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Li F, Wang W, Cheng H, Li M. Genome-wide analysis reveals the contributors to fast molecular evolution of the Chinese hook snout carp ( Opsariichthys bidens). Comput Struct Biotechnol J 2024; 23:2465-2477. [PMID: 38882676 PMCID: PMC11179538 DOI: 10.1016/j.csbj.2024.05.048] [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: 03/07/2024] [Revised: 05/21/2024] [Accepted: 05/29/2024] [Indexed: 06/18/2024] Open
Abstract
Variations in molecular evolutionary rate have been widely investigated among lineages and genes. However, it remains an open question whether fast rate of molecular evolution is driven by natural selection or random drift, and how the fast rate is linked to metabolic rate. Additionally, previous studies on fast molecular evolution have been largely restricted to concatenated matrix of genes or a few specifically selected genes, but less is known for individual genes at the genome-wide level. Here we addressed these questions using more than 5000 single-copy orthologous (SCO) genes through comparative genomic and phylogenetic analyses among fishes, with a special focus on a newly-sequenced clupeocephalan fish the Chinese hook snout carp Opsariichthys bidens. We showed O. bidens displays significantly higher mean substitution rate and more fast-evolving SCO genes (2172 genes) than most fishes studied here. The rapidly evolving genes are enriched in highly conserved and very basic functions such as translation and ribosome that are critical for biological fitness. We further revealed that ∼25 % of these fast-evolving genes exhibit a constant increase of substitution rate from the common ancestor down to the present, suggesting a neglected but important contribution from ancestral states. Model fitting showed that ∼85 % of fast-evolving genes exclusive to O. bidens and related species follow the adaptive evolutionary model rather than random-drift model, and 7.6 % of fast-evolving genes identified in O. bidens have experienced positive selection, both indicating the reflection of adaptive selection. Finally, metabolic rate was observed to be linked with substitution rate in a gene-specific manner. Overall, our findings reveal fast molecular evolution of SCO genes at genome-wide level in O. bidens, and uncover the evolutionary and ecological contributors to it.
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Affiliation(s)
- Fengbo Li
- Zhejiang Institute of Freshwater Fisheries, 999 Hangchangqiao South Road, Huzhou 313001, China
| | - Wei Wang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, 1 Beichen West Road, Beijing 100101, China
| | - Haihua Cheng
- Zhejiang Institute of Freshwater Fisheries, 999 Hangchangqiao South Road, Huzhou 313001, China
| | - Ming Li
- Jinhua Fisheries Technology Extension Center, 828 Shuanglong South Street, Jinhua 321013, China
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2
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Li Y, Dong T, Wan S, Xiong R, Jin S, Dai Y, Guan C. Application of multi-omics techniques to androgenetic alopecia: Current status and perspectives. Comput Struct Biotechnol J 2024; 23:2623-2636. [PMID: 39021583 PMCID: PMC11253216 DOI: 10.1016/j.csbj.2024.06.026] [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: 03/10/2024] [Revised: 06/17/2024] [Accepted: 06/18/2024] [Indexed: 07/20/2024] Open
Abstract
The rapid advancement of sequencing technologies has enabled the generation of vast datasets, allowing for the in-depth analysis of sequencing data. This analysis has facilitated the validation of novel pathogenesis hypotheses for understanding and treating diseases through ex vivo and in vivo experiments. Androgenetic alopecia (AGA), a common hair loss disorder, has been a key focus of investigators attempting to uncover its underlying mechanisms. Abnormal changes in mRNA, proteins, and metabolites have been identified in individuals with AGA, and future developments in sequencing technologies may reveal new biomarkers for AGA. By integrating multiple omics analysis datasets such as genomics, transcriptomics, proteomics, and metabolomics-along with clinical phenotype data-we can achieve a comprehensive understanding of the molecular underpinnings of AGA. This review summarizes the data-mining studies conducted on various omics analysis datasets as related to AGA that have been adopted to interpret the biological data obtained from different omics layers. We herein discuss the challenges of integrative omics analyses, and suggest that collaborative multi-omics studies can enhance the understanding of the complete pathomechanism(s) of AGA by focusing on the interaction networks comprising DNA, RNA, proteins, and metabolites.
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Affiliation(s)
- Yujie Li
- Hangzhou Third Hospital Affiliated to Zhejiang Chinese Medical University, Hangzhou 310009, China
| | - Tingru Dong
- Hangzhou Third Hospital Affiliated to Zhejiang Chinese Medical University, Hangzhou 310009, China
| | - Sheng Wan
- Hangzhou Third Hospital Affiliated to Zhejiang Chinese Medical University, Hangzhou 310009, China
- Department of Dermatology, Hangzhou Third People's Hospital, Hangzhou 310009, China
| | - Renxue Xiong
- Hangzhou Third Hospital Affiliated to Zhejiang Chinese Medical University, Hangzhou 310009, China
- Department of Dermatology, Hangzhou Third People's Hospital, Hangzhou 310009, China
| | - Shiyu Jin
- Hangzhou Third Hospital Affiliated to Zhejiang Chinese Medical University, Hangzhou 310009, China
| | - Yeqin Dai
- Hangzhou Third Hospital Affiliated to Zhejiang Chinese Medical University, Hangzhou 310009, China
- Department of Dermatology, Hangzhou Third People's Hospital, Hangzhou 310009, China
| | - Cuiping Guan
- Hangzhou Third Hospital Affiliated to Zhejiang Chinese Medical University, Hangzhou 310009, China
- Department of Dermatology, Hangzhou Third People's Hospital, Hangzhou 310009, China
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3
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Canesin LEC, Vilaça ST, Oliveira RRM, Al-Ajli F, Tracey A, Sims Y, Formenti G, Fedrigo O, Banhos A, Sanaiotti TM, Farias IP, Jarvis ED, Oliveira G, Hrbek T, Solferini V, Aleixo A. A reference genome for the Harpy Eagle reveals steady demographic decline and chromosomal rearrangements in the origin of Accipitriformes. Sci Rep 2024; 14:19925. [PMID: 39261501 PMCID: PMC11390914 DOI: 10.1038/s41598-024-70305-w] [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: 05/14/2024] [Accepted: 08/14/2024] [Indexed: 09/13/2024] Open
Abstract
The Harpy Eagle (Harpia harpyja) is an iconic species that inhabits forested landscapes in Neotropical regions, with decreasing population trends mainly due to habitat loss, and currently classified as vulnerable. Here, we report on a chromosome-scale genome assembly for a female individual combining long reads, optical mapping, and chromatin conformation capture reads. The final assembly spans 1.35 Gb, with N50scaffold equal to 58.1 Mb and BUSCO completeness of 99.7%. We built the first extensive transposable element (TE) library for the Accipitridae to date and identified 7,228 intact TEs. We found a burst of an unknown TE ~ 13-22 million years ago (MYA), coincident with the split of the Harpy Eagle from other Harpiinae eagles. We also report a burst of solo-LTRs and CR1 retrotransposons ~ 31-33 MYA, overlapping with the split of the ancestor to all Harpiinae from other Accipitridae subfamilies. Comparative genomics with other Accipitridae, the closely related Cathartidae and Galloanserae revealed major chromosome-level rearrangements at the basal Accipitriformes genome, in contrast to a conserved ancient genome architecture for the latter two groups. A historical demography reconstruction showed a rapid decline in effective population size over the last 20,000 years. This reference genome serves as a crucial resource for future conservation efforts towards the Harpy Eagle.
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Affiliation(s)
| | - Sibelle T Vilaça
- Instituto Tecnológico Vale - Desenvolvimento Sustentável (ITV-DS), Belém, Brazil
| | - Renato R M Oliveira
- Instituto Tecnológico Vale - Desenvolvimento Sustentável (ITV-DS), Belém, Brazil
| | - Farooq Al-Ajli
- Rockefeller University, New York, USA
- Katara Biodiversity Genomics Program, Katara Cultural Village Foundation, Doha, Qatar
| | | | - Ying Sims
- Rockefeller University, New York, USA
| | | | | | - Aureo Banhos
- Universidade Federal do Espírito Santo (UFES), Alegre, Brazil
| | | | | | - Erich D Jarvis
- Rockefeller University, New York, USA
- Howard Hughes Medical Institute (HHMI), New York, USA
| | - Guilherme Oliveira
- Instituto Tecnológico Vale - Desenvolvimento Sustentável (ITV-DS), Belém, Brazil
| | - Tomas Hrbek
- Universidade Federal do Amazonas (UFAM), Manaus, Brazil
- Trinity University, San Antonio, USA
| | - Vera Solferini
- Universidade Estadual de Campinas (Unicamp), Campinas, Brazil
| | - Alexandre Aleixo
- Instituto Tecnológico Vale - Desenvolvimento Sustentável (ITV-DS), Belém, Brazil.
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4
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Bjornson S, Verbruggen H, Upham NS, Steenwyk JL. Reticulate evolution: Detection and utility in the phylogenomics era. Mol Phylogenet Evol 2024; 201:108197. [PMID: 39270765 DOI: 10.1016/j.ympev.2024.108197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2024] [Revised: 08/13/2024] [Accepted: 09/08/2024] [Indexed: 09/15/2024]
Abstract
Phylogenomics has enriched our understanding that the Tree of Life can have network-like or reticulate structures among some taxa and genes. Two non-vertical modes of evolution - hybridization/introgression and horizontal gene transfer - deviate from a strictly bifurcating tree model, causing non-treelike patterns. However, these reticulate processes can produce similar patterns to incomplete lineage sorting or recombination, potentially leading to ambiguity. Here, we present a brief overview of a phylogenomic workflow for inferring organismal histories and compare methods for distinguishing modes of reticulate evolution. We discuss how the timing of coalescent events can help disentangle introgression from incomplete lineage sorting and how horizontal gene transfer events can help determine the relative timing of speciation events. In doing so, we identify pitfalls of certain methods and discuss how to extend their utility across the Tree of Life. Workflows, methods, and future directions discussed herein underscore the need to embrace reticulate evolutionary patterns for understanding the timing and rates of evolutionary events, providing a clearer view of life's history.
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Affiliation(s)
- Saelin Bjornson
- School of BioSciences, University of Melbourne, Victoria, Australia
| | - Heroen Verbruggen
- School of BioSciences, University of Melbourne, Victoria, Australia; CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
| | - Nathan S Upham
- School of Life Sciences, Arizona State University, Tempe, AZ, USA.
| | - Jacob L Steenwyk
- Howards Hughes Medical Institute and the Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.
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5
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Homberger DG. Reconstructive evolutionary morphology: Tracing the historical process of modifications of complex systems driven by natural selection through changing ecological conditions. J Morphol 2024; 285:e21763. [PMID: 39248452 DOI: 10.1002/jmor.21763] [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: 03/06/2024] [Revised: 07/14/2024] [Accepted: 08/05/2024] [Indexed: 09/10/2024]
Abstract
There is general consensus among evolutionary biologists that natural selection drives phenotypic modifications within populations over generational time. How to reconstruct this historical process, however, has been discussed mostly in theoretical terms, and recommendations and explanations on how to translate such theoretical insights into practice are needed. The present study aims at providing a theory-supported practical guide on how to reconstruct historical evolutionary processes by applying a morphology-centered approach through a series of interdependent steps of descriptive morphology, functional analysis, ecological observation, integration of paleoecological data, and evolutionary synthesis. Special attention is given to the development of tests regarding the accuracy, closeness to reality, and plausibility of the hypotheses at every level of the reconstructive process. This morphology-centered approach had its beginnings in the wake of the evolutionary synthesis and is part of the scientifically necessary process of reciprocal testing of hypotheses generated by different methods and data for the reconstruction of evolutionary history.
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Affiliation(s)
- Dominique G Homberger
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, USA
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6
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Silver LW, Stojanovic D, Farquharson KA, Alexander L, Peel E, Belov K, Hogg CJ. A reference genome, mitochondrial genome and associated transcriptomes for the critically endangered swift parrot ( Lathamus discolor). F1000Res 2024; 13:251. [PMID: 39301273 PMCID: PMC11411239 DOI: 10.12688/f1000research.144352.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/21/2024] [Indexed: 09/22/2024] Open
Abstract
The swift parrot ( Lathamus discolor) is a Critically Endangered migratory parrot that breeds in Tasmania and winters on the Australian mainland. Here we provide a reference genome assembly for the swift parrot. We sequence PacBio HiFi reads to create a high-quality reference assembly and identify a complete mitochondrial sequence. We also generate a reference transcriptome from five organs to inform genome annotation. The genome was 1.24 Gb in length and consisted of 847 contigs with a contig N50 of 18.97 Gb and L50 of 20 contigs. This study provides an annotated reference assembly and transcriptomic resources for the swift parrot to assist in future conservation genomic research.
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Affiliation(s)
- Luke W Silver
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, 2006, Australia
| | - Dejan Stojanovic
- Fenner School of Environment and Society, Australian National University, Acton, Australian Capital Territory, 2601, Australia
| | - Katherine A Farquharson
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, 2006, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science,, The University of Sydney, Sydney, New South Wales, 2006, Australia
| | - Lauren Alexander
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, 2006, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science,, The University of Sydney, Sydney, New South Wales, 2006, Australia
| | - Emma Peel
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, 2006, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science,, The University of Sydney, Sydney, New South Wales, 2006, Australia
| | - Katherine Belov
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, 2006, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science,, The University of Sydney, Sydney, New South Wales, 2006, Australia
| | - Carolyn J Hogg
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, 2006, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science,, The University of Sydney, Sydney, New South Wales, 2006, Australia
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7
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Mc Cartney AM, Scholz AH, Groussin M, Staunton C. Benefit-Sharing by Design: A Call to Action for Human Genomics Research. Annu Rev Genomics Hum Genet 2024; 25:369-395. [PMID: 38608642 DOI: 10.1146/annurev-genom-021623-104241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/14/2024]
Abstract
The ethical standards for the responsible conduct of human research have come a long way; however, concerns surrounding equity remain in human genetics and genomics research. Addressing these concerns will help society realize the full potential of human genomics research. One outstanding concern is the fair and equitable sharing of benefits from research on human participants. Several international bodies have recognized that benefit-sharing can be an effective tool for ethical research conduct, but international laws, including the Convention on Biological Diversity and its Nagoya Protocol on Access and Benefit-Sharing, explicitly exclude human genetic and genomic resources. These agreements face significant challenges that must be considered and anticipated if similar principles are applied in human genomics research. We propose that benefit-sharing from human genomics research can be a bottom-up effort and embedded into the existing research process. We propose the development of a "benefit-sharing by design" framework to address concerns of fairness and equity in the use of human genomic resources and samples and to learn from the aspirations and decade of implementation of the Nagoya Protocol.
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Affiliation(s)
- Ann M Mc Cartney
- Genomics Institute, University of California, Santa Cruz, California, USA;
| | - Amber Hartman Scholz
- Department of Science Policy and Internationalisation, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany;
| | - Mathieu Groussin
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany;
| | - Ciara Staunton
- School of Law, University of KwaZulu-Natal, Durban, South Africa
- Institute for Biomedicine, Eurac Research, Bolzano, Italy;
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8
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Conklin JR, Verkuil YI, Lefebvre MJM, Battley PF, Bom RA, Gill RE, Hassell CJ, Ten Horn J, Ruthrauff DR, Tibbitts TL, Tomkovich PS, Warnock N, Piersma T, Fontaine MC. High dispersal ability versus migratory traditions: Fine-scale population structure and post-glacial colonisation in bar-tailed godwits. Mol Ecol 2024; 33:e17452. [PMID: 38970373 DOI: 10.1111/mec.17452] [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: 12/08/2023] [Revised: 05/15/2024] [Accepted: 05/30/2024] [Indexed: 07/08/2024]
Abstract
In migratory animals, high mobility may reduce population structure through increased dispersal and enable adaptive responses to environmental change, whereas rigid migratory routines predict low dispersal, increased structure, and limited flexibility to respond to change. We explore the global population structure and phylogeographic history of the bar-tailed godwit, Limosa lapponica, a migratory shorebird known for making the longest non-stop flights of any landbird. Using nextRAD sequencing of 14,318 single-nucleotide polymorphisms and scenario-testing in an Approximate Bayesian Computation framework, we infer that bar-tailed godwits existed in two main lineages at the last glacial maximum, when much of their present-day breeding range persisted in a vast, unglaciated Siberian-Beringian refugium, followed by admixture of these lineages in the eastern Palearctic. Subsequently, population structure developed at both longitudinal extremes: in the east, a genetic cline exists across latitude in the Alaska breeding range of subspecies L. l. baueri; in the west, one lineage diversified into three extant subspecies L. l. lapponica, taymyrensis, and yamalensis, the former two of which migrate through previously glaciated western Europe. In the global range of this long-distance migrant, we found evidence of both (1) fidelity to rigid behavioural routines promoting fine-scale geographic population structure (in the east) and (2) flexibility to colonise recently available migratory flyways and non-breeding areas (in the west). Our results suggest that cultural traditions in highly mobile vertebrates can override the expected effects of high dispersal ability on population structure, and provide insights for the evolution and flexibility of some of the world's longest migrations.
