avian and mammalian species across the Antarctic region. We also speculate on the threat to specific populations following recent reports in the area.
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Affiliation(s)
- Ashley C Banyard
- Department of Virology, Animal and Plant Health Agency (APHA-Weybridge), Woodham Lane, Addlestone, Surrey, KT15 3NB, UK.
- WOAH/FAO International Reference Laboratory for Avian Influenza, Animal and Plant Health Agency (APHA-Weybridge), Woodham Lane, Addlestone, Surrey, KT15 3NB, UK.
| | - Ashley Bennison
- British Antarctic Survey, Madingley Road, Cambridge, CB3 0ET, UK
| | - Alexander M P Byrne
- Department of Virology, Animal and Plant Health Agency (APHA-Weybridge), Woodham Lane, Addlestone, Surrey, KT15 3NB, UK
- Worldwide Influenza Centre, The Francis Crick Institute, Midland Road, London, NW1 1AT, UK
| | - Scott M Reid
- Department of Virology, Animal and Plant Health Agency (APHA-Weybridge), Woodham Lane, Addlestone, Surrey, KT15 3NB, UK
| | - Joshua G Lynton-Jenkins
- Department of Virology, Animal and Plant Health Agency (APHA-Weybridge), Woodham Lane, Addlestone, Surrey, KT15 3NB, UK
- WOAH/FAO International Reference Laboratory for Avian Influenza, Animal and Plant Health Agency (APHA-Weybridge), Woodham Lane, Addlestone, Surrey, KT15 3NB, UK
| | - Benjamin Mollett
- Department of Virology, Animal and Plant Health Agency (APHA-Weybridge), Woodham Lane, Addlestone, Surrey, KT15 3NB, UK
| | - Dilhani De Silva
- Department of Virology, Animal and Plant Health Agency (APHA-Weybridge), Woodham Lane, Addlestone, Surrey, KT15 3NB, UK
| | - Jacob Peers-Dent
- Department of Virology, Animal and Plant Health Agency (APHA-Weybridge), Woodham Lane, Addlestone, Surrey, KT15 3NB, UK
| | - Kim Finlayson
- KEMH Pathology and Food, Water & Environmental Laboratory, St Mary's Walk, Stanley, FIQQ 1ZZ, Falkland Islands
| | - Rosamund Hall
- British Antarctic Survey, Madingley Road, Cambridge, CB3 0ET, UK
| | - Freya Blockley
- British Antarctic Survey, Madingley Road, Cambridge, CB3 0ET, UK
| | - Marcia Blyth
- British Antarctic Survey, Madingley Road, Cambridge, CB3 0ET, UK
| | - Marco Falchieri
- Department of Virology, Animal and Plant Health Agency (APHA-Weybridge), Woodham Lane, Addlestone, Surrey, KT15 3NB, UK
| | - Zoe Fowler
- Department of Agriculture, Bypass Road, Stanley, FIQQ 1ZZ, Falkland Islands
| | | | - Ian H Brown
- Department of Virology, Animal and Plant Health Agency (APHA-Weybridge), Woodham Lane, Addlestone, Surrey, KT15 3NB, UK
- WOAH/FAO International Reference Laboratory for Avian Influenza, Animal and Plant Health Agency (APHA-Weybridge), Woodham Lane, Addlestone, Surrey, KT15 3NB, UK
| | - Joe James
- Department of Virology, Animal and Plant Health Agency (APHA-Weybridge), Woodham Lane, Addlestone, Surrey, KT15 3NB, UK.
- WOAH/FAO International Reference Laboratory for Avian Influenza, Animal and Plant Health Agency (APHA-Weybridge), Woodham Lane, Addlestone, Surrey, KT15 3NB, UK.