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Affiliation(s)
- Jesse R Conklin
- Conservation Ecology Group, Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Groningen, The Netherlands
- BirdEyes, Centre for Global Ecological Change at the Faculties of Science & Engineering and Campus Fryslân, University of Groningen, Leeuwarden, The Netherlands
| | - Yvonne I Verkuil
- Conservation Ecology Group, Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Groningen, The Netherlands
- BirdEyes, Centre for Global Ecological Change at the Faculties of Science & Engineering and Campus Fryslân, University of Groningen, Leeuwarden, The Netherlands
| | | | - Phil F Battley
- Zoology and Ecology Group, School of Food Technology and Natural Sciences, Massey University, Palmerston North, New Zealand
| | - Roeland A Bom
- BirdEyes, Centre for Global Ecological Change at the Faculties of Science & Engineering and Campus Fryslân, University of Groningen, Leeuwarden, The Netherlands
- Department of Coastal Systems, NIOZ Royal Netherlands Institute for Sea Research, Texel, The Netherlands
| | - Robert E Gill
- U.S. Geological Survey, Alaska Science Center, Anchorage, Alaska, USA
| | | | - Job Ten Horn
- Department of Coastal Systems, NIOZ Royal Netherlands Institute for Sea Research, Texel, The Netherlands
| | | | - T Lee Tibbitts
- U.S. Geological Survey, Alaska Science Center, Anchorage, Alaska, USA
| | - Pavel S Tomkovich
- Zoological Museum, Moscow MV Lomonosov State University, Moscow, Russia
| | - Nils Warnock
- Audubon Canyon Ranch, Cypress Grove Research Center, Marshall, California, USA
| | - Theunis Piersma
- Conservation Ecology Group, Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Groningen, The Netherlands
- BirdEyes, Centre for Global Ecological Change at the Faculties of Science & Engineering and Campus Fryslân, University of Groningen, Leeuwarden, The Netherlands
- Department of Coastal Systems, NIOZ Royal Netherlands Institute for Sea Research, Texel, The Netherlands
| | - Michaël C Fontaine
- MiVEGEC, CNRS, IRD, University of Montpellier, Montpellier, France
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Groningen, The Netherlands
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9
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Zhang D, She H, Wang S, Wang H, Li S, Cheng Y, Song G, Jia C, Qu Y, Rheindt FE, Olsson U, Alström P, Lei F. Phylogenetic Conflict Between Species Tree and Maternally Inherited Gene Trees in a Clade of Emberiza Buntings (Aves: Emberizidae). Syst Biol 2024; 73:279-289. [PMID: 38157277 DOI: 10.1093/sysbio/syad078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 12/06/2023] [Accepted: 12/27/2023] [Indexed: 01/03/2024] Open
Abstract
Different genomic regions may reflect conflicting phylogenetic topologies primarily due to incomplete lineage sorting and/or gene flow. Genomic data are necessary to reconstruct the true species tree and explore potential causes of phylogenetic conflict. Here, we investigate the phylogenetic relationships of 4 Emberiza species (Aves: Emberizidae) and discuss the potential causes of the observed mitochondrial non-monophyly of Emberiza godlewskii (Godlewski's bunting) using phylogenomic analyses based on whole genome resequencing data from 41 birds. Analyses based on both the whole mitochondrial genome and ~39 kilobases from the non-recombining W chromosome reveal sister relationships between each the northern and southern populations of E. godlewskii with E. cioides and E. cia, respectively. In contrast, the monophyly of E. godlewskii is reflected by the phylogenetic signal of autosomal and Z chromosomal sequence data as well as demographic inference analyses, which-in combination-support the following tree topology: ([{E. godlewskii, E. cia}, E. cioides], E. jankowskii). Using D-statistics, we detected multiple gene flow events among different lineages, indicating pervasive introgressive hybridization within this clade. Introgression from an unsampled lineage that is sister to E. cioides or introgression from an unsampled mitochondrial + W chromosomal lineage of E. cioides into northern E. godlewskii may explain the phylogenetic conflict between the species tree estimated from genome-wide data versus mtDNA/W tree topologies. These results underscore the importance of using genomic data for phylogenetic reconstruction and species delimitation.
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Affiliation(s)
- Dezhi Zhang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China
| | - Huishang She
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China
| | - Shangyu Wang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Haitao Wang
- School of Life Sciences, Jilin Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun 130024, China
| | - Shi Li
- College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China
| | - Yalin Cheng
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China
| | - Gang Song
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China
| | - Chenxi Jia
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China
| | - Yanhua Qu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China
| | - Frank E Rheindt
- Department of Biological Sciences, National University of Singapore, Singapore 117543, Republic of Singapore
| | - Urban Olsson
- Department of Biology and Environmental Science, University of Gothenburg, Box 463, SE-405 30 Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Box 461, SE-405 30 Gothenburg, Sweden
| | - Per Alström
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China
- Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18 D, SE-752 36 Uppsala, Sweden
| | - Fumin Lei
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, 100049 Beijing, China
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10
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Blom MP, Peona V, Prost S, Christidis L, Benz BW, Jønsson KA, Suh A, Irestedt M. Hybridization in birds-of-paradise: Widespread ancestral gene flow despite strong sexual selection in a lek-mating system. iScience 2024; 27:110300. [PMID: 39055907 PMCID: PMC11269930 DOI: 10.1016/j.isci.2024.110300] [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: 02/16/2024] [Revised: 05/08/2024] [Accepted: 06/14/2024] [Indexed: 07/28/2024] Open
Abstract
Sexual selection can directly contribute to reproductive isolation and is an important mechanism that can lead to speciation. Lek-mating is one of the most extreme forms of sexual selection, but surprisingly does not seem to preclude occasional hybridization in nature. However, hybridization among lekking species may still be trivial if selection against offspring with intermediate phenotypes prohibits introgression. Here we investigate this further by sequencing the genomes of nearly all bird-of-paradise (Paradisaeidae) species and 10 museum specimens of putative hybrid origin. We find that intergeneric hybridization indeed still takes place despite extreme differentiation in form, plumage, and behavior. In parallel, the genomes of contemporary species contain widespread signatures of past introgression, demonstrating that hybridization has repeatedly resulted in shared genetic variation despite strong sexual isolation. Our study raises important questions about extrinsic factors that modulate hybridization probability and the evolutionary consequences of introgressive hybridization between lekking species.
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Affiliation(s)
- Mozes P.K. Blom
- Department for Evolutionary Diversity Dynamics, Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Research, 10115 Berlin, Germany
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, 114 18 Stockholm, Sweden
| | - Valentina Peona
- Department of Organismal Biology – Systematic Biology, Evolutionary Biology Centre, Science for Life Laboratory, Uppsala University, 752 36 Uppsala, Sweden
| | - Stefan Prost
- Ecology and Genetics Research Unit, University of Oulu, 90014 Oulu, Finland
| | - Les Christidis
- Faculty of Science and Engineering, Southern Cross University, Coffs Harbour, NSW 2450, Australia
| | - Brett W. Benz
- Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, Ann Arbor, MI 48108, USA
| | - Knud A. Jønsson
- Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, 114 18 Stockholm, Sweden
| | - Alexander Suh
- Department of Organismal Biology – Systematic Biology, Evolutionary Biology Centre, Science for Life Laboratory, Uppsala University, 752 36 Uppsala, Sweden
| | - Martin Irestedt
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, 114 18 Stockholm, Sweden
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11
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Chromosomal-level genome assembly and single-nucleotide polymorphism sites of black-faced spoonbill Platalea minor. GIGABYTE 2024; 2024:1-13. [PMID: 39071178 PMCID: PMC11273517 DOI: 10.46471/gigabyte.130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Accepted: 07/04/2024] [Indexed: 07/30/2024] Open
Abstract
Platalea minor, or black-faced spoonbill (Threskiornithidae), is a wading bird confined to coastal areas in East Asia. Due to habitat destruction, it was classified as globally endangered by the International Union for Conservation of Nature. However, the lack of genomic resources for this species hinders the understanding of its biology and diversity, and the development of conservation measures. Here, we report the first chromosomal-level genome assembly of P. minor using a combination of PacBio SMRT and Omni-C scaffolding technologies. The assembled genome (1.24 Gb) contains 95.33% of the sequences anchored to 31 pseudomolecules. The genome assembly has high sequence continuity with scaffold length N50 = 53 Mb. We predicted 18,780 protein-coding genes and measured high BUSCO score completeness (97.3%). Finally, we revealed 6,155,417 bi-allelic single nucleotide polymorphisms, accounting for ∼5% of the genome. This resource offers new opportunities for studying the black-faced spoonbill and developing conservation measures for this species.
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Spurgin LG, Bosse M, Adriaensen F, Albayrak T, Barboutis C, Belda E, Bushuev A, Cecere JG, Charmantier A, Cichon M, Dingemanse NJ, Doligez B, Eeva T, Erikstad KE, Fedorov V, Griggio M, Heylen D, Hille S, Hinde CA, Ivankina E, Kempenaers B, Kerimov A, Krist M, Kvist L, Laine VN, Mänd R, Matthysen E, Nager R, Nikolov BP, Norte AC, Orell M, Ouyang J, Petrova-Dinkova G, Richner H, Rubolini D, Slagsvold T, Tilgar V, Török J, Tschirren B, Vágási CI, Yuta T, Groenen MAM, Visser ME, van Oers K, Sheldon BC, Slate J. The great tit HapMap project: A continental-scale analysis of genomic variation in a songbird. Mol Ecol Resour 2024; 24:e13969. [PMID: 38747336 DOI: 10.1111/1755-0998.13969] [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: 12/13/2023] [Revised: 04/10/2024] [Accepted: 04/29/2024] [Indexed: 06/04/2024]
Abstract
A major aim of evolutionary biology is to understand why patterns of genomic diversity vary within taxa and space. Large-scale genomic studies of widespread species are useful for studying how environment and demography shape patterns of genomic divergence. Here, we describe one of the most geographically comprehensive surveys of genomic variation in a wild vertebrate to date; the great tit (Parus major) HapMap project. We screened ca 500,000 SNP markers across 647 individuals from 29 populations, spanning ~30 degrees of latitude and 40 degrees of longitude - almost the entire geographical range of the European subspecies. Genome-wide variation was consistent with a recent colonisation across Europe from a South-East European refugium, with bottlenecks and reduced genetic diversity in island populations. Differentiation across the genome was highly heterogeneous, with clear 'islands of differentiation', even among populations with very low levels of genome-wide differentiation. Low local recombination rates were a strong predictor of high local genomic differentiation (FST), especially in island and peripheral mainland populations, suggesting that the interplay between genetic drift and recombination causes highly heterogeneous differentiation landscapes. We also detected genomic outlier regions that were confined to one or more peripheral great tit populations, probably as a result of recent directional selection at the species' range edges. Haplotype-based measures of selection were related to recombination rate, albeit less strongly, and highlighted population-specific sweeps that likely resulted from positive selection. Our study highlights how comprehensive screens of genomic variation in wild organisms can provide unique insights into spatio-temporal evolutionary dynamics.
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Affiliation(s)
- Lewis G Spurgin
- School of Biological Sciences, Norwich Research Park, University of East Anglia, Norwich, UK
- Department of Biology, Edward Grey Institute, University of Oxford, Oxford, UK
| | - Mirte Bosse
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
- Animal Breeding and Genomics, Wageningen University and Research, Wageningen, The Netherlands
- Department of Ecological Science, Animal Ecology Group, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Frank Adriaensen
- Evolutionary Ecology Group, Department of Biology, University of Antwerp, Antwerp, Belgium
| | - Tamer Albayrak
- Department of Biology, Science and art Faculty, Mehmet Akif Ersoy University, Istiklal Yerleskesi, Burdur, Turkey
- Biology Education, Buca Faculty of Education, Mathematics and Science Education, Dokuz Eylül University, İzmir, Turkey
| | | | - Eduardo Belda
- Institut d'Investigació per a la Gestió Integrada de Zones Costaneres, Campus de Gandia, Universitat Politècnica de València, València, Spain
| | - Andrey Bushuev
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Jacopo G Cecere
- Area Avifauna Migratrice, Istituto Superiore per la Protezione e la Ricerca Ambientale (ISPRA), Ozzano Emilia, Italy
| | | | - Mariusz Cichon
- Institute of Environmental Sciences, Jagiellonian University, Kraków, Poland
| | - Niels J Dingemanse
- Behavioural Ecology, Faculty of Biology, LMU München, Planegg-Martinsried, Germany
| | - Blandine Doligez
- UMR CNRS 5558-LBBE, Biométrie et Biologie Évolutive, Villeurbanne, France
- Department of Ecology and Evolution, Animal Ecology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Tapio Eeva
- Department of Biology, University of Turku, Turku, Finland
| | - Kjell Einar Erikstad
- Norwegian Institute for Nature Research, FRAM-High North Research Centre for Climate and the Environment, Tromsø, Norway
| | | | - Matteo Griggio
- Department of Biology, University of Padova, Padova, Italy
| | - Dieter Heylen
- Department of Biology, Edward Grey Institute, University of Oxford, Oxford, UK
- Evolutionary Ecology Group, Department of Biology, University of Antwerp, Antwerp, Belgium
- Interuniversity Institute for Biostatistics and Statistical Bioinformatics, Hasselt University, Diepenbeek, Belgium
| | - Sabine Hille
- Institute of Wildlife Biology and Game Management, University of Natural Resources and Life Science, Vienna, Austria
| | - Camilla A Hinde
- Behavioural Ecology Group, Department of Life Sciences, Anglia Ruskin University, Cambridgeshire, UK
| | - Elena Ivankina
- Faculty of Biology, Zvenigorod Biological Station, Lomonosov Moscow State University, Moscow, Russia
| | - Bart Kempenaers
- Department of Ornithology, Max Planck Institute for Biological Intelligence, Seewiesen, Germany
| | - Anvar Kerimov
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Milos Krist
- Department of Zoology, Faculty of Science, Palacký University, Olomouc, Czech Republic
| | - Laura Kvist
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland
| | - Veronika N Laine
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
- Zoology Unit, Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
| | - Raivo Mänd
- Department of Zoology, University of Tartu, Tartu, Estonia
| | - Erik Matthysen
- Evolutionary Ecology Group, Department of Biology, University of Antwerp, Antwerp, Belgium
| | - Ruedi Nager
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow, UK
| | - Boris P Nikolov
- Bulgarian Ornithological Centre, Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Ana Claudia Norte
- MARE - Marine and Environmental Sciences Centre, Department of Life Sciences, Faculty of Sciences and Technology, University of Coimbra, Coimbra, Portugal
| | - Markku Orell
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland
| | | | - Gergana Petrova-Dinkova
- Bulgarian Ornithological Centre, Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Heinz Richner
- Evolutionary Ecology Lab, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Diego Rubolini
- Dipartimento di Scienze e Politiche Ambientali, Università Degli Studi di Milano, Milan, Italy
| | - Tore Slagsvold
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Vallo Tilgar
- Department of Zoology, University of Tartu, Tartu, Estonia
| | - János Török
- Behavioural Ecology Group, Department of Systematic Zoology and Ecology, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Barbara Tschirren
- Centre for Ecology and Conservation, University of Exeter, Penryn, UK
| | - Csongor I Vágási
- Evolutionary Ecology Group, Hungarian Department of Biology and Ecology, Babeș-Bolyai University, Cluj-Napoca, Romania
| | - Teru Yuta
- Yamashina Institute for Ornithology, Abiko, Japan
| | - Martien A M Groenen
- Animal Breeding and Genomics, Wageningen University and Research, Wageningen, The Netherlands
| | - Marcel E Visser
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
- Animal Breeding and Genomics, Wageningen University and Research, Wageningen, The Netherlands
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Groningen, the Netherlands
| | - Kees van Oers
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - Ben C Sheldon
- Department of Biology, Edward Grey Institute, University of Oxford, Oxford, UK
| | - Jon Slate
- School of Biosciences, University of Sheffield, Sheffield, UK
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13
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Wu X, Zhang Z, Li Y, Zhao Y, Ren Y, Tian Y, Hou M, Guo Y, Li Q, Tian W, Jiang R, Zhang Y, Gong Y, Li H, Li G, Liu X, Kang X, Li D, Tian Y. Estrogen promotes gonadotropin-releasing hormone expression by regulating tachykinin 3 and prodynorphin systems in chicken. Poult Sci 2024; 103:103820. [PMID: 38759565 PMCID: PMC11127269 DOI: 10.1016/j.psj.2024.103820] [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: 01/23/2024] [Revised: 04/12/2024] [Accepted: 05/02/2024] [Indexed: 05/19/2024] Open
Abstract
The "KNDy neurons" located in the hypothalamic arcuate nucleus (ARC) of mammals are known to co-express kisspeptin, neurokinin B (NKB), and dynorphin (DYN), and have been identified as key mediators of the feedback regulation of steroid hormones on gonadotropin-releasing hormone (GnRH). However, in birds, the genes encoding kisspeptin and its receptor GPR54 are genomic lost, leaving unclear mechanisms for feedback regulation of GnRH by steroid hormones. Here, the genes tachykinin 3 (TAC3) and prodynorphin (PDYN) encoding chicken NKB and DYN neuropeptides were successfully cloned. Temporal expression profiling indicated that TAC3, PDYN and their receptor genes (TACR3, OPRK1) were mainly expressed in the hypothalamus, with significantly higher expression at 30W than at 15W. Furthermore, overexpression or interference of TAC3 and PDYN can regulate the GnRH mRNA expression. In addition, in vivo and in vitro assays showed that estrogen (E2) could promote the mRNA expression of TAC3, PDYN, and GnRH, as well as the secretion of GnRH/LH. Mechanistically, E2 could dimerize the nuclear estrogen receptor 1 (ESR1) to regulate the expression of TAC3 and PDYN, which promoted the mRNA and protein expression of GnRH gene as well as the secretion of GnRH. In conclusion, these results revealed that E2 could regulate the GnRH expression through TAC3 and PDYN systems, providing novel insights for reproductive regulation in chickens.
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Affiliation(s)
- Xing Wu
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Zihao Zhang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Yijie Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Yudian Zhao
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Yangguang Ren
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Yixiang Tian
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Meng Hou
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Yulong Guo
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Qi Li
- Henan zhumadian agricultural school, zhumadian, 463000, China
| | - Weihua Tian
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China; Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Zhengzhou 450046, China
| | - Ruirui Jiang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China; Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Zhengzhou 450046, China
| | - Yanhua Zhang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China; Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Zhengzhou 450046, China
| | - Yujie Gong
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China; Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Zhengzhou 450046, China
| | - Hong Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China; Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Zhengzhou 450046, China
| | - Guoxi Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China; Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Zhengzhou 450046, China
| | - Xiaojun Liu
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China; Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Zhengzhou 450046, China
| | - Xiangtao Kang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China; Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Zhengzhou 450046, China
| | - Donghua Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China; Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Zhengzhou 450046, China
| | - Yadong Tian
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China; Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Zhengzhou 450046, China.
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14
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Alves Barcellos S, Kretschmer R, Santos de Souza M, Tura V, Pozzobon LC, Ochotorena de Freitas TR, Griffin DK, O'Connor R, Gunski RJ, Del Valle Garnero A. Understanding microchromosomal organization and evolution in four representative woodpeckers (Picidae, Piciformes) through BAC-FISH analysis. Genome 2024; 67:223-232. [PMID: 38742652 DOI: 10.1139/gen-2023-0096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
The genome organization of woodpeckers has several distinctive features e.g., an uncommon accumulation of repetitive sequences, enlarged Z chromosomes, and atypical diploid numbers. Despite the large diversity of species, there is a paucity of detailed cytogenomic studies for this group and we thus aimed to rectify this. Genome organization patterns and hence evolutionary change in the microchromosome formation of four species (Colaptes campestris, Veniliornis spilogaster, Melanerpes candidus, and Picumnus nebulosus) was established through fluorescence in situ hybridization using bacterial artificial chromosomes originally derived from Gallus gallus and Taeniopygia guttata. Findings suggest that P. nebulosus (2n = 110), which was described for the first time, had the most basal karyotype among species of Picidae studied here, and probably arose as a result of fissions of avian ancestral macrochromosomes. We defined a new chromosomal number for V. spilogaster (2n = 88) and demonstrated microchromosomal rearrangements involving C. campestris plus a single, unique hitherto undescribed rearrangement in V. spilogaster. This comprised an inversion after a fusion involving the ancestral microchromosome 12 (homologous to chicken microchromosome 12). We also determined that the low diploid number of M. candidus is related to microchromosome fusions. Woodpeckers thus exhibit significantly rearranged karyotypes compared to the putative ancestral karyotype.
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Affiliation(s)
- Suziane Alves Barcellos
- Laboratório de Diversidade Genética Animal, Universidade Federal do Pampa, São Gabriel 97300-162, RS, Brazil
| | - Rafael Kretschmer
- Departamento de Ecologia, Zoologia e Genética, Instituto de Biologia, Universidade Federal de Pelotas, Pelotas 96010-900, RS, Brazil
| | - Marcelo Santos de Souza
- Laboratório de Diversidade Genética Animal, Universidade Federal do Pampa, São Gabriel 97300-162, RS, Brazil
| | - Victoria Tura
- Laboratório de Diversidade Genética Animal, Universidade Federal do Pampa, São Gabriel 97300-162, RS, Brazil
| | - Luciano Cesar Pozzobon
- Departamento de Genética, Laboratório de Citogenética e Evolução, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre 91509-900, RS, Brazil
| | - Thales Renato Ochotorena de Freitas
- Departamento de Genética, Laboratório de Citogenética e Evolução, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre 91509-900, RS, Brazil
| | - Darren K Griffin
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK
| | - Rebecca O'Connor
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK
| | - Ricardo José Gunski
- Laboratório de Diversidade Genética Animal, Universidade Federal do Pampa, São Gabriel 97300-162, RS, Brazil
| | - Analía Del Valle Garnero
- Laboratório de Diversidade Genética Animal, Universidade Federal do Pampa, São Gabriel 97300-162, RS, Brazil
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15
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Dittrich C, Hoelzl F, Smith S, Fouilloux CA, Parker DJ, O’Connell LA, Knowles LS, Hughes M, Fewings A, Morgan R, Rojas B, Comeault AA. Genome Assembly of the Dyeing Poison Frog Provides Insights into the Dynamics of Transposable Element and Genome-Size Evolution. Genome Biol Evol 2024; 16:evae109. [PMID: 38753031 PMCID: PMC11152451 DOI: 10.1093/gbe/evae109] [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] [Accepted: 05/12/2024] [Indexed: 06/07/2024] Open
Abstract
Genome size varies greatly across the tree of life and transposable elements are an important contributor to this variation. Among vertebrates, amphibians display the greatest variation in genome size, making them ideal models to explore the causes and consequences of genome size variation. However, high-quality genome assemblies for amphibians have, until recently, been rare. Here, we generate a high-quality genome assembly for the dyeing poison frog, Dendrobates tinctorius. We compare this assembly to publicly available frog genomes and find evidence for both large-scale conserved synteny and widespread rearrangements between frog lineages. Comparing conserved orthologs annotated in these genomes revealed a strong correlation between genome size and gene size. To explore the cause of gene-size variation, we quantified the location of transposable elements relative to gene features and find that the accumulation of transposable elements in introns has played an important role in the evolution of gene size in D. tinctorius, while estimates of insertion times suggest that many insertion events are recent and species-specific. Finally, we carry out population-scale mobile-element sequencing and show that the diversity and abundance of transposable elements in poison frog genomes can complicate genotyping from repetitive element sequence anchors. Our results show that transposable elements have clearly played an important role in the evolution of large genome size in D. tinctorius. Future studies are needed to fully understand the dynamics of transposable element evolution and to optimize primer or bait design for cost-effective population-level genotyping in species with large, repetitive genomes.
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Affiliation(s)
- Carolin Dittrich
- Department of Biology and Environmental Sciences, University of Jyväskylä, Jyväskylä, Finland
- Department of Interdisciplinary Life Sciences, Konrad Lorenz Institute of Ethology, University of Veterinary Medicine, Vienna, Austria
| | - Franz Hoelzl
- Department of Interdisciplinary Life Sciences, Konrad Lorenz Institute of Ethology, University of Veterinary Medicine, Vienna, Austria
| | - Steve Smith
- Department of Interdisciplinary Life Sciences, Konrad Lorenz Institute of Ethology, University of Veterinary Medicine, Vienna, Austria
| | - Chloe A Fouilloux
- Department of Biology and Environmental Sciences, University of Jyväskylä, Jyväskylä, Finland
| | - Darren J Parker
- School of Environmental and Natural Sciences, Molecular Ecology & Evolution Group, Bangor University, Bangor, UK
| | | | - Lucy S Knowles
- NERC Environmental Omics Facility, University of Sheffield, Sheffield, UK
| | - Margaret Hughes
- Centre for Genomic Research, University of Liverpool, Liverpool, UK
| | - Ade Fewings
- Supercomputing Wales, Digital Services, Bangor University, Bangor, UK
| | - Rhys Morgan
- School of Environmental and Natural Sciences, Molecular Ecology & Evolution Group, Bangor University, Bangor, UK
| | - Bibiana Rojas
- Department of Biology and Environmental Sciences, University of Jyväskylä, Jyväskylä, Finland
- Department of Interdisciplinary Life Sciences, Konrad Lorenz Institute of Ethology, University of Veterinary Medicine, Vienna, Austria
| | - Aaron A Comeault
- School of Environmental and Natural Sciences, Molecular Ecology & Evolution Group, Bangor University, Bangor, UK
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16
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Recuerda M, Campagna L. How structural variants shape avian phenotypes: Lessons from model systems. Mol Ecol 2024; 33:e17364. [PMID: 38651830 DOI: 10.1111/mec.17364] [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: 11/06/2023] [Revised: 04/04/2024] [Accepted: 04/09/2024] [Indexed: 04/25/2024]
Abstract
Despite receiving significant recent attention, the relevance of structural variation (SV) in driving phenotypic diversity remains understudied, although recent advances in long-read sequencing, bioinformatics and pangenomic approaches have enhanced SV detection. We review the role of SVs in shaping phenotypes in avian model systems, and identify some general patterns in SV type, length and their associated traits. We found that most of the avian SVs so far identified are short indels in chickens, which are frequently associated with changes in body weight and plumage colouration. Overall, we found that relatively short SVs are more frequently detected, likely due to a combination of their prevalence compared to large SVs, and a detection bias, stemming primarily from the widespread use of short-read sequencing and associated analytical methods. SVs most commonly involve non-coding regions, especially introns, and when patterns of inheritance were reported, SVs associated primarily with dominant discrete traits. We summarise several examples of phenotypic convergence across different species, mediated by different SVs in the same or different genes and different types of changes in the same gene that can lead to various phenotypes. Complex rearrangements and supergenes, which can simultaneously affect and link several genes, tend to have pleiotropic phenotypic effects. Additionally, SVs commonly co-occur with single-nucleotide polymorphisms, highlighting the need to consider all types of genetic changes to understand the basis of phenotypic traits. We end by summarising expectations for when long-read technologies become commonly implemented in non-model birds, likely leading to an increase in SV discovery and characterisation. The growing interest in this subject suggests an increase in our understanding of the phenotypic effects of SVs in upcoming years.
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Affiliation(s)
- María Recuerda
- Fuller Evolutionary Biology Program, Cornell Lab of Ornithology, Ithaca, New York, USA
| | - Leonardo Campagna
- Fuller Evolutionary Biology Program, Cornell Lab of Ornithology, Ithaca, New York, USA
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
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17
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Nagashima A, Torii K, Ota C, Kato A. slc26a12-A novel member of the slc26 family, is located in tandem with slc26a2 in coelacanths, amphibians, reptiles, and birds. Physiol Rep 2024; 12:e16089. [PMID: 38828713 PMCID: PMC11145369 DOI: 10.14814/phy2.16089] [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: 03/26/2024] [Revised: 05/16/2024] [Accepted: 05/16/2024] [Indexed: 06/05/2024] Open
Abstract
Solute carrier family 26 (Slc26) is a family of anion exchangers with 11 members in mammals (named Slc26a1-a11). Here, we identified a novel member of the slc26 family, slc26a12, located in tandem with slc26a2 in the genomes of several vertebrate lineages. BLAST and synteny analyses of various jawed vertebrate genome databases revealed that slc26a12 is present in coelacanths, amphibians, reptiles, and birds but not in cartilaginous fishes, lungfish, mammals, or ray-finned fishes. In some avian and reptilian lineages such as owls, penguins, egrets, and ducks, and most turtles examined, slc26a12 was lost or pseudogenized. Phylogenetic analysis showed that Slc26a12 formed an independent branch with the other Slc26 members and Slc26a12, Slc26a1 and Slc26a2 formed a single branch, suggesting that these three members formed a subfamily in Slc26. In jawless fish, hagfish have two genes homologous to slc26a2 and slc26a12, whereas lamprey has a single gene homologous to slc26a2. African clawed frogs express slc26a12 in larval gills, skin, and fins. These results show that slc26a12 was present at least before the separation of lobe-finned fish and tetrapods; the name slc26a12 is appropriate because the gene duplication occurred in the distant past.
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Affiliation(s)
- Ayumi Nagashima
- School of Life Science and TechnologyTokyo Institute of TechnologyYokohamaJapan
| | - Kota Torii
- School of Life Science and TechnologyTokyo Institute of TechnologyYokohamaJapan
| | - Chihiro Ota
- School of Life Science and TechnologyTokyo Institute of TechnologyYokohamaJapan
| | - Akira Kato
- School of Life Science and TechnologyTokyo Institute of TechnologyYokohamaJapan
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18
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Zhang R, Drummond AJ, Mendes FK. Fast Bayesian Inference of Phylogenies from Multiple Continuous Characters. Syst Biol 2024; 73:102-124. [PMID: 38085256 PMCID: PMC11129596 DOI: 10.1093/sysbio/syad067] [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: 11/06/2023] [Revised: 03/23/2023] [Accepted: 11/07/2023] [Indexed: 05/28/2024] Open
Abstract
Time-scaled phylogenetic trees are an ultimate goal of evolutionary biology and a necessary ingredient in comparative studies. The accumulation of genomic data has resolved the tree of life to a great extent, yet timing evolutionary events remain challenging if not impossible without external information such as fossil ages and morphological characters. Methods for incorporating morphology in tree estimation have lagged behind their molecular counterparts, especially in the case of continuous characters. Despite recent advances, such tools are still direly needed as we approach the limits of what molecules can teach us. Here, we implement a suite of state-of-the-art methods for leveraging continuous morphology in phylogenetics, and by conducting extensive simulation studies we thoroughly validate and explore our methods' properties. While retaining model generality and scalability, we make it possible to estimate absolute and relative divergence times from multiple continuous characters while accounting for uncertainty. We compile and analyze one of the most data-type diverse data sets to date, comprised of contemporaneous and ancient molecular sequences, and discrete and continuous morphological characters from living and extinct Carnivora taxa. We conclude by synthesizing lessons about our method's behavior, and suggest future research venues.
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Affiliation(s)
- Rong Zhang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School 169857, Singapore
| | - Alexei J Drummond
- Centre for Computational Evolution, The University of Auckland, Auckland 1010, New Zealand
- School of Biological Sciences, The University of Auckland, Auckland 1010, New Zealand
| | - Fábio K Mendes
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA
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Khurana MP, Scheidwasser-Clow N, Penn MJ, Bhatt S, Duchêne DA. The Limits of the Constant-rate Birth-Death Prior for Phylogenetic Tree Topology Inference. Syst Biol 2024; 73:235-246. [PMID: 38153910 PMCID: PMC11129600 DOI: 10.1093/sysbio/syad075] [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: 02/06/2023] [Revised: 12/20/2023] [Accepted: 12/27/2023] [Indexed: 12/30/2023] Open
Abstract
Birth-death models are stochastic processes describing speciation and extinction through time and across taxa and are widely used in biology for inference of evolutionary timescales. Previous research has highlighted how the expected trees under the constant-rate birth-death (crBD) model tend to differ from empirical trees, for example, with respect to the amount of phylogenetic imbalance. However, our understanding of how trees differ between the crBD model and the signal in empirical data remains incomplete. In this Point of View, we aim to expose the degree to which the crBD model differs from empirically inferred phylogenies and test the limits of the model in practice. Using a wide range of topology indices to compare crBD expectations against a comprehensive dataset of 1189 empirically estimated trees, we confirm that crBD model trees frequently differ topologically compared with empirical trees. To place this in the context of standard practice in the field, we conducted a meta-analysis for a subset of the empirical studies. When comparing studies that used Bayesian methods and crBD priors with those that used other non-crBD priors and non-Bayesian methods (i.e., maximum likelihood methods), we do not find any significant differences in tree topology inferences. To scrutinize this finding for the case of highly imbalanced trees, we selected the 100 trees with the greatest imbalance from our dataset, simulated sequence data for these tree topologies under various evolutionary rates, and re-inferred the trees under maximum likelihood and using the crBD model in a Bayesian setting. We find that when the substitution rate is low, the crBD prior results in overly balanced trees, but the tendency is negligible when substitution rates are sufficiently high. Overall, our findings demonstrate the general robustness of crBD priors across a broad range of phylogenetic inference scenarios but also highlight that empirically observed phylogenetic imbalance is highly improbable under the crBD model, leading to systematic bias in data sets with limited information content.