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246
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Pietluch F, Mackiewicz P, Ludwig K, Gagat P. A New Model and Dating for the Evolution of Complex Plastids of Red Alga Origin. Genome Biol Evol 2024; 16:evae192. [PMID: 39240751 DOI: 10.1093/gbe/evae192] [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: 11/10/2023] [Revised: 08/14/2024] [Accepted: 08/31/2024] [Indexed: 09/08/2024] Open
Abstract
Complex plastids, characterized by more than two bounding membranes, still present an evolutionary puzzle for the traditional endosymbiotic theory. Unlike primary plastids that directly evolved from cyanobacteria, complex plastids originated from green or red algae. The Chromalveolata hypothesis proposes a single red alga endosymbiosis that involved the ancestor of all the Chromalveolata lineages: cryptophytes, haptophytes, stramenopiles, and alveolates. As extensive phylogenetic analyses contradict the monophyly of Chromalveolata, serial plastid endosymbiosis models were proposed, suggesting a single secondary red alga endosymbiosis within Cryptophyta, followed by subsequent plastid transfers to other chromalveolates. Our findings based on 97 plastid-encoded markers, 112 species, and robust phylogenetic methods challenge all the existing models. They reveal two independent secondary endosymbioses, one within Cryptophyta and one within stramenopiles, precisely the phylum Ochrophyta, with two different groups of red algae. Consequently, we propose a new model for the emergence of red alga plastid-containing lineages and, through molecular clock analyses, estimate their ages.
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Affiliation(s)
- Filip Pietluch
- Department of Bioinformatics and Genomics, Faculty of Biotechnology, University of Wroclaw, 50-383 Wroclaw, Poland
| | - Paweł Mackiewicz
- Department of Bioinformatics and Genomics, Faculty of Biotechnology, University of Wroclaw, 50-383 Wroclaw, Poland
| | - Kacper Ludwig
- Department of Bioinformatics and Genomics, Faculty of Biotechnology, University of Wroclaw, 50-383 Wroclaw, Poland
| | - Przemysław Gagat
- Department of Bioinformatics and Genomics, Faculty of Biotechnology, University of Wroclaw, 50-383 Wroclaw, Poland
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247
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Valerio F, Martel C, Stefanescu C, van Nouhuys S, Kankare M, Duplouy A. Wolbachia strain diversity in a complex group of sympatric cryptic parasitoid wasp species. BMC Microbiol 2024; 24:319. [PMID: 39223450 PMCID: PMC11368008 DOI: 10.1186/s12866-024-03470-7] [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: 11/22/2023] [Accepted: 08/20/2024] [Indexed: 09/04/2024] Open
Abstract
BACKGROUND Maternally-inherited symbionts can induce pre-mating and/or post-mating reproductive isolation between sympatric host lineages, and speciation, by modifying host reproductive phenotypes. The large parasitoid wasp genus Cotesia (Braconidae) includes a diversity of cryptic species, each specialized in parasitizing one to few related Lepidoptera host species. Here, we characterized the infection status of an assemblage of 21 Cotesia species from 15 countries by several microbial symbionts, as a first step toward investigating whether symbionts may provide a barrier to gene flow between these parasitoid host lineages. RESULTS The symbiotic microbes Arsenophonus, Cardinium, Microsporidium and Spiroplasma were not detected in the Cotesia wasps. However, the endosymbiotic bacterium Wolbachia was present in at least eight Cotesia species, and hence we concentrated on it upon screening additional DNA extracts and SRAs from NCBI. Some of the closely related Cotesia species carry similar Wolbachia strains, but most Wolbachia strains showed patterns of horizontal transfer between phylogenetically distant host lineages. CONCLUSIONS The lack of co-phylogenetic signal between Wolbachia and Cotesia suggests that the symbiont and hosts have not coevolved to an extent that would drive species divergence between the Cotesia host lineages. However, as the most common facultative symbiont of Cotesia species, Wolbachia may still function as a key-player in the biology of the parasitoid wasps. Its precise role in the evolution of this complex clade of cryptic species remains to be experimentally investigated.
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Affiliation(s)
- Federica Valerio
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, Helsinki, Finland
| | | | | | - Saskya van Nouhuys
- Centre for Ecological Sciences, Indian Institute of Science, Bangalore, India
| | - Maaria Kankare
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | - Anne Duplouy
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, Helsinki, Finland.
- Department of Biology, Lund University, Lund, Sweden.
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248
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Godwe C, Goni OH, San JE, Sonela N, Tchakoute M, Nanfack A, Koro FK, Butel C, Vidal N, Duerr R, Martin DP, de Oliveira T, Peeters M, Altfeld M, Ayouba A, Ndung’u T, Tongo M. Phylogenetic evidence of extensive spatial mixing of diverse HIV-1 group M lineages within Cameroon but not between its neighbours. Virus Evol 2024; 10:veae070. [PMID: 39386075 PMCID: PMC11463025 DOI: 10.1093/ve/veae070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 07/12/2024] [Accepted: 08/28/2024] [Indexed: 10/12/2024] Open
Abstract
From the perspective of developing relevant interventions for treating HIV and controlling its spread, it is particularly important to comprehensively understand the underlying diversity of the virus, especially in countries where the virus has been present and evolving since the cross-species transmission event that triggered the global pandemic. Here, we generate and phylogenetically analyse sequences derived from the gag-protease (2010 bp; n = 115), partial integrase (345 bp; n = 36), and nef (719 bp; n = 321) genes of HIV-1 group M (HIV-1M) isolates sampled between 2000 and 2022 from two cosmopolitan cities and 40 remote villages of Cameroon. While 52.4% of all sequenced viruses belonged to circulating recombinant form (CRF) 02_AG (CRF02_AG), the remainder were highly diverse, collectively representing seven subtypes and sub-subtypes, eight CRFs, and 36 highly divergent lineages that fall outside the established HIV-1M classification. Additionally, in 77 samples for which at least two genes were typed, 31% of the studied viruses apparently had fragments from viruses belonging to different clades. Furthermore, we found that the distribution of HIV-1M populations is similar between different regions of Cameroon. In contrast, HIV-1M demographics in Cameroon differ significantly from those in its neighbouring countries in the Congo Basin (CB). In phylogenetic trees, viral sequences cluster according to the countries where they were sampled, suggesting that while there are minimal geographical or social barriers to viral dissemination throughout Cameroon, there is strongly impeded dispersal of HIV-1M lineages between Cameroon and other locations of the CB. This suggests that the apparent stability of highly diverse Cameroonian HIV-1M populations may be attributable to the extensive mixing of human populations within the country and the concomitant trans-national movements of major lineages with very similar degrees of fitness; coupled with the relatively infrequent inter-national transmission of these lineages from neighbouring countries in the CB.
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Affiliation(s)
- Célestin Godwe
- Center of Research for Emerging and Re-Emerging Diseases (CREMER), Institute of Medical Research and Study of Medicinal Plants (IMPM), Yaoundé, PO Box. 906 Yaoundé, Cameroon
- Department of Biochemistry, University of Douala, Douala, PO Box. 24157 Douala, Cameroon
| | - Oumarou H Goni
- Center of Research for Emerging and Re-Emerging Diseases (CREMER), Institute of Medical Research and Study of Medicinal Plants (IMPM), Yaoundé, PO Box. 906 Yaoundé, Cameroon
- Department of Microbiology, Faculty of Sciences, University of Yaoundé 1, Yaoundé, PO Box. 812 Yaoundé, Cameroon
| | - James E San
- KwaZulu-Natal Research Innovation and Sequencing Platform, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban 4001, South Africa
- Duke Human Vaccine Institute, Duke University, Durham, NC 27710, United States
| | - Nelson Sonela
- Center of Research for Emerging and Re-Emerging Diseases (CREMER), Institute of Medical Research and Study of Medicinal Plants (IMPM), Yaoundé, PO Box. 906 Yaoundé, Cameroon
- Chantal BIYA International Reference Centre for Research on HIV/AIDS prevention and management (CIRCB), Yaoundé PO Box. 3077 Yaoundé, Cameroon
- Weill Cornell Medical College, Department of Medicine, Cornell University, New York, NY 10021, United States
| | - Mérimé Tchakoute
- Programmes de Santé et développement au sein du Groupement de la Filière Bois du Cameroun, PO Box 495, Yaoundé, Cameroon
| | - Aubin Nanfack
- Chantal BIYA International Reference Centre for Research on HIV/AIDS prevention and management (CIRCB), Yaoundé PO Box. 3077 Yaoundé, Cameroon
| | - Francioli K Koro
- Department of Biochemistry, University of Douala, Douala, PO Box. 24157 Douala, Cameroon