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Affiliation(s)
- Mark P Khurana
- Section of Epidemiology, Department of Public Health, University of Copenhagen, 1352 Copenhagen, Denmark
| | - Neil Scheidwasser-Clow
- Section of Epidemiology, Department of Public Health, University of Copenhagen, 1352 Copenhagen, Denmark
| | - Matthew J Penn
- Department of Statistics, University of Oxford, OX1 3LB, Oxford, UK
| | - Samir Bhatt
- Section of Epidemiology, Department of Public Health, University of Copenhagen, 1352 Copenhagen, Denmark
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, SW7 2AZ, London, UK
| | - David A Duchêne
- Centre for Evolutionary Hologenomics, University of Copenhagen, 1352 Copenhagen, Denmark
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20
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Musher LJ, Del-Rio G, Marcondes RS, Brumfield RT, Bravo GA, Thom G. Geogenomic Predictors of Genetree Heterogeneity Explain Phylogeographic and Introgression History: A Case Study in an Amazonian Bird (Thamnophilus aethiops). Syst Biol 2024; 73:36-52. [PMID: 37804132 DOI: 10.1093/sysbio/syad061] [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: 12/20/2022] [Revised: 09/14/2023] [Accepted: 10/04/2023] [Indexed: 10/08/2023] Open
Abstract
Can knowledge about genome architecture inform biogeographic and phylogenetic inference? Selection, drift, recombination, and gene flow interact to produce a genomic landscape of divergence wherein patterns of differentiation and genealogy vary nonrandomly across the genomes of diverging populations. For instance, genealogical patterns that arise due to gene flow should be more likely to occur on smaller chromosomes, which experience high recombination, whereas those tracking histories of geographic isolation (reduced gene flow caused by a barrier) and divergence should be more likely to occur on larger and sex chromosomes. In Amazonia, populations of many bird species diverge and introgress across rivers, resulting in reticulated genomic signals. Herein, we used reduced representation genomic data to disentangle the evolutionary history of 4 populations of an Amazonian antbird, Thamnophilus aethiops, whose biogeographic history was associated with the dynamic evolution of the Madeira River Basin. Specifically, we evaluate whether a large river capture event ca. 200 Ka, gave rise to reticulated genealogies in the genome by making spatially explicit predictions about isolation and gene flow based on knowledge about genomic processes. We first estimated chromosome-level phylogenies and recovered 2 primary topologies across the genome. The first topology (T1) was most consistent with predictions about population divergence and was recovered for the Z-chromosome. The second (T2), was consistent with predictions about gene flow upon secondary contact. To evaluate support for these topologies, we trained a convolutional neural network to classify our data into alternative diversification models and estimate demographic parameters. The best-fit model was concordant with T1 and included gene flow between non-sister taxa. Finally, we modeled levels of divergence and introgression as functions of chromosome length and found that smaller chromosomes experienced higher gene flow. Given that (1) genetrees supporting T2 were more likely to occur on smaller chromosomes and (2) we found lower levels of introgression on larger chromosomes (and especially the Z-chromosome), we argue that T1 represents the history of population divergence across rivers and T2 the history of secondary contact due to barrier loss. Our results suggest that a significant portion of genomic heterogeneity arises due to extrinsic biogeographic processes such as river capture interacting with intrinsic processes associated with genome architecture. Future phylogeographic studies would benefit from accounting for genomic processes, as different parts of the genome reveal contrasting, albeit complementary histories, all of which are relevant for disentangling the intricate geogenomic mechanisms of biotic diversification. [Amazonia; biogeography; demographic modeling; gene flow; gene tree; genome architecture; geogenomics; introgression; linked selection; neural network; phylogenomic; phylogeography; reproductive isolation; speciation; species tree.].
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Affiliation(s)
- Lukas J Musher
- Department of Ornithology, The Academy of Natural Sciences of Drexel University, Philadelphia, PA 19103, USA
- Department of Ornithology, American Museum of Natural History, New York, NY 10024, USA
| | - Glaucia Del-Rio
- Cornell Laboratory of Ornithology and Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14853, USA
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | - Rafael S Marcondes
- Department of Biology and Museum of Natural Science, Louisiana State University, Baton Rouge, LA 70803, USA
- Department of BioSciences, Rice University, Houston, TX 77005, USA
| | - Robb T Brumfield
- Department of Biology and Museum of Natural Science, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Gustavo A Bravo
- Sección de Ornitología, Colecciones Biológicas, Instituto de Investigación de Recursos Biológicos Alexander von Humboldt, Claustro de San Agustín, Villa de Leyva, Boyacá 111311, Colombia
- Museum of Comparative Zoology and Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Gregory Thom
- Department of Biology and Museum of Natural Science, Louisiana State University, Baton Rouge, LA 70803, USA
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21
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Edwards SV, Cloutier A, Cockburn G, Driver R, Grayson P, Katoh K, Baldwin MW, Sackton TB, Baker AJ. A nuclear genome assembly of an extinct flightless bird, the little bush moa. SCIENCE ADVANCES 2024; 10:eadj6823. [PMID: 38781323 DOI: 10.1126/sciadv.adj6823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 04/17/2024] [Indexed: 05/25/2024]
Abstract
We present a draft genome of the little bush moa (Anomalopteryx didiformis)-one of approximately nine species of extinct flightless birds from Aotearoa, New Zealand-using ancient DNA recovered from a fossil bone from the South Island. We recover a complete mitochondrial genome at 249.9× depth of coverage and almost 900 megabases of a male moa nuclear genome at ~4 to 5× coverage, with sequence contiguity sufficient to identify more than 85% of avian universal single-copy orthologs. We describe a diverse landscape of transposable elements and satellite repeats, estimate a long-term effective population size of ~240,000, identify a diverse suite of olfactory receptor genes and an opsin repertoire with sensitivity in the ultraviolet range, show that the wingless moa phenotype is likely not attributable to gene loss or pseudogenization, and identify potential function-altering coding sequence variants in moa that could be synthesized for future functional assays. This genomic resource should support further studies of avian evolution and morphological divergence.
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Affiliation(s)
- Scott V Edwards
- Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
- Museum of Comparative Zoology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
| | - Alison Cloutier
- Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
| | - Glenn Cockburn
- Evolution of Sensory Systems Research Group, Max Planck Institute for Biological Intelligence, 82319 Seewiesen, Germany
| | - Robert Driver
- Department of Biology, East Carolina University, E 5th Street, Greenville, NC 27605, USA
| | - Phil Grayson
- Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
- Museum of Comparative Zoology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
| | - Kazutaka Katoh
- Department of Genome Informatics, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita 565-0871, Japan
| | - Maude W Baldwin
- Evolution of Sensory Systems Research Group, Max Planck Institute for Biological Intelligence, 82319 Seewiesen, Germany
| | - Timothy B Sackton
- Informatics Group, Harvard University, 38 Oxford Street, Cambridge, MA 02138, USA
| | - Allan J Baker
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcox Street, Toronto, ON M5S 3B2, Canada
- Department of Natural History, Royal Ontario Museum, 100 Queen's Park, Toronto, ON M5S 2C6, Canada
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22
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Wang Y, Zhai J, Tang B, Dong Y, Sun S, He S, Zhao W, Lancuo Z, Jia Q, Wang W. Metagenomic comparison of gut communities between wild and captive Himalayan griffons. Front Vet Sci 2024; 11:1403932. [PMID: 38784654 PMCID: PMC11112026 DOI: 10.3389/fvets.2024.1403932] [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: 03/20/2024] [Accepted: 04/29/2024] [Indexed: 05/25/2024] Open
Abstract
Introduction Himalayan griffons (Gyps himalayensis), known as the scavenger of nature, are large scavenging raptors widely distributed on the Qinghai-Tibetan Plateau and play an important role in maintaining the balance of the plateau ecosystem. The gut microbiome is essential for host health, helping to maintain homeostasis, improving digestive efficiency, and promoting the development of the immune system. Changes in environment and diet can affect the composition and function of gut microbiota, ultimately impacting the host health and adaptation. Captive rearing is considered to be a way to protect Himalayan griffons and increase their population size. However, the effects of captivity on the structure and function of the gut microbial communities of Himalayan griffons are poorly understood. Still, availability of sequenced metagenomes and functional information for most griffons gut microbes remains limited. Methods In this study, metagenome sequencing was used to analyze the composition and functional structures of the gut microbiota of Himalayan griffons under wild and captive conditions. Results Our results showed no significant differences in the alpha diversity between the two groups, but significant differences in beta diversity. Taxonomic classification revealed that the most abundant phyla in the gut of Himalayan griffons were Fusobacteriota, Proteobacteria, Firmicutes_A, Bacteroidota, Firmicutes, Actinobacteriota, and Campylobacterota. At the functional level, a series of Kyoto Encyclopedia of Genes and Genome (KEGG) functional pathways, carbohydrate-active enzymes (CAZymes) categories, virulence factor genes (VFGs), and pathogen-host interactions (PHI) were annotated and compared between the two groups. In addition, we recovered nearly 130 metagenome-assembled genomes (MAGs). Discussion In summary, the present study provided a first inventory of the microbial genes and metagenome-assembled genomes related to the Himalayan griffons, marking a crucial first step toward a wider investigation of the scavengers microbiomes with the ultimate goal to contribute to the conservation and management strategies for this near threatened bird.
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Affiliation(s)
- You Wang
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, Qinghai, China
- College of Eco-Environmental Engineering, Qinghai University, Xining, Qinghai, China
| | - Jundie Zhai
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, Qinghai, China
- College of Eco-Environmental Engineering, Qinghai University, Xining, Qinghai, China
| | - Boyu Tang
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, Qinghai, China
- College of Eco-Environmental Engineering, Qinghai University, Xining, Qinghai, China
| | - Yonggang Dong
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, Qinghai, China
- College of Eco-Environmental Engineering, Qinghai University, Xining, Qinghai, China
| | - Shengzhen Sun
- Animal Disease Prevention and Control Center of Qinghai Province, Xining, Qinghai, China
| | - Shunfu He
- Xining Wildlife Park of Qinghai Province, Xining, Qinghai, China
| | - Wenxin Zhao
- Xining Wildlife Park of Qinghai Province, Xining, Qinghai, China
| | - Zhuoma Lancuo
- College of Finance and Economics, Qinghai University, Xining, Qinghai, China
| | - Qiangqiang Jia
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, Qinghai, China
| | - Wen Wang
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, Qinghai, China
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23
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Forest T, Achaz G, Marbouty M, Bignaud A, Thierry A, Koszul R, Milhes M, Lledo J, Pons JM, Fuchs J. Chromosome-level genome assembly of the European green woodpecker Picus viridis. G3 (BETHESDA, MD.) 2024; 14:jkae042. [PMID: 38537260 PMCID: PMC11075563 DOI: 10.1093/g3journal/jkae042] [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: 12/17/2023] [Accepted: 02/15/2024] [Indexed: 05/08/2024]
Abstract
The European green woodpecker, Picus viridis, is a widely distributed species found in the Western Palearctic region. Here, we assembled a highly contiguous genome assembly for this species using a combination of short- and long-read sequencing and scaffolded with chromatin conformation capture (Hi-C). The final genome assembly was 1.28 Gb and features a scaffold N50 of 37 Mb and a scaffold L50 of 39.165 Mb. The assembly incorporates 89.4% of the genes identified in birds in OrthoDB. Gene and repetitive content annotation on the assembly detected 15,805 genes and a ∼30.1% occurrence of repetitive elements, respectively. Analysis of synteny demonstrates the fragmented nature of the P. viridis genome when compared to the chicken (Gallus gallus). The assembly and annotations produced in this study will certainly help for further research into the genomics of P. viridis and the comparative evolution of woodpeckers. Five historical and seven contemporary samples have been resequenced and may give insights on the population history of this species.
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Affiliation(s)
- Thomas Forest
- Éco-anthropologie, Muséum national d’Histoire naturelle, CNRS UMR 7206, 75005 Paris, France
- CIRB, Collège de France, Université PSL, CNRS, INSERM, 75005 Paris, France
- Institut de Systématique Evolution Biodiversité, Muséum national d’Histoire naturelle CNRS SU EPHE UA, CP 51, 75005 Paris, France
| | - Guillaume Achaz
- CIRB, Collège de France, Université PSL, CNRS, INSERM, 75005 Paris, France
- Université Paris-Cité, 75006 Paris, France
| | - Martial Marbouty
- Institut Pasteur, CNRS UMR 3525, Université Paris Cité, Unité Régulation Spatiale des Génomes, 75015 Paris, France
| | - Amaury Bignaud
- Institut Pasteur, CNRS UMR 3525, Université Paris Cité, Unité Régulation Spatiale des Génomes, 75015 Paris, France
| | - Agnès Thierry
- Institut Pasteur, CNRS UMR 3525, Université Paris Cité, Unité Régulation Spatiale des Génomes, 75015 Paris, France
| | - Romain Koszul
- Institut Pasteur, CNRS UMR 3525, Université Paris Cité, Unité Régulation Spatiale des Génomes, 75015 Paris, France
| | - Marine Milhes
- PlaGe, INRAE, Genotoul, 31320 Castanet-Tolosan, France
| | - Joanna Lledo
- PlaGe, INRAE, Genotoul, 31320 Castanet-Tolosan, France
| | - Jean-Marc Pons
- Institut de Systématique Evolution Biodiversité, Muséum national d’Histoire naturelle CNRS SU EPHE UA, CP 51, 75005 Paris, France
| | - Jérôme Fuchs
- Institut de Systématique Evolution Biodiversité, Muséum national d’Histoire naturelle CNRS SU EPHE UA, CP 51, 75005 Paris, France
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24
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Anchundia DJ, Lam AW, Henderson JB, Van Dam MH, Dumbacher JP. Genome Assembly of Pyrocephalus nanus: A Step Toward the Genetic Conservation of the Endangered Little Vermilion Flycatcher of the Galapagos Islands. Genome Biol Evol 2024; 16:evae083. [PMID: 38652799 PMCID: PMC11077314 DOI: 10.1093/gbe/evae083] [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: 01/29/2024] [Revised: 04/03/2024] [Accepted: 04/13/2024] [Indexed: 04/25/2024] Open
Abstract
Incredibly powerful whole genome studies of conservation genetics, evolution, and biogeography become possible for non-model organisms when reference genomes are available. Here, we report the sequence and assembly of the whole genome of the little vermilion flycatcher (Pyrocephalus nanus; family Tyrannidae), which is an endemic, endangered, and declining species of the Galapagos Islands. Using PacBio HiFi reads to assemble long contigs and Hi-C reads for scaffolding, we assembled a genome of 1.07 Gb comprising 267 contigs in 152 scaffolds, scaffold N50 74 M, contig N50 17.8 M, with 98.9% assigned to candidate chromosomal sequences and 99.72% of the BUSCO passeriformes 10,844 single-copy orthologs present. In addition, we used the novel HiFiMiTie pipeline to fully assemble and verify all portions of the mitochondrial genome from HiFi reads, obtaining a mitogenome of 17,151 bases, containing 13 protein-coding genes, 22 tRNAs, 2 rRNAs, two control regions, and a unique structure of control region duplication and repeats. These genomes will be a critical tool for much-needed studies of phylogenetics, population genetics, biogeography, and conservation genetics of Pyrocephalus and related genera. This genome and other studies that use it will be able to provide recommendations for conservation management, taxonomic improvement, and to understand the evolution and diversification of this genus within the Galapagos Islands.
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Affiliation(s)
- David J Anchundia
- Department of Behavioral and Cognitive Biology, University of Vienna, Vienna 1030, Austria
- Charles Darwin Research Station, Charles Darwin Foundation, Santa Cruz, Galapagos, Ecuador
- Institute for Biodiversity Sciences and Sustainability, California Academy of Sciences, San Francisco, CA 94118, USA
| | - Athena W Lam
- Institute for Biodiversity Sciences and Sustainability, California Academy of Sciences, San Francisco, CA 94118, USA
| | - James B Henderson
- Institute for Biodiversity Sciences and Sustainability, California Academy of Sciences, San Francisco, CA 94118, USA
| | - Matthew H Van Dam
- Institute for Biodiversity Sciences and Sustainability, California Academy of Sciences, San Francisco, CA 94118, USA
| | - John P Dumbacher
- Institute for Biodiversity Sciences and Sustainability, California Academy of Sciences, San Francisco, CA 94118, USA
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25
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Buthasane W, Shotelersuk V, Chetruengchai W, Srichomthong C, Assawapitaksakul A, Tangphatsornruang S, Pootakham W, Sonthirod C, Tongsima S, Wangkumhang P, Wilantho A, Thongphakdee A, Sanannu S, Poksawat C, Nipanunt T, Kasorndorkbua C, Koepfli KP, Pukazhenthi BS, Suriyaphol P, Wongsurawat T, Jenjaroenpun P, Suriyaphol G. Comprehensive genome assembly reveals genetic diversity and carcass consumption insights in critically endangered Asian king vultures. Sci Rep 2024; 14:9455. [PMID: 38658744 PMCID: PMC11043450 DOI: 10.1038/s41598-024-59990-9] [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: 11/23/2023] [Accepted: 04/17/2024] [Indexed: 04/26/2024] Open
Abstract
The Asian king vulture (AKV), a vital forest scavenger, is facing globally critical endangerment. This study aimed to construct a reference genome to unveil the mechanisms underlying its scavenger abilities and to assess the genetic relatedness of the captive population in Thailand. A reference genome of a female AKV was assembled from sequencing reads obtained from both PacBio long-read and MGI short-read sequencing platforms. Comparative genomics with New World vultures (NWVs) and other birds in the Family Accipitridae revealed unique gene families in AKV associated with retroviral genome integration and feather keratin, contrasting with NWVs' genes related to olfactory reception. Expanded gene families in AKV were linked to inflammatory response, iron regulation and spermatogenesis. Positively selected genes included those associated with anti-apoptosis, immune response and muscle cell development, shedding light on adaptations for carcass consumption and high-altitude soaring. Using restriction site-associated DNA sequencing (RADseq)-based genome-wide single nucleotide polymorphisms (SNPs), genetic relatedness and inbreeding status of five captive AKVs were determined, revealing high genomic inbreeding in two females. In conclusion, the AKV reference genome was established, providing insights into its unique characteristics. Additionally, the potential of RADseq-based genome-wide SNPs for selecting AKV breeders was demonstrated.
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Affiliation(s)
- Wannapol Buthasane
- Biochemistry Unit, Department of Physiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Vorasuk Shotelersuk
- Center of Excellence for Medical Genomics, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Henri Dunant Road, Pathumwan, Bangkok, 10330, Thailand
- Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok, 10330, Thailand
| | - Wanna Chetruengchai
- Center of Excellence for Medical Genomics, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Henri Dunant Road, Pathumwan, Bangkok, 10330, Thailand
- Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok, 10330, Thailand
| | - Chalurmpon Srichomthong
- Center of Excellence for Medical Genomics, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Henri Dunant Road, Pathumwan, Bangkok, 10330, Thailand
- Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok, 10330, Thailand
| | - Adjima Assawapitaksakul
- Center of Excellence for Medical Genomics, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Henri Dunant Road, Pathumwan, Bangkok, 10330, Thailand
- Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok, 10330, Thailand
| | - Sithichoke Tangphatsornruang
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, 12120, Thailand
| | - Wirulda Pootakham
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, 12120, Thailand
| | - Chutima Sonthirod
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, 12120, Thailand
| | - Sissades Tongsima
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, 12120, Thailand
| | - Pongsakorn Wangkumhang
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, 12120, Thailand
| | - Alisa Wilantho
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, 12120, Thailand
| | - Ampika Thongphakdee
- Animal Conservation and Research Institute, The Zoological Park Organization of Thailand under the Royal Patronage of H.M. The King, Bangkok, 10300, Thailand
| | - Saowaphang Sanannu
- Animal Conservation and Research Institute, The Zoological Park Organization of Thailand under the Royal Patronage of H.M. The King, Bangkok, 10300, Thailand
| | - Chaianan Poksawat
- Animal Conservation and Research Institute, The Zoological Park Organization of Thailand under the Royal Patronage of H.M. The King, Bangkok, 10300, Thailand
| | - Tarasak Nipanunt
- Huai Kha Khaeng Wildlife Breeding Center, Department of National Parks, Wildlife and Plant Conservation, Uthai Thani, 61160, Thailand
| | - Chaiyan Kasorndorkbua
- Laboratory of Raptor Research and Conservation Medicine, Department of Pathology, Faculty of Veterinary Medicine, Kasetsart University, Bangkok, 10900, Thailand
| | - Klaus-Peter Koepfli
- Smithsonian-Mason School of Conservation, George Mason University, Front Royal, VA, 22630, USA
- Center for Species Survival, Smithsonian Conservation Biology Institute, National Zoological Park, Front Royal, VA, 22630, USA
| | - Budhan S Pukazhenthi
- Center for Species Survival, Smithsonian Conservation Biology Institute, National Zoological Park, Front Royal, VA, 22630, USA
| | - Prapat Suriyaphol
- Division of Medical Bioinformatics, Department of Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
| | - Thidathip Wongsurawat
- Division of Medical Bioinformatics, Department of Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
| | - Piroon Jenjaroenpun
- Division of Medical Bioinformatics, Department of Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
| | - Gunnaporn Suriyaphol
- Biochemistry Unit, Department of Physiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand.
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26
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Sebastianelli M, Lukhele SM, Secomandi S, de Souza SG, Haase B, Moysi M, Nikiforou C, Hutfluss A, Mountcastle J, Balacco J, Pelan S, Chow W, Fedrigo O, Downs CT, Monadjem A, Dingemanse NJ, Jarvis ED, Brelsford A, vonHoldt BM, Kirschel ANG. A genomic basis of vocal rhythm in birds. Nat Commun 2024; 15:3095. [PMID: 38653976 DOI: 10.1038/s41467-024-47305-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 03/22/2024] [Indexed: 04/25/2024] Open
Abstract
Vocal rhythm plays a fundamental role in sexual selection and species recognition in birds, but little is known of its genetic basis due to the confounding effect of vocal learning in model systems. Uncovering its genetic basis could facilitate identifying genes potentially important in speciation. Here we investigate the genomic underpinnings of rhythm in vocal non-learning Pogoniulus tinkerbirds using 135 individual whole genomes distributed across a southern African hybrid zone. We find rhythm speed is associated with two genes that are also known to affect human speech, Neurexin-1 and Coenzyme Q8A. Models leveraging ancestry reveal these candidate loci also impact rhythmic stability, a trait linked with motor performance which is an indicator of quality. Character displacement in rhythmic stability suggests possible reinforcement against hybridization, supported by evidence of asymmetric assortative mating in the species producing faster, more stable rhythms. Because rhythm is omnipresent in animal communication, candidate genes identified here may shape vocal rhythm across birds and other vertebrates.
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Affiliation(s)
- Matteo Sebastianelli
- Department of Biological Sciences, University of Cyprus, PO Box 20537, Nicosia, 1678, Cyprus.
- Department of Medical Biochemistry and Microbiology, Uppsala University, Box 582, 751 23, Uppsala, Sweden.
| | - Sifiso M Lukhele
- Department of Biological Sciences, University of Cyprus, PO Box 20537, Nicosia, 1678, Cyprus
| | - Simona Secomandi
- Department of Biological Sciences, University of Cyprus, PO Box 20537, Nicosia, 1678, Cyprus
| | - Stacey G de Souza
- Department of Biological Sciences, University of Cyprus, PO Box 20537, Nicosia, 1678, Cyprus
| | - Bettina Haase
- Vertebrate Genome Lab, The Rockefeller University, New York, NY, USA
| | - Michaella Moysi
- Department of Biological Sciences, University of Cyprus, PO Box 20537, Nicosia, 1678, Cyprus
| | - Christos Nikiforou
- Department of Biological Sciences, University of Cyprus, PO Box 20537, Nicosia, 1678, Cyprus
| | - Alexander Hutfluss
- Behavioural Ecology, Faculty of Biology, LMU Munich (LMU), 82152, Planegg-Martinsried, Germany
| | | | - Jennifer Balacco
- Vertebrate Genome Lab, The Rockefeller University, New York, NY, USA
| | | | | | - Olivier Fedrigo
- Vertebrate Genome Lab, The Rockefeller University, New York, NY, USA
| | - Colleen T Downs
- Centre for Functional Biodiversity, School of Life Sciences, University of KwaZulu-Natal, Pietermaritzburg, 3209, South Africa
| | - Ara Monadjem
- Department of Biological Sciences, University of Eswatini, Kwaluseni, Eswatini
- Mammal Research Institute, Department of Zoology & Entomology, University of Pretoria, Private Bag 20, Hatfield, 0028, Pretoria, South Africa
| | - Niels J Dingemanse
- Behavioural Ecology, Faculty of Biology, LMU Munich (LMU), 82152, Planegg-Martinsried, Germany
| | - Erich D Jarvis
- Vertebrate Genome Lab, The Rockefeller University, New York, NY, USA
- Laboratory of Neurogenetics of Language, The Rockefeller University, New York, NY, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Alan Brelsford
- Department of Evolution, Ecology and Organismal Biology, University of California Riverside, Riverside, CA, 92521, USA
| | - Bridgett M vonHoldt
- Department of Ecology & Evolutionary Biology, Princeton University, Princeton, NJ, 08544, USA
| | - Alexander N G Kirschel
- Department of Biological Sciences, University of Cyprus, PO Box 20537, Nicosia, 1678, Cyprus.
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Chen G, Yu D, Yang Y, Li X, Wang X, Sun D, Lu Y, Ke R, Zhang G, Cui J, Feng S. Adaptive expansion of ERVK solo-LTRs is associated with Passeriformes speciation events. Nat Commun 2024; 15:3151. [PMID: 38605055 PMCID: PMC11009239 DOI: 10.1038/s41467-024-47501-3] [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: 09/29/2023] [Accepted: 04/02/2024] [Indexed: 04/13/2024] Open
Abstract
Endogenous retroviruses (ERVs) are ancient retroviral remnants integrated in host genomes, and commonly deleted through unequal homologous recombination, leaving solitary long terminal repeats (solo-LTRs). This study, analysing the genomes of 362 bird species and their reptilian and mammalian outgroups, reveals an unusually higher level of solo-LTRs formation in birds, indicating evolutionary forces might have purged ERVs during evolution. Strikingly in the order Passeriformes, and especially the parvorder Passerida, endogenous retrovirus K (ERVK) solo-LTRs showed bursts of formation and recurrent accumulations coinciding with speciation events over past 22 million years. Moreover, our results indicate that the ongoing expansion of ERVK solo-LTRs in these bird species, marked by high transcriptional activity of ERVK retroviral genes in reproductive organs, caused variation of solo-LTRs between individual zebra finches. We experimentally demonstrated that cis-regulatory activity of recently evolved ERVK solo-LTRs may significantly increase the expression level of ITGA2 in the brain of zebra finches compared to chickens. These findings suggest that ERVK solo-LTRs expansion may introduce novel genomic sequences acting as cis-regulatory elements and contribute to adaptive evolution. Overall, our results underscore that the residual sequences of ancient retroviruses could influence the adaptive diversification of species by regulating host gene expression.
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Affiliation(s)
- Guangji Chen
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- Center for Evolutionary & Organismal Biology, Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou, China
- BGI Research, Wuhan, China
| | - Dan Yu
- Center for Evolutionary & Organismal Biology, Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou, China
- Center for Genomic Research, International Institutes of Medicine, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, Zhejiang, China
| | - Yu Yang
- School of Medicine, Huaqiao University, Xiamen, Fujian, 361021, China
| | - Xiang Li
- CAS Key Laboratory of Molecular Virology & Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China
| | - Xiaojing Wang
- CAS Key Laboratory of Molecular Virology & Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China
| | - Danyang Sun
- Center for Evolutionary & Organismal Biology, Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou, China
- Center for Genomic Research, International Institutes of Medicine, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, Zhejiang, China
| | - Yanlin Lu
- Center for Evolutionary & Organismal Biology, Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou, China
- Center for Genomic Research, International Institutes of Medicine, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, Zhejiang, China
| | - Rongqin Ke
- School of Medicine, Huaqiao University, Xiamen, Fujian, 361021, China
| | - Guojie Zhang
- Center for Evolutionary & Organismal Biology, Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou, China
- Innovation Center of Yangtze River Delta, Zhejiang University, Jiashan, China
| | - Jie Cui
- Department of Infectious Diseases, National Medical Center for Infectious Diseases, Huashan Hospital, Institute of Infection and Health Research, Fudan University, Shanghai, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, China.
- Shanghai Sci-Tech Inno Center for Infection & Immunity, Shanghai, 200052, China.
- Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Huashan Hospital, Fudan University, Shanghai, China.
| | - Shaohong Feng
- Center for Evolutionary & Organismal Biology, Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou, China.
- Innovation Center of Yangtze River Delta, Zhejiang University, Jiashan, China.
- Department of General Surgery of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.
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28
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Zheng W, Gojobori J, Suh A, Satta Y. Different Host-Endogenous Retrovirus Relationships between Mammals and Birds Reflected in Genome-Wide Evolutionary Interaction Patterns. Genome Biol Evol 2024; 16:evae065. [PMID: 38527852 PMCID: PMC11005779 DOI: 10.1093/gbe/evae065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 02/25/2024] [Accepted: 03/21/2024] [Indexed: 03/27/2024] Open
Abstract
Mammals and birds differ largely in their average endogenous retrovirus loads, namely the proportion of endogenous retrovirus in the genome. The host-endogenous retrovirus relationships, including conflict and co-option, have been hypothesized among the causes of this difference. However, there has not been studies about the genomic evolutionary signal of constant host-endogenous retrovirus interactions in a long-term scale and how such interactions could lead to the endogenous retrovirus load difference. Through a phylogeny-controlled correlation analysis on ∼5,000 genes between the dN/dS ratio of each gene and the load of endogenous retrovirus in 12 mammals and 21 birds, separately, we detected genes that may have evolved in association with endogenous retrovirus loads. Birds have a higher proportion of genes with strong correlation between dN/dS and the endogenous retrovirus load than mammals. Strong evidence of association is found between the dN/dS of the coding gene for leucine-rich repeat-containing protein 23 and endogenous retrovirus load in birds. Gene set enrichment analysis shows that gene silencing rather than immunity and DNA recombination may have a larger contribution to the association between dN/dS and the endogenous retrovirus load for both mammals and birds. The above results together showing different evolutionary patterns between bird and mammal genes can partially explain the apparently lower endogenous retrovirus loads of birds, while gene silencing may be a universal mechanism that plays a remarkable role in the evolutionary interaction between the host and endogenous retrovirus. In summary, our study presents signals that the host genes might have driven or responded to endogenous retrovirus load changes in long-term evolution.
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Affiliation(s)
- Wanjing Zheng
- Department of Evolutionary Studies of Biosystems, School of Advanced Sciences, SOKENDAI (The Graduate University for Advanced Studies), Kanagawa 240-0193, Japan
- School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Jun Gojobori
- Department of Evolutionary Studies of Biosystems, School of Advanced Sciences, SOKENDAI (The Graduate University for Advanced Studies), Kanagawa 240-0193, Japan
- Research Center for Integrative Evolutionary Science, SOKENDAI (The Graduate University for Advanced Studies), Kanagawa 240-0193, Japan
| | - Alexander Suh
- Department of Organismal Biology—Systematic Biology, Evolutionary Biology Centre (EBC), Uppsala University, Uppsala 75236, Sweden
- School of Biological Sciences—Organisms and the Environment, University of East Anglia, Norwich, UK
| | - Yoko Satta
- Department of Evolutionary Studies of Biosystems, School of Advanced Sciences, SOKENDAI (The Graduate University for Advanced Studies), Kanagawa 240-0193, Japan
- Research Center for Integrative Evolutionary Science, SOKENDAI (The Graduate University for Advanced Studies), Kanagawa 240-0193, Japan
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29
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Karollus A, Hingerl J, Gankin D, Grosshauser M, Klemon K, Gagneur J. Species-aware DNA language models capture regulatory elements and their evolution. Genome Biol 2024; 25:83. [PMID: 38566111 PMCID: PMC10985990 DOI: 10.1186/s13059-024-03221-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 03/20/2024] [Indexed: 04/04/2024] Open
Abstract
BACKGROUND The rise of large-scale multi-species genome sequencing projects promises to shed new light on how genomes encode gene regulatory instructions. To this end, new algorithms are needed that can leverage conservation to capture regulatory elements while accounting for their evolution. RESULTS Here, we introduce species-aware DNA language models, which we trained on more than 800 species spanning over 500 million years of evolution. Investigating their ability to predict masked nucleotides from context, we show that DNA language models distinguish transcription factor and RNA-binding protein motifs from background non-coding sequence. Owing to their flexibility, DNA language models capture conserved regulatory elements over much further evolutionary distances than sequence alignment would allow. Remarkably, DNA language models reconstruct motif instances bound in vivo better than unbound ones and account for the evolution of motif sequences and their positional constraints, showing that these models capture functional high-order sequence and evolutionary context. We further show that species-aware training yields improved sequence representations for endogenous and MPRA-based gene expression prediction, as well as motif discovery. CONCLUSIONS Collectively, these results demonstrate that species-aware DNA language models are a powerful, flexible, and scalable tool to integrate information from large compendia of highly diverged genomes.
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Affiliation(s)
- Alexander Karollus
- School of Computation, Information and Technology, Technical University of Munich, Garching, Germany
- Munich Center for Machine Learning, Munich, Germany
| | - Johannes Hingerl
- School of Computation, Information and Technology, Technical University of Munich, Garching, Germany
| | - Dennis Gankin
- School of Computation, Information and Technology, Technical University of Munich, Garching, Germany
| | - Martin Grosshauser
- School of Computation, Information and Technology, Technical University of Munich, Garching, Germany
| | - Kristian Klemon
- School of Computation, Information and Technology, Technical University of Munich, Garching, Germany
| | - Julien Gagneur
- School of Computation, Information and Technology, Technical University of Munich, Garching, Germany.
- Munich Center for Machine Learning, Munich, Germany.
- Institute of Human Genetics, School of Medicine and Health, Technical University of Munich, Munich, Germany.
- Computational Health Center, Helmholtz Center Munich, Neuherberg, Germany.
- Munich Data Science Institute, Technical University of Munich, Garching, Germany.
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30
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Benham PM, Cicero C, Escalona M, Beraut E, Fairbairn C, Marimuthu MPA, Nguyen O, Sahasrabudhe R, King BL, Thomas WK, Kovach AI, Nachman MW, Bowie RCK. Remarkably High Repeat Content in the Genomes of Sparrows: The Importance of Genome Assembly Completeness for Transposable Element Discovery. Genome Biol Evol 2024; 16:evae067. [PMID: 38566597 PMCID: PMC11088854 DOI: 10.1093/gbe/evae067] [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: 11/02/2023] [Revised: 03/01/2024] [Accepted: 03/23/2024] [Indexed: 04/04/2024] Open
Abstract
Transposable elements (TE) play critical roles in shaping genome evolution. Highly repetitive TE sequences are also a major source of assembly gaps making it difficult to fully understand the impact of these elements on host genomes. The increased capacity of long-read sequencing technologies to span highly repetitive regions promises to provide new insights into patterns of TE activity across diverse taxa. Here we report the generation of highly contiguous reference genomes using PacBio long-read and Omni-C technologies for three species of Passerellidae sparrow. We compared these assemblies to three chromosome-level sparrow assemblies and nine other sparrow assemblies generated using a variety of short- and long-read technologies. All long-read based assemblies were longer (range: 1.12 to 1.41 Gb) than short-read assemblies (0.91 to 1.08 Gb) and assembly length was strongly correlated with the amount of repeat content. Repeat content for Bell's sparrow (31.2% of genome) was the highest level ever reported within the order Passeriformes, which comprises over half of avian diversity. The highest levels of repeat content (79.2% to 93.7%) were found on the W chromosome relative to other regions of the genome. Finally, we show that proliferation of different TE classes varied even among species with similar levels of repeat content. These patterns support a dynamic model of TE expansion and contraction even in a clade where TEs were once thought to be fairly depauperate and static. Our work highlights how the resolution of difficult-to-assemble regions of the genome with new sequencing technologies promises to transform our understanding of avian genome evolution.