| | - Christelle Butel
- TransVIHMI, Université de Montpellier, IRD, INSERM, 911 Avenue Agropolis, Montpellier, Montpellier cedex 34394, France
| | - Nicole Vidal
- TransVIHMI, Université de Montpellier, IRD, INSERM, 911 Avenue Agropolis, Montpellier, Montpellier cedex 34394, France
| | - Ralf Duerr
- Department of Medicine, Division of Infectious Diseases and Immunology, NYU Grossman School of Medicine, New York, NY 10016, United States
- Vaccine Center, NYU Grossman School of Medicine, New York, NY 10016, United States
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY 10016, United States
| | - Darren P Martin
- Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, Cape Town 7700, South Africa
| | - Tulio de Oliveira
- KwaZulu-Natal Research Innovation and Sequencing Platform, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban 4001, South Africa
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch 7600, South Africa
| | - Martine Peeters
- TransVIHMI, Université de Montpellier, IRD, INSERM, 911 Avenue Agropolis, Montpellier, Montpellier cedex 34394, France
| | - Marcus Altfeld
- Universitätsklinikum Hamburg-Eppendorf, Hamburg, Hamburg 20251, Germany
| | - Ahidjo Ayouba
- Center of Research for Emerging and Re-Emerging Diseases (CREMER), Institute of Medical Research and Study of Medicinal Plants (IMPM), Yaoundé, PO Box. 906 Yaoundé, Cameroon
- TransVIHMI, Université de Montpellier, IRD, INSERM, 911 Avenue Agropolis, Montpellier, Montpellier cedex 34394, France
| | - Thumbi Ndung’u
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, University of KwaZulu Natal, Durban 4013, South Africa
- Africa Health Research Institute (AHRI), Durban 4001, South Africa
- Ragon Institute of MGH, MIT and Harvard University, Cambridge MA 02139, United States
- Division of Infection and Immunity, University College London, London WC1E 6BT, United Kingdom
| | - Marcel Tongo
- Center of Research for Emerging and Re-Emerging Diseases (CREMER), Institute of Medical Research and Study of Medicinal Plants (IMPM), Yaoundé, PO Box. 906 Yaoundé, Cameroon
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, University of KwaZulu Natal, Durban 4013, South Africa
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249
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Hassanin A, Tu VT, Görföl T, Ngon LQ, Pham PV, Hang CT, Tuan TA, Prot M, Simon-Lorière E, Kemenesi G, Tóth GE, Moulin L, Wurtzer S. Phylogeography of horseshoe bat sarbecoviruses in Vietnam and neighbouring countries. Implications for the origins of SARS-CoV and SARS-CoV-2. Mol Ecol 2024; 33:e17486. [PMID: 39161178 DOI: 10.1111/mec.17486] [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: 03/13/2024] [Revised: 07/16/2024] [Accepted: 07/19/2024] [Indexed: 08/21/2024]
Abstract
Previous studies on horseshoe bats (Rhinolophus spp.) have described many coronaviruses related to SARS-CoV (SARSCoVr) in China and only a few coronaviruses related to SARS-CoV-2 (SARSCoV2r) in Yunnan (southern China), Cambodia, Laos and Thailand. Here, we report the results of several field missions carried out in 2017, 2021 and 2022 across Vietnam during which 1218 horseshoe bats were sampled from 19 locations. Sarbecoviruses were detected in 11% of faecal RNA extracts, with much more positives among Rhinolophus thomasi (46%). We assembled 38 Sarbecovirus genomes, including 32 SARSCoVr, four SARSCoV2r, and two recombinants of SARSCoVr and SARSCoV2r (RecSar), one showing a Spike protein very similar to SARS-CoV-2. We detected a bat co-infected with four coronaviruses, including two sarbecoviruses. Our analyses revealed that Sarbecovirus genomes evolve in Vietnam under strong geographical and host constraints. First, we found evidence for a deep separation between viruses from northern Vietnam and those from central and southern Vietnam. Second, we detected only SARSCoVr in Rhinolophus thomasi, both SARSCoVr and SARSCoV2r in Rhinolophus affinis, and only RecSar in Rhinolophus pusillus captured close to the border with China. Third, the bias in favour of Uracil in synonymous third codon positions of SARSCoVr extracted from R. thomasi showed a negative correlation with latitudes. Our results also provided support for an emergence of SARS-CoV in horseshoe bats from northern Yunnan and emergence of SARS-CoV-2 in horseshoe bats from northern Indochina subtropical forests (southern Yunnan, northern Laos and north-western Vietnam).