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Affiliation(s)
- Phred M Benham
- Museum of Vertebrate Zoology, University of California Berkeley, Berkeley, CA 94720, USA
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Carla Cicero
- Museum of Vertebrate Zoology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Merly Escalona
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Eric Beraut
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Colin Fairbairn
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Mohan P A Marimuthu
- DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California-Davis, Davis, CA 95616, USA
| | - Oanh Nguyen
- DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California-Davis, Davis, CA 95616, USA
| | - Ruta Sahasrabudhe
- DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California-Davis, Davis, CA 95616, USA
| | - Benjamin L King
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, ME 04469, USA
| | - W Kelley Thomas
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH 03824, USA
| | - Adrienne I Kovach
- Department of Natural Resources and the Environment, University of New Hampshire, Durham, NH 03824, USA
| | - Michael W Nachman
- Museum of Vertebrate Zoology, University of California Berkeley, Berkeley, CA 94720, USA
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Rauri C K Bowie
- Museum of Vertebrate Zoology, University of California Berkeley, Berkeley, CA 94720, USA
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA 94720, USA
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31
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Tang L, Dong S, Xing X. Comparative Genomics Reveal Phylogenetic Relationship and Chromosomal Evolutionary Events of Eight Cervidae Species. Animals (Basel) 2024; 14:1063. [PMID: 38612302 PMCID: PMC11010878 DOI: 10.3390/ani14071063] [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: 02/26/2024] [Revised: 03/25/2024] [Accepted: 03/27/2024] [Indexed: 04/14/2024] Open
Abstract
Cervidae represents a family that is not only rich in species diversity but also exhibits a wide range of karyotypes. The controversies regarding the phylogeny and classification of Cervidae still persist. The flourishing development of the genomic era has made it possible to address these issues at the genomic level. Here, the genomes of nine species were used to explore the phylogeny and chromosomal evolutionary events of Cervidae. By conducting whole-genome comparisons, we identified single-copy orthologous genes across the nine species and constructed a phylogenetic tree based on the single-copy orthologous genes sequences, providing new insights into the phylogeny of Cervidae, particularly the phylogenetic relationship among sika deer, red deer, wapiti and Tarim red deer. Gene family analysis revealed contractions in the olfactory receptor gene family and expansions in the histone gene family across eight Cervidae species. Furthermore, synteny analysis was used to explore the chromosomal evolutionary events of Cervidae species, revealing six chromosomal fissions during the evolutionary process from Bovidae to Cervidae. Notably, specific chromosomal fusion events were found in four species of Cervus, and a unique chromosomal fusion event was identified in Muntiacus reevesi. Our study further completed the phylogenetic relationship within the Cervidae and demonstrated the feasibility of inferring species phylogeny at the whole-genome level. Additionally, our findings on gene family evolution and the chromosomal evolutionary events in eight Cervidae species lay a foundation for comprehensive research of the evolution of Cervidae.
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Affiliation(s)
| | | | - Xiumei Xing
- State Key Laboratory for Molecular Biology of Special Economic Animals, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China; (L.T.); (S.D.)
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32
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McComish BJ, Charleston MA, Parks M, Baroni C, Salvatore MC, Li R, Zhang G, Millar CD, Holland BR, Lambert DM. Ancient and Modern Genomes Reveal Microsatellites Maintain a Dynamic Equilibrium Through Deep Time. Genome Biol Evol 2024; 16:evae017. [PMID: 38412309 PMCID: PMC10972684 DOI: 10.1093/gbe/evae017] [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: 04/05/2023] [Revised: 12/22/2023] [Accepted: 01/23/2024] [Indexed: 02/29/2024] Open
Abstract
Microsatellites are widely used in population genetics, but their evolutionary dynamics remain poorly understood. It is unclear whether microsatellite loci drift in length over time. This is important because the mutation processes that underlie these important genetic markers are central to the evolutionary models that employ microsatellites. We identify more than 27 million microsatellites using a novel and unique dataset of modern and ancient Adélie penguin genomes along with data from 63 published chordate genomes. We investigate microsatellite evolutionary dynamics over 2 timescales: one based on Adélie penguin samples dating to ∼46.5 ka and the other dating to the diversification of chordates aged more than 500 Ma. We show that the process of microsatellite allele length evolution is at dynamic equilibrium; while there is length polymorphism among individuals, the length distribution for a given locus remains stable. Many microsatellites persist over very long timescales, particularly in exons and regulatory sequences. These often retain length variability, suggesting that they may play a role in maintaining phenotypic variation within populations.
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Affiliation(s)
- Bennet J McComish
- School of Natural Sciences, University of Tasmania, Hobart, TAS 7001, Australia
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS 7001, Australia
| | | | - Matthew Parks
- Australian Research Centre for Human Evolution, Griffith University, Nathan, QLD 4111, Australia
- Department of Biology, University of Central Oklahoma, Edmond, OK 73034, USA
| | - Carlo Baroni
- Dipartimento di Scienze della Terra, University of Pisa, Pisa, Italy
- CNR-IGG, Institute of Geosciences and Earth Resources, Pisa, Italy
| | - Maria Cristina Salvatore
- Dipartimento di Scienze della Terra, University of Pisa, Pisa, Italy
- CNR-IGG, Institute of Geosciences and Earth Resources, Pisa, Italy
| | - Ruiqiang Li
- Novogene Bioinformatics Technology Co. Ltd., Beijing 100083, China
| | - Guojie Zhang
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
- Department of Biology, Centre for Social Evolution, University of Copenhagen, Copenhagen DK-2100, Denmark
| | - Craig D Millar
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Barbara R Holland
- School of Natural Sciences, University of Tasmania, Hobart, TAS 7001, Australia
| | - David M Lambert
- Australian Research Centre for Human Evolution, Griffith University, Nathan, QLD 4111, Australia
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33
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Sin SYW, Ke F, Chen G, Huang PY, Enbody ED, Karubian J, Webster MS, Edwards SV. Genetic Basis and Evolution of Structural Color Polymorphism in an Australian Songbird. Mol Biol Evol 2024; 41:msae046. [PMID: 38415852 PMCID: PMC10962638 DOI: 10.1093/molbev/msae046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 02/02/2024] [Accepted: 02/22/2024] [Indexed: 02/29/2024] Open
Abstract
Island organisms often evolve phenotypes divergent from their mainland counterparts, providing a useful system for studying adaptation under differential selection. In the white-winged fairywren (Malurus leucopterus), subspecies on two islands have a black nuptial plumage whereas the subspecies on the Australian mainland has a blue nuptial plumage. The black subspecies have a feather nanostructure that could in principle produce a blue structural color, suggesting a blue ancestor. An earlier study proposed independent evolution of melanism on the islands based on the history of subspecies divergence. However, the genetic basis of melanism and the origin of color differentiation in this group are still unknown. Here, we used whole-genome resequencing to investigate the genetic basis of melanism by comparing the blue and black M. leucopterus subspecies to identify highly divergent genomic regions. We identified a well-known pigmentation gene ASIP and four candidate genes that may contribute to feather nanostructure development. Contrary to the prediction of convergent evolution of island melanism, we detected signatures of a selective sweep in genomic regions containing ASIP and SCUBE2 not in the black subspecies but in the blue subspecies, which possesses many derived SNPs in these regions, suggesting that the mainland subspecies has re-evolved a blue plumage from a black ancestor. This proposed re-evolution was likely driven by a preexisting female preference. Our findings provide new insight into the evolution of plumage coloration in island versus continental populations, and, importantly, we identify candidate genes that likely play roles in the development and evolution of feather structural coloration.
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Affiliation(s)
- Simon Yung Wa Sin
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Fushi Ke
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China
| | - Guoling Chen
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China
| | - Pei-Yu Huang
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China
| | - Erik D Enbody
- Department of Ecology and Evolutionary Biology, Tulane University, New Orleans, LA 70118, USA
| | - Jordan Karubian
- Department of Ecology and Evolutionary Biology, Tulane University, New Orleans, LA 70118, USA
| | - Michael S Webster
- Cornell Lab of Ornithology and Department of Neurobiology and Behavior, Cornell University, Ithaca, NY 14853, USA
| | - Scott V Edwards
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
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34
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Wollenberg Valero KC. Brief Communication: The Predictable Network Topology of Evolutionary Genomic Constraint. Mol Biol Evol 2024; 41:msae033. [PMID: 38366776 PMCID: PMC10906983 DOI: 10.1093/molbev/msae033] [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: 07/25/2023] [Revised: 01/03/2024] [Accepted: 02/09/2024] [Indexed: 02/18/2024] Open
Abstract
Large-scale comparative genomics studies offer valuable resources for understanding both functional and evolutionary rate constraints. It is suggested that constraint aligns with the topology of genomic networks, increasing toward the center, with intermediate nodes combining relaxed constraint with higher contributions to the phenotype due to pleiotropy. However, this pattern has yet to be demonstrated in vertebrates. This study shows that constraint intensifies toward the network's center in placental mammals. Genes with rate changes associated with emergence of hibernation cluster mostly toward intermediate positions, with higher constraint in faster-evolving genes, which is indicative of a "sweet spot" for adaptation. If this trend holds universally, network node metrics could predict high-constraint regions even in clades lacking empirical constraint data.
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35
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Xu L, Ren Y, Wu J, Cui T, Dong R, Huang C, Feng Z, Zhang T, Yang P, Yuan J, Xu X, Liu J, Wang J, Chen W, Mi D, Irwin DM, Yan Y, Xu L, Yu X, Li G. Evolution and expression patterns of the neo-sex chromosomes of the crested ibis. Nat Commun 2024; 15:1670. [PMID: 38395916 PMCID: PMC10891136 DOI: 10.1038/s41467-024-46052-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: 06/21/2023] [Accepted: 02/08/2024] [Indexed: 02/25/2024] Open
Abstract
Bird sex chromosomes play a unique role in sex-determination, and affect the sexual morphology and behavior of bird species. Core waterbirds, a major clade of birds, share the common characteristics of being sexually monomorphic and having lower levels of inter-sexual conflict, yet their sex chromosome evolution remains poorly understood. Here, by we analyse of a chromosome-level assembly of a female crested ibis (Nipponia nippon), a typical core waterbird. We identify neo-sex chromosomes resulting from fusion of microchromosomes with ancient sex chromosomes. These fusion events likely occurred following the divergence of Threskiornithidae and Ardeidae. The neo-W chromosome of the crested ibis exhibits the characteristics of slow degradation, which is reflected in its retention of abundant gametologous genes. Neo-W chromosome genes display an apparent ovary-biased gene expression, which is largely driven by genes that are retained on the crested ibis W chromosome but lost in other bird species. These results provide new insights into the evolutionary history and expression patterns for the sex chromosomes of bird species.
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Affiliation(s)
- Lulu Xu
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Yandong Ren
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Jiahong Wu
- MOE Key Laboratory of Freshwater Fish Reproduction and Development, School of Life Sciences, Southwest University, Chongqing, China
| | - Tingting Cui
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Rong Dong
- Research Center for Qinling Giant Panda, Shaanxi Academy of Forestry, Xi'an, China
| | - Chen Huang
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Zhe Feng
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Tianmin Zhang
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Peng Yang
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Jiaqing Yuan
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Xiao Xu
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Jiao Liu
- MOE Key Laboratory of Freshwater Fish Reproduction and Development, School of Life Sciences, Southwest University, Chongqing, China
| | - Jinhong Wang
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Wu Chen
- Guangzhou Wildlife Research Center, Guangzhou Zoo, Guangzhou, China
| | - Da Mi
- Xi'an Haorui Genomics Technology Co., LTD, Xi'an, China
| | - David M Irwin
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Yaping Yan
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Luohao Xu
- MOE Key Laboratory of Freshwater Fish Reproduction and Development, School of Life Sciences, Southwest University, Chongqing, China.
| | - Xiaoping Yu
- College of Life Sciences, Shaanxi Normal University, Xi'an, China.
| | - Gang Li
- College of Life Sciences, Shaanxi Normal University, Xi'an, China.
- Guangzhou Wildlife Research Center, Guangzhou Zoo, Guangzhou, China.
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36
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Fromm B, Sorger T. Rapid adaptation of cellular metabolic rate to the MicroRNA complements of mammals and its relevance to the evolution of endothermy. iScience 2024; 27:108740. [PMID: 38327773 PMCID: PMC10847693 DOI: 10.1016/j.isci.2023.108740] [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: 11/28/2022] [Revised: 09/13/2023] [Accepted: 12/12/2023] [Indexed: 02/09/2024] Open
Abstract
The metabolic efficiency of mammalian cells depends on the attenuation of intrinsic translation noise by microRNAs. We devised a metric of cellular metabolic rate (cMR), rMR/Mexp optimally fit to the number of microRNA families (mirFam), that is robust to variation in mass and sensitive to body temperature (Tb), consistent with the heat dissipation limit theory of Speakman and Król (2010). Using mirFam as predictor, an Ornstein-Uhlenbeck process of stabilizing selection, with an adaptive shift at the divergence of Boreoeutheria, accounted for 95% of the variation in cMR across mammals. Branchwise rates of evolution of cMR, mirFam and Tb concurrently increased 6- to 7-fold at the divergence of Boreoeutheria, independent of mass. Cellular MR variation across placental mammals was also predicted by the sum of model conserved microRNA-target interactions, revealing an unexpected degree of integration of the microRNA-target apparatus into the energy economy of the mammalian cell.
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Affiliation(s)
- Bastian Fromm
- The Arctic University Museum of Norway, UiT- The Arctic University of Norway, Tromsø, Norway
| | - Thomas Sorger
- Department of Biology, Roger Williams University, Bristol, RI 02809, USA
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37
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Langebrake C, Manthey G, Frederiksen A, Lugo Ramos JS, Dutheil JY, Chetverikova R, Solov'yov IA, Mouritsen H, Liedvogel M. Adaptive evolution and loss of a putative magnetoreceptor in passerines. Proc Biol Sci 2024; 291:20232308. [PMID: 38320616 PMCID: PMC10846946 DOI: 10.1098/rspb.2023.2308] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 01/08/2024] [Indexed: 02/08/2024] Open
Abstract
Migratory birds possess remarkable accuracy in orientation and navigation, which involves various compass systems including the magnetic compass. Identifying the primary magnetosensor remains a fundamental open question. Cryptochromes (Cry) have been shown to be magnetically sensitive, and Cry4a from a migratory songbird seems to show enhanced magnetic sensitivity in vitro compared to Cry4a from resident species. We investigate Cry and their potential involvement in magnetoreception in a phylogenetic framework, integrating molecular evolutionary analyses with protein dynamics modelling. Our analysis is based on 363 bird genomes and identifies different selection regimes in passerines. We show that Cry4a is characterized by strong positive selection and high variability, typical characteristics of sensor proteins. We identify key sites that are likely to have facilitated the evolution of an optimized sensory protein for night-time orientation in songbirds. Additionally, we show that Cry4 was lost in hummingbirds, parrots and Tyranni (Suboscines), and thus identified a gene deletion, which might facilitate testing the function of Cry4a in birds. In contrast, the other avian Cry (Cry1 and Cry2) were highly conserved across all species, indicating basal, non-sensory functions. Our results support a specialization or functional differentiation of Cry4 in songbirds which could be magnetosensation.
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Affiliation(s)
- Corinna Langebrake
- Institute of Avian Research ‘Vogelwarte Helgoland’, 26386 Wilhelmshaven, Germany
- MPRG Behavioural Genomics, MPI Evolutionary Biology, 24306 Plön, Germany
| | - Georg Manthey
- Institute of Avian Research ‘Vogelwarte Helgoland’, 26386 Wilhelmshaven, Germany
- Department of Physics, Carl von Ossietzky Universität Oldenburg, 26129 Oldenburg
| | - Anders Frederiksen
- Department of Physics, Carl von Ossietzky Universität Oldenburg, 26129 Oldenburg
| | - Juan S. Lugo Ramos
- MPRG Behavioural Genomics, MPI Evolutionary Biology, 24306 Plön, Germany
- The Francis Crick Institute, London NW1 1AT, UK
| | - Julien Y. Dutheil
- Research Group Molecular Systems Evolution, MPI Evolutionary Biology, 24306 Plön, Germany
| | - Raisa Chetverikova
- Biology and Environmental Sciences Department, Carl von Ossietzky Universität Oldenburg, 26129 Oldenburg
| | - Ilia A. Solov'yov
- Department of Physics, Carl von Ossietzky Universität Oldenburg, 26129 Oldenburg
- Research Centre for Neurosensory Sciences, Carl von Ossietzky Universität Oldenburg, 26129 Oldenburg
- Center for Nanoscale Dynamics (CENAD), Carl von Ossietzky Universität Oldenburg, 26129 Oldenburg
| | - Henrik Mouritsen
- Biology and Environmental Sciences Department, Carl von Ossietzky Universität Oldenburg, 26129 Oldenburg
- Research Centre for Neurosensory Sciences, Carl von Ossietzky Universität Oldenburg, 26129 Oldenburg
| | - Miriam Liedvogel
- Institute of Avian Research ‘Vogelwarte Helgoland’, 26386 Wilhelmshaven, Germany
- MPRG Behavioural Genomics, MPI Evolutionary Biology, 24306 Plön, Germany
- Biology and Environmental Sciences Department, Carl von Ossietzky Universität Oldenburg, 26129 Oldenburg
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38
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Zhou H, Huang X, Liu J, Ding J, Xu K, Zhu W, He C, Yang L, Zhu J, Han C, Qin C, Luo H, Chen K, Jiang S, Shi Y, Zeng J, Weng Z, Xu Y, Wang Q, Zhong M, Du B, Song S, Meng H. De novo Phased Genome Assembly, Annotation and Population Genotyping of Alectoris Chukar. Sci Data 2024; 11:162. [PMID: 38307880 PMCID: PMC10837146 DOI: 10.1038/s41597-024-02991-0] [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: 09/25/2023] [Accepted: 01/22/2024] [Indexed: 02/04/2024] Open
Abstract
The Alectoris Chukar (chukar) is the most geographically widespread partridge species in the world, demonstrating exceptional adaptability to diverse ecological environments. However, the scarcity of genetic resources for chukar has hindered research into its adaptive evolution and molecular breeding. In this study, we have sequenced and assembled a high-quality, phased chukar genome that consists of 31 pairs of relatively complete diploid chromosomes. Our BUSCO analysis reported a high completeness score of 96.8% and 96.5%, with respect to universal single-copy orthologs and a low duplication rate (0.3% and 0.5%) for two assemblies. Through resequencing and population genomic analyses of six subspecies, we have curated invaluable genotype data that underscores the adaptive evolution of chukar in response to both arid and high-altitude environments. These data will significantly contribute to research on how chukars adaptively evolve to cope with desertification and alpine climates.
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Affiliation(s)
- Hao Zhou
- Shanghai Collaborative Innovation Center of Agri-Seeds/School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xunhe Huang
- Jiaying University/Guangdong Provincial Key Laboratory of Conservation and Precision Utilization of Characteristic Agricultural Resources in Mountainous Areas, Meizhou, 514015, China
| | - Jiajia Liu
- Shanghai Collaborative Innovation Center of Agri-Seeds/School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jinmei Ding
- Shanghai Collaborative Innovation Center of Agri-Seeds/School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Ke Xu
- Shanghai Collaborative Innovation Center of Agri-Seeds/School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Wenqi Zhu
- Shanghai Collaborative Innovation Center of Agri-Seeds/School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Chuan He
- Shanghai Collaborative Innovation Center of Agri-Seeds/School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Lingyu Yang
- Shanghai Collaborative Innovation Center of Agri-Seeds/School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jianshen Zhu
- Shanghai Collaborative Innovation Center of Agri-Seeds/School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Chengxiao Han
- Shanghai Collaborative Innovation Center of Agri-Seeds/School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Chao Qin
- Shanghai Collaborative Innovation Center of Agri-Seeds/School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Huaixi Luo
- Shanghai Collaborative Innovation Center of Agri-Seeds/School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Kangchun Chen
- Shanghai Collaborative Innovation Center of Agri-Seeds/School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Shengyao Jiang
- Shanghai Collaborative Innovation Center of Agri-Seeds/School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yurou Shi
- School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Jinyuan Zeng
- School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Zhuoxian Weng
- Jiaying University/Guangdong Provincial Key Laboratory of Conservation and Precision Utilization of Characteristic Agricultural Resources in Mountainous Areas, Meizhou, 514015, China
| | - Yongjie Xu
- Jiaying University/Guangdong Provincial Key Laboratory of Conservation and Precision Utilization of Characteristic Agricultural Resources in Mountainous Areas, Meizhou, 514015, China
| | - Qing Wang
- Jiaying University/Guangdong Provincial Key Laboratory of Conservation and Precision Utilization of Characteristic Agricultural Resources in Mountainous Areas, Meizhou, 514015, China
| | - Ming Zhong
- Jiaying University/Guangdong Provincial Key Laboratory of Conservation and Precision Utilization of Characteristic Agricultural Resources in Mountainous Areas, Meizhou, 514015, China
| | - Bingwang Du
- Jiaying University/Guangdong Provincial Key Laboratory of Conservation and Precision Utilization of Characteristic Agricultural Resources in Mountainous Areas, Meizhou, 514015, China.
- Department of Animal Science, Guangdong Ocean University, Huguangyan East, Zhanjiang, Guangdong, 524088, China.
| | - Sen Song
- School of Life Sciences, Lanzhou University, Lanzhou, 730000, China.
| | - He Meng
- Shanghai Collaborative Innovation Center of Agri-Seeds/School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China.
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Xu X, Wang C, Xu C, Yuan J, Wang G, Wu Y, Huang C, Jing H, Yang P, Xu L, Peng S, Shan F, Xia X, Jin F, Hou F, Wang J, Mi D, Ren Y, Liu Y, Irwin DM, Li X, Chen W, Li G. Genomic evolution of island birds from the view of the Swinhoe's pheasant (Lophura swinhoii). Mol Ecol Resour 2024; 24:e13896. [PMID: 37955396 DOI: 10.1111/1755-0998.13896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 10/26/2023] [Accepted: 10/31/2023] [Indexed: 11/14/2023]
Abstract
Island endemic birds account for the majority of extinct vertebrates in the past few centuries. To date, the evolutionary characteristics of island endemic bird's is poorly known. In this research, we de novo assembled a high-quality chromosome-level reference genome for the Swinhoe's pheasant, which is a typical endemic island bird. Results of collinearity tests suggest rapid ancient chromosome rearrangement that may have contributed to the initial species radiation within Phasianidae, and a role for the insertions of CR1 transposable elements in rearranging chromosomes in Phasianidae. During the evolution of the Swinhoe's pheasant, natural selection positively selected genes involved in fecundity and body size functions, at both the species and population levels, which reflect genetic variation associated with island adaptation. We further tested for variation in population genomic traits between the Swinhoe's pheasant and its phylogenetically closely related mainland relative the silver pheasant, and found higher levels of genetic drift and inbreeding in the Swinhoe's pheasant genome. Divergent demographic histories of insular and mainland bird species during the last glacial period may reflect the differing impact of insular and continental climates on the evolution of species. Our research interprets the natural history and population genetic characteristics of the insular endemic bird the Swinhoe's pheasant, at a genome-wide scale, provides a broader perspective on insular speciation, and adaptive evolution and contributes to the genetic conservation of island endemic birds.
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Affiliation(s)
- Xiao Xu
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Chen Wang
- Guangzhou Zoo, Guangzhou, China
- Guangzhou Collaborative Innovation Center on Science-Tech of Ecology and Landscape, Guangzhou, China
| | - Chunzhong Xu
- Shanghai Wild Animal Park Development Co., Ltd, Shanghai, China
| | - Jiaqing Yuan
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Guiqiang Wang
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Yajiang Wu
- Guangzhou Zoo, Guangzhou, China
- Guangzhou Collaborative Innovation Center on Science-Tech of Ecology and Landscape, Guangzhou, China
| | - Chen Huang
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Haohao Jing
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Peng Yang
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Lulu Xu
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Shiming Peng
- Guangzhou Zoo, Guangzhou, China
- Guangzhou Collaborative Innovation Center on Science-Tech of Ecology and Landscape, Guangzhou, China
| | - Fen Shan
- Guangzhou Zoo, Guangzhou, China
- Guangzhou Collaborative Innovation Center on Science-Tech of Ecology and Landscape, Guangzhou, China
| | - Xiaochao Xia
- Guangdong Wildlife Monitoring, Rescue and Conservation Center, Guangzhou, China
| | - Fuyuan Jin
- Guangdong Maoming Forest Park Administrative Office, Maoming, China
| | - Fanghui Hou
- Shanghai Wild Animal Park Development Co., Ltd, Shanghai, China
| | - Jinhong Wang
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Da Mi
- Xi'an Haorui Genomics Technology Co., Ltd, Xi'an, China
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China
| | - Yandong Ren
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Yang Liu
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - David M Irwin
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Xuejuan Li
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Wu Chen
- Guangzhou Zoo, Guangzhou, China
- Guangzhou Collaborative Innovation Center on Science-Tech of Ecology and Landscape, Guangzhou, China
| | - Gang Li
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
- Guangzhou Zoo, Guangzhou, China
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40
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Wang S, Zhang P, Fei F, Tong T, Zhou X, Zhou Y, Zhang J, Wei M, Zhang Y, Zhang L, Huang Y, Zhang L, Zhang X, Cai T, Xie C. Unexpected divergence in magnetoreceptor MagR from robin and pigeon linked to two sequence variations. Zool Res 2024; 45:69-78. [PMID: 38114434 PMCID: PMC10839668 DOI: 10.24272/j.issn.2095-8137.2023.138] [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: 10/11/2023] [Accepted: 11/28/2023] [Indexed: 12/21/2023] Open
Abstract
Birds exhibit extraordinary mobility and remarkable navigational skills, obtaining guidance cues from the Earth's magnetic field for orientation and long-distance movement. Bird species also show tremendous diversity in navigation strategies, with considerable differences even within the same taxa and among individuals from the same population. The highly conserved iron and iron-sulfur cluster binding magnetoreceptor (MagR) protein is suggested to enable animals, including birds, to detect the geomagnetic field and navigate accordingly. Notably, MagR is also implicated in other functions, such as electron transfer and biogenesis of iron-sulfur clusters, raising the question of whether variability exists in its biochemical and biophysical features among species, particularly birds. In the current study, we conducted a comparative analysis of MagR from two different bird species, including the migratory European robin and the homing pigeon. Sequence alignment revealed an extremely high degree of similarity between the MagRs of these species, with only three sequence variations. Nevertheless, two of these variations underpinned significant differences in metal binding capacity, oligomeric state, and magnetic properties. These findings offer compelling evidence for the marked differences in MagR between the two avian species, potentially explaining how a highly conserved protein can mediate such diverse functions.
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Affiliation(s)
- Shun Wang
- Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui 230039, China
- High Magnetic Field Laboratory, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Science Island, Hefei, Anhui 230031, China
| | - Peng Zhang
- High Magnetic Field Laboratory, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Science Island, Hefei, Anhui 230031, China
- Science Island Branch of Graduate School, University of Science and Technology of China, Hefei, Anhui 230036, China
| | - Fan Fei
- High Magnetic Field Laboratory, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Science Island, Hefei, Anhui 230031, China
- Science Island Branch of Graduate School, University of Science and Technology of China, Hefei, Anhui 230036, China
| | - Tianyang Tong
- High Magnetic Field Laboratory, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Science Island, Hefei, Anhui 230031, China
- Department of Anatomy, Anhui Medical University, Hefei, Anhui 230032, China
| | - Xiujuan Zhou
- High Magnetic Field Laboratory, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Science Island, Hefei, Anhui 230031, China
- Science Island Branch of Graduate School, University of Science and Technology of China, Hefei, Anhui 230036, China
| | - Yajie Zhou
- Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui 230039, China
- High Magnetic Field Laboratory, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Science Island, Hefei, Anhui 230031, China
| | - Jing Zhang
- High Magnetic Field Laboratory, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Science Island, Hefei, Anhui 230031, China
- Science Island Branch of Graduate School, University of Science and Technology of China, Hefei, Anhui 230036, China
| | - Mengke Wei
- Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui 230039, China
- High Magnetic Field Laboratory, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Science Island, Hefei, Anhui 230031, China
| | - Yanqi Zhang
- High Magnetic Field Laboratory, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Science Island, Hefei, Anhui 230031, China
- Science Island Branch of Graduate School, University of Science and Technology of China, Hefei, Anhui 230036, China
| | - Lei Zhang
- High Magnetic Field Laboratory, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Science Island, Hefei, Anhui 230031, China
- Science Island Branch of Graduate School, University of Science and Technology of China, Hefei, Anhui 230036, China
| | - Yulong Huang
- Department of Mechanical and Aerospace Engineering, University at Buffalo, State University of New York, Buffalo, NY 14260 USA
| | - Lin Zhang
- High Magnetic Field Laboratory, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Science Island, Hefei, Anhui 230031, China
| | - Xin Zhang
- Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui 230039, China
- High Magnetic Field Laboratory, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Science Island, Hefei, Anhui 230031, China
- Science Island Branch of Graduate School, University of Science and Technology of China, Hefei, Anhui 230036, China
- International Magnetobiology Frontier Research Center, Science Island, Hefei, Anhui 230031, China
| | - Tiantian Cai
- High Magnetic Field Laboratory, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Science Island, Hefei, Anhui 230031, China
- Science Island Branch of Graduate School, University of Science and Technology of China, Hefei, Anhui 230036, China. E-mail:
| | - Can Xie
- High Magnetic Field Laboratory, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Science Island, Hefei, Anhui 230031, China
- Science Island Branch of Graduate School, University of Science and Technology of China, Hefei, Anhui 230036, China
- International Magnetobiology Frontier Research Center, Science Island, Hefei, Anhui 230031, China. E-mail:
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41
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Bredeson JV, Mudd AB, Medina-Ruiz S, Mitros T, Smith OK, Miller KE, Lyons JB, Batra SS, Park J, Berkoff KC, Plott C, Grimwood J, Schmutz J, Aguirre-Figueroa G, Khokha MK, Lane M, Philipp I, Laslo M, Hanken J, Kerdivel G, Buisine N, Sachs LM, Buchholz DR, Kwon T, Smith-Parker H, Gridi-Papp M, Ryan MJ, Denton RD, Malone JH, Wallingford JB, Straight AF, Heald R, Hockemeyer D, Harland RM, Rokhsar DS. Conserved chromatin and repetitive patterns reveal slow genome evolution in frogs. Nat Commun 2024; 15:579. [PMID: 38233380 PMCID: PMC10794172 DOI: 10.1038/s41467-023-43012-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 10/27/2023] [Indexed: 01/19/2024] Open
Abstract
Frogs are an ecologically diverse and phylogenetically ancient group of anuran amphibians that include important vertebrate cell and developmental model systems, notably the genus Xenopus. Here we report a high-quality reference genome sequence for the western clawed frog, Xenopus tropicalis, along with draft chromosome-scale sequences of three distantly related emerging model frog species, Eleutherodactylus coqui, Engystomops pustulosus, and Hymenochirus boettgeri. Frog chromosomes have remained remarkably stable since the Mesozoic Era, with limited Robertsonian (i.e., arm-preserving) translocations and end-to-end fusions found among the smaller chromosomes. Conservation of synteny includes conservation of centromere locations, marked by centromeric tandem repeats associated with Cenp-a binding surrounded by pericentromeric LINE/L1 elements. This work explores the structure of chromosomes across frogs, using a dense meiotic linkage map for X. tropicalis and chromatin conformation capture (Hi-C) data for all species. Abundant satellite repeats occupy the unusually long (~20 megabase) terminal regions of each chromosome that coincide with high rates of recombination. Both embryonic and differentiated cells show reproducible associations of centromeric chromatin and of telomeres, reflecting a Rabl-like configuration. Our comparative analyses reveal 13 conserved ancestral anuran chromosomes from which contemporary frog genomes were constructed.
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Affiliation(s)
- Jessen V Bredeson
- Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA
- DOE-Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Austin B Mudd
- Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA
| | - Sofia Medina-Ruiz
- Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA
| | - Therese Mitros
- Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA
| | - Owen Kabnick Smith
- Department of Biochemistry, Stanford University School of Medicine, 279 Campus Drive, Beckman Center 409, Stanford, CA, 94305-5307, USA
| | - Kelly E Miller
- Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA
| | - Jessica B Lyons
- Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA
| | - Sanjit S Batra
- Computer Science Division, University of California Berkeley, 2626 Hearst Avenue, Berkeley, CA, 94720, USA
| | - Joseph Park
- Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA
| | - Kodiak C Berkoff
- Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA
| | - Christopher Plott
- HudsonAlpha Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Jane Grimwood
- HudsonAlpha Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Jeremy Schmutz
- HudsonAlpha Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Guadalupe Aguirre-Figueroa
- Department of Biochemistry, Stanford University School of Medicine, 279 Campus Drive, Beckman Center 409, Stanford, CA, 94305-5307, USA
| | - Mustafa K Khokha
- Pediatric Genomics Discovery Program, Departments of Pediatrics and Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT, 06510, USA
| | - Maura Lane
- Pediatric Genomics Discovery Program, Departments of Pediatrics and Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT, 06510, USA
| | - Isabelle Philipp
- Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA
| | - Mara Laslo
- Department of Organismic and Evolutionary Biology, and Museum of Comparative Zoology, Harvard University, Cambridge, MA, 02138, USA
| | - James Hanken
- Department of Organismic and Evolutionary Biology, and Museum of Comparative Zoology, Harvard University, Cambridge, MA, 02138, USA
| | - Gwenneg Kerdivel
- Département Adaptation du Vivant, UMR 7221 CNRS, Muséum National d'Histoire Naturelle, Paris, France
| | - Nicolas Buisine
- Département Adaptation du Vivant, UMR 7221 CNRS, Muséum National d'Histoire Naturelle, Paris, France
| | - Laurent M Sachs
- Département Adaptation du Vivant, UMR 7221 CNRS, Muséum National d'Histoire Naturelle, Paris, France
| | - Daniel R Buchholz
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, USA
| | - Taejoon Kwon
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology, Ulsan, 44919, Republic of Korea
- Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan, 44919, Republic of Korea
| | - Heidi Smith-Parker
- Department of Integrative Biology, Patterson Labs, 2401 Speedway, University of Texas, Austin, TX, 78712, USA
| | - Marcos Gridi-Papp
- Department of Biological Sciences, University of the Pacific, 3601 Pacific Avenue, Stockton, CA, 95211, USA
| | - Michael J Ryan
- Department of Integrative Biology, Patterson Labs, 2401 Speedway, University of Texas, Austin, TX, 78712, USA
| | - Robert D Denton
- Department of Molecular and Cell Biology and Institute of Systems Genomics, University of Connecticut, 181 Auditorium Road, Unit 3197, Storrs, CT, 06269, USA
| | - John H Malone
- Department of Molecular and Cell Biology and Institute of Systems Genomics, University of Connecticut, 181 Auditorium Road, Unit 3197, Storrs, CT, 06269, USA
| | - John B Wallingford
- Department of Molecular Biosciences, Patterson Labs, 2401 Speedway, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Aaron F Straight
- Department of Biochemistry, Stanford University School of Medicine, 279 Campus Drive, Beckman Center 409, Stanford, CA, 94305-5307, USA
| | - Rebecca Heald
- Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA
| | - Dirk Hockemeyer
- Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, 94720, USA
- Chan-Zuckerberg BioHub, 499 Illinois Street, San Francisco, CA, 94158, USA
| | - Richard M Harland
- Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA
| | - Daniel S Rokhsar
- Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA.