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Affiliation(s)
- Alexandre Hassanin
- Institut de Systématique, Évolution, Biodiversité (ISYEB), SU, MNHN, CNRS, EPHE, UA, Sorbonne Université, Paris, France
| | - Vuong Tan Tu
- Institute of Ecology and Biological Resources, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Tamás Görföl
- National Laboratory of Virology, Szentágothai Research Centre, University of Pécs, Pécs, Hungary
| | - Lam Quang Ngon
- Institute of Ecology and Biological Resources, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Phu Van Pham
- Institute of Ecology and Biological Resources, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Chu Thi Hang
- Institute of Ecology and Biological Resources, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Tran Anh Tuan
- Institute of Ecology and Biological Resources, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Mathieu Prot
- G5 Evolutionary Genomics of RNA Viruses, Institut Pasteur, Université Paris Cité, Paris, France
| | - Etienne Simon-Lorière
- G5 Evolutionary Genomics of RNA Viruses, Institut Pasteur, Université Paris Cité, Paris, France
| | - Gábor Kemenesi
- National Laboratory of Virology, Szentágothai Research Centre, University of Pécs, Pécs, Hungary
| | - Gábor Endre Tóth
- National Laboratory of Virology, Szentágothai Research Centre, University of Pécs, Pécs, Hungary
| | - Laurent Moulin
- R&D Laboratory, Direction Recherche, Développement et Qualité de l'Eau, Eau de Paris, Ivry-sur-Seine, France
| | - Sébastien Wurtzer
- R&D Laboratory, Direction Recherche, Développement et Qualité de l'Eau, Eau de Paris, Ivry-sur-Seine, France
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250
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Horton DM, Feleke Y, Pasquet RS, Javadi F, Melville KA, Delgado-Salinas A, Thulin M, Mithen RF, Gepts P, Egan AN. Phylogenetic systematics of Vigna sensu stricto in the context of Physostigma and allies. AMERICAN JOURNAL OF BOTANY 2024; 111:e16381. [PMID: 39107933 DOI: 10.1002/ajb2.16381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 05/14/2024] [Accepted: 05/15/2024] [Indexed: 11/06/2024]
Abstract
PREMISE Vigna includes economically vital crops and wild species. Molecular systematic studies of Vigna species resulted in generic segregates of many New World (NW) species. However, limited Old World (OW) sampling left questions regarding inter- and intraspecific relationships in Vigna s.s. METHODS African species, including the putative sister genus Physostigma, were comprehensively sampled within the context of NW relatives. Maximum likelihood and Bayesian inference analyses of the chloroplast matK-trnK and nuclear ribosomal ITS/5.8 S (ITS) DNA regions were undertaken to resolve OW Vigna taxonomic questions. Divergence dates were estimated using BEAST to date key nodes in the phylogeny. RESULTS Analyses of matK and ITS data supported five clades of Vigna s.s.: subg. Lasiospron, a reduced subg. Vigna, subg. Haydonia, subg. Ceratotropis, an enlarged subg. Plectrotropis, and a clade including V. kirkii and V. stenophylla. Genome size estimates of 601 Mb for V. kirkii are near the overall mean of the genus, whereas V. stenophylla had a larger genome (810 Mb), similar to some Vigna subg. Ceratotropis or Plectrotropis species. CONCLUSIONS Former subg. Vigna is reduced to yellow- and blue-flowered species and subg. Plectrotropis is enlarged to mostly all white-, pink-, and purple-flowered species. The age of the split between NW and OW Vigna lineages is ~6-7 Myr. Genome size estimates cannot rule out a polyploid or hybrid origin for V. stenophylla, potentially involving extinct lineage ancestors of Vigna subg. Ceratotropis or Plectrotropis, as indicated by network and phylogenetic analyses. Taxonomic revisions are suggested based on these results.
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Affiliation(s)
- Dasha M Horton
- Department of Biology, Utah Valley University, Orem, 84058, UT, USA
| | - Yonas Feleke
- Department of Plant Sciences, Section of Crop and Ecosystem Sciences, University of California, Davis, CA, USA
| | | | - Firouzeh Javadi
- Institute of Decision Science for a Sustainable Society, Kyushu University, Fukuoka, Japan
- Kyushu University Museum, Kyushu University, Fukuoka, Japan
| | | | - Alfonso Delgado-Salinas
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Apartado postal 70-233, CDMX, 04510, México
| | - Mats Thulin
- Systematic Biology, Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, Uppsala, SE-75236, Sweden
| | | | - Paul Gepts
- Department of Plant Sciences, Section of Crop and Ecosystem Sciences, University of California, Davis, CA, USA
| | - Ashley N Egan
- Department of Biology, Utah Valley University, Orem, 84058, UT, USA
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