- DOE-Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA, 94720, USA.
- Innovative Genomics Institute, University of California, Berkeley, CA, 94720, USA.
- Chan-Zuckerberg BioHub, 499 Illinois Street, San Francisco, CA, 94158, USA.
- Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 9040495, Japan.
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Bascón-Cardozo K, Bours A, Manthey G, Durieux G, Dutheil JY, Pruisscher P, Odenthal-Hesse L, Liedvogel M. Fine-Scale Map Reveals Highly Variable Recombination Rates Associated with Genomic Features in the Eurasian Blackcap. Genome Biol Evol 2024; 16:evad233. [PMID: 38198800 PMCID: PMC10781513 DOI: 10.1093/gbe/evad233] [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] [Accepted: 12/12/2023] [Indexed: 01/12/2024] Open
Abstract
Recombination is responsible for breaking up haplotypes, influencing genetic variability, and the efficacy of selection. Bird genomes lack the protein PR domain-containing protein 9, a key determinant of recombination dynamics in most metazoans. Historical recombination maps in birds show an apparent stasis in positioning recombination events. This highly conserved recombination pattern over long timescales may constrain the evolution of recombination in birds. At the same time, extensive variation in recombination rate is observed across the genome and between different species of birds. Here, we characterize the fine-scale historical recombination map of an iconic migratory songbird, the Eurasian blackcap (Sylvia atricapilla), using a linkage disequilibrium-based approach that accounts for population demography. Our results reveal variable recombination rates among and within chromosomes, which associate positively with nucleotide diversity and GC content and negatively with chromosome size. Recombination rates increased significantly at regulatory regions but not necessarily at gene bodies. CpG islands are associated strongly with recombination rates, though their specific position and local DNA methylation patterns likely influence this relationship. The association with retrotransposons varied according to specific family and location. Our results also provide evidence of heterogeneous intrachromosomal conservation of recombination maps between the blackcap and its closest sister taxon, the garden warbler. These findings highlight the considerable variability of recombination rates at different scales and the role of specific genomic features in shaping this variation. This study opens the possibility of further investigating the impact of recombination on specific population-genomic features.
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Affiliation(s)
- Karen Bascón-Cardozo
- MPRG Behavioural Genomics, Max Planck Institute for Evolutionary Biology, Plön 24306, Germany
| | - Andrea Bours
- MPRG Behavioural Genomics, Max Planck Institute for Evolutionary Biology, Plön 24306, Germany
| | - Georg Manthey
- Institute of Avian Research “Vogelwarte Helgoland”, Wilhelmshaven 26386, Germany
| | - Gillian Durieux
- MPRG Behavioural Genomics, Max Planck Institute for Evolutionary Biology, Plön 24306, Germany
| | - Julien Y Dutheil
- Department for Theoretical Biology, Max Planck Institute for Evolutionary Biology, Plön 24306, Germany
| | - Peter Pruisscher
- MPRG Behavioural Genomics, Max Planck Institute for Evolutionary Biology, Plön 24306, Germany
- Department of Zoology, Stockholm University, Stockholm SE-106 91, Sweden
| | - Linda Odenthal-Hesse
- Department Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Plön 24306, Germany
| | - Miriam Liedvogel
- MPRG Behavioural Genomics, Max Planck Institute for Evolutionary Biology, Plön 24306, Germany
- Institute of Avian Research “Vogelwarte Helgoland”, Wilhelmshaven 26386, Germany
- Department of Biology and Environmental Sciences, Carl von Ossietzky University of Oldenburg, Oldenburg 26129, Germany
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43
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Thom G, Moreira LR, Batista R, Gehara M, Aleixo A, Smith BT. Genomic Architecture Predicts Tree Topology, Population Structuring, and Demographic History in Amazonian Birds. Genome Biol Evol 2024; 16:evae002. [PMID: 38236173 PMCID: PMC10823491 DOI: 10.1093/gbe/evae002] [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: 05/09/2023] [Revised: 10/26/2023] [Accepted: 12/12/2023] [Indexed: 01/19/2024] Open
Abstract
Geographic barriers are frequently invoked to explain genetic structuring across the landscape. However, inferences on the spatial and temporal origins of population variation have been largely limited to evolutionary neutral models, ignoring the potential role of natural selection and intrinsic genomic processes known as genomic architecture in producing heterogeneity in differentiation across the genome. To test how variation in genomic characteristics (e.g. recombination rate) impacts our ability to reconstruct general patterns of differentiation between species that cooccur across geographic barriers, we sequenced the whole genomes of multiple bird populations that are distributed across rivers in southeastern Amazonia. We found that phylogenetic relationships within species and demographic parameters varied across the genome in predictable ways. Genetic diversity was positively associated with recombination rate and negatively associated with species tree support. Gene flow was less pervasive in genomic regions of low recombination, making these windows more likely to retain patterns of population structuring that matched the species tree. We further found that approximately a third of the genome showed evidence of selective sweeps and linked selection, skewing genome-wide estimates of effective population sizes and gene flow between populations toward lower values. In sum, we showed that the effects of intrinsic genomic characteristics and selection can be disentangled from neutral processes to elucidate spatial patterns of population differentiation.
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Affiliation(s)
- Gregory Thom
- Department of Ornithology, American Museum of Natural History, New York, NY, USA
- Museum of Natural Science, Louisiana State University, Baton Rouge, LA, USA
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
| | - Lucas Rocha Moreira
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Department of Vertebrate Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Romina Batista
- Programa de Coleções Biológicas, Instituto Nacional de Pesquisas da Amazônia, Manaus, Brazil
- School of Science, Engineering and Environment, University of Salford, Manchester, UK
| | - Marcelo Gehara
- Department of Earth and Environmental Sciences, Rutgers University, Newark, NJ, USA
| | - Alexandre Aleixo
- Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
- Department of Environmental Genomics, Instituto Tecnológico Vale, Belém, Brazil
| | - Brian Tilston Smith
- Department of Ornithology, American Museum of Natural History, New York, NY, USA
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44
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Zancolli G, von Reumont BM, Anderluh G, Caliskan F, Chiusano ML, Fröhlich J, Hapeshi E, Hempel BF, Ikonomopoulou MP, Jungo F, Marchot P, de Farias TM, Modica MV, Moran Y, Nalbantsoy A, Procházka J, Tarallo A, Tonello F, Vitorino R, Zammit ML, Antunes A. Web of venom: exploration of big data resources in animal toxin research. Gigascience 2024; 13:giae054. [PMID: 39250076 PMCID: PMC11382406 DOI: 10.1093/gigascience/giae054] [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: 05/14/2024] [Revised: 07/01/2024] [Accepted: 07/13/2024] [Indexed: 09/10/2024] Open
Abstract
Research on animal venoms and their components spans multiple disciplines, including biology, biochemistry, bioinformatics, pharmacology, medicine, and more. Manipulating and analyzing the diverse array of data required for venom research can be challenging, and relevant tools and resources are often dispersed across different online platforms, making them less accessible to nonexperts. In this article, we address the multifaceted needs of the scientific community involved in venom and toxin-related research by identifying and discussing web resources, databases, and tools commonly used in this field. We have compiled these resources into a comprehensive table available on the VenomZone website (https://venomzone.expasy.org/10897). Furthermore, we highlight the challenges currently faced by researchers in accessing and using these resources and emphasize the importance of community-driven interdisciplinary approaches. We conclude by underscoring the significance of enhancing standards, promoting interoperability, and encouraging data and method sharing within the venom research community.
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Affiliation(s)
- Giulia Zancolli
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
- SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Björn Marcus von Reumont
- Goethe University Frankfurt, Faculty of Biological Sciences, 60438 Frankfurt, Germany
- LOEWE Centre for Translational Biodiversity Genomics, 60325 Frankfurt, Germany
| | - Gregor Anderluh
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, 1000 Ljubljana, Slovenia
| | - Figen Caliskan
- Department of Biology, Faculty of Science, Eskisehir Osmangazi University, 26040 Eskişehir, Turkey
| | - Maria Luisa Chiusano
- Department of Agricultural Sciences, University Federico II of Naples, 80055 Portici, Naples, Italy
- Department of Research Infrastructures for Marine Biological Resources, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
| | - Jacob Fröhlich
- Veterinary Center for Resistance Research (TZR), Freie Universität Berlin, 14163 Berlin, Germany
| | - Evroula Hapeshi
- Department of Health Sciences, School of Life and Health Sciences, University of Nicosia, 1700 Nicosia, Cyprus
| | - Benjamin-Florian Hempel
- Veterinary Center for Resistance Research (TZR), Freie Universität Berlin, 14163 Berlin, Germany
| | - Maria P Ikonomopoulou
- Madrid Institute of Advanced Studies in Food, Precision Nutrition & Aging Program, 28049 Madrid, Spain
| | - Florence Jungo
- SIB Swiss Institute of Bioinformatics, Swiss-Prot Group, 1211 Geneva, Switzerland
| | - Pascale Marchot
- Laboratory Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille University, Centre National de la Recherche Scientifique, Faculté des Sciences, Campus Luminy, 13288 Marseille, France
| | - Tarcisio Mendes de Farias
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
- SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Maria Vittoria Modica
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, 00198 Rome, Italy
| | - Yehu Moran
- Department of Ecology, Evolution and Behavior, Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, 9190401 Jerusalem, Israel
| | - Ayse Nalbantsoy
- Engineering Faculty, Bioengineering Department, Ege University, 35100 Bornova-Izmir, Turkey
| | - Jan Procházka
- Laboratory of Transgenic Models of Diseases, Institute of Molecular Genetics of the Czech Academy of Sciences, 252 50 Vestec, Czech Republic
| | - Andrea Tarallo
- Institute of Research on Terrestrial Ecosystems (IRET), National Research Council (CNR), 73100 Lecce, Italy
| | - Fiorella Tonello
- Neuroscience Institute, National Research Council (CNR), 35131 Padua, Italy
| | - Rui Vitorino
- Department of Medical Sciences, iBiMED, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Mark Lawrence Zammit
- Department of Clinical Pharmacology & Therapeutics, Faculty of Medicine & Surgery, University of Malta, 2090 Msida, Malta
- Malta National Poisons Centre, Malta Life Sciences Park, 3000 San Ġwann, Malta
| | - Agostinho Antunes
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, 4450-208 Porto, Portugal
- Department of Biology, Faculty of Sciences, University of Porto, 4169-007 Porto, Portugal
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45
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Stuart KC, Johnson RN, Major RE, Atsawawaranunt K, Ewart KM, Rollins LA, Santure AW, Whibley A. The genome of a globally invasive passerine, the common myna, Acridotheres tristis. DNA Res 2024; 31:dsae005. [PMID: 38366840 PMCID: PMC10917472 DOI: 10.1093/dnares/dsae005] [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: 08/24/2023] [Revised: 02/13/2024] [Accepted: 02/15/2024] [Indexed: 02/18/2024] Open
Abstract
In an era of global climate change, biodiversity conservation is receiving increased attention. Conservation efforts are greatly aided by genetic tools and approaches, which seek to understand patterns of genetic diversity and how they impact species health and their ability to persist under future climate regimes. Invasive species offer vital model systems in which to investigate questions regarding adaptive potential, with a particular focus on how changes in genetic diversity and effective population size interact with novel selection regimes. The common myna (Acridotheres tristis) is a globally invasive passerine and is an excellent model species for research both into the persistence of low-diversity populations and the mechanisms of biological invasion. To underpin research on the invasion genetics of this species, we present the genome assembly of the common myna. We describe the genomic landscape of this species, including genome wide allelic diversity, methylation, repeats, and recombination rate, as well as an examination of gene family evolution. Finally, we use demographic analysis to identify that some native regions underwent a dramatic population increase between the two most recent periods of glaciation, and reveal artefactual impacts of genetic bottlenecks on demographic analysis.
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Affiliation(s)
- Katarina C Stuart
- School of Biological Sciences, University of Auckland, Auckland, Aotearoa, New Zealand
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, Australia
| | - Rebecca N Johnson
- National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Richard E Major
- Australian Museum Research Institute, Australian Museum, Sydney, Australia
| | | | - Kyle M Ewart
- Australian Museum Research Institute, Australian Museum, Sydney, Australia
- School of Life and Environmental Sciences,University of Sydney, Sydney, Australia
| | - Lee A Rollins
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, Australia
| | - Anna W Santure
- School of Biological Sciences, University of Auckland, Auckland, Aotearoa, New Zealand
| | - Annabel Whibley
- School of Biological Sciences, University of Auckland, Auckland, Aotearoa, New Zealand
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46
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Fandiño S, Gomez-Lucia E, Benítez L, Doménech A. Comparison of Endogenous Alpharetroviruses (ALV-like) across Galliform Species: New Distant Proviruses. Microorganisms 2023; 12:86. [PMID: 38257913 PMCID: PMC10820513 DOI: 10.3390/microorganisms12010086] [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: 11/25/2023] [Revised: 12/22/2023] [Accepted: 12/25/2023] [Indexed: 01/24/2024] Open
Abstract
The Genus Alpharetrovirus contains viruses pathogenic mainly for chickens, forming the Avian Sarcoma and Leukosis Virus group (ASLV). Cells of most Galliform species, besides chickens, contain genetic elements (endogenous retroviruses, ERVs) that could recombine with other alpharetroviruses or express proteins, complementing defective ASLV, which may successfully replicate and cause disease. However, they are quite unknown, and only ALV-F, from ring-necked pheasants, has been partially published. Upon scrutiny of 53 genomes of different avian species, we found Alpharetrovirus-like sequences only in 12 different Galliformes, including six full-length (7.4-7.6 Kbp) and 27 partial sequences. Phylogenetic studies of the regions studied (LTR, gag, pol, and env) consistently resulted in five almost identical clades containing the same ERVs: Clade I (presently known ASLVs); Clade II (Callipepla spp. ERVs); Clade IIIa (Phasianus colchicus ERVs); Clade IIIb (Alectoris spp. ERVs); and Clade IV (Centrocercus spp. ERVs). The low pol identity scores suggested that each of these Clades may be considered a different species. ORF analysis revealed that putatively encoded proteins would be very similar in length and domains to those of other alpharetroviruses and thus potentially functional. This will undoubtedly contribute to better understanding the biology of defective viruses, especially in wild Galliformes, their evolution, and the danger they may represent for other wild species and the poultry industry.
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Affiliation(s)
- Sergio Fandiño
- Department of Animal Health, Veterinary Faculty, Complutense University of Madrid, Av. Puerta de Hierro s/n, 28040 Madrid, Spain; (S.F.); (A.D.)
- Department of Genetics, Physiology and Microbiology, Faculty of Biological Sciences, Complutense University of Madrid (UCM), C. de José Antonio Novais 12, 28040 Madrid, Spain;
- Research Group, “Animal Viruses” of Complutense University of Madrid, 28040 Madrid, Spain
| | - Esperanza Gomez-Lucia
- Department of Animal Health, Veterinary Faculty, Complutense University of Madrid, Av. Puerta de Hierro s/n, 28040 Madrid, Spain; (S.F.); (A.D.)
- Research Group, “Animal Viruses” of Complutense University of Madrid, 28040 Madrid, Spain
| | - Laura Benítez
- Department of Genetics, Physiology and Microbiology, Faculty of Biological Sciences, Complutense University of Madrid (UCM), C. de José Antonio Novais 12, 28040 Madrid, Spain;
- Research Group, “Animal Viruses” of Complutense University of Madrid, 28040 Madrid, Spain
| | - Ana Doménech
- Department of Animal Health, Veterinary Faculty, Complutense University of Madrid, Av. Puerta de Hierro s/n, 28040 Madrid, Spain; (S.F.); (A.D.)
- Research Group, “Animal Viruses” of Complutense University of Madrid, 28040 Madrid, Spain
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47
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Li X, Wang X, Yu X, Yang C, Lin L, Huang Y. The draft genome of the Temminck's tragopan (Tragopan temminckii) with evolutionary implications. BMC Genomics 2023; 24:751. [PMID: 38062370 PMCID: PMC10702090 DOI: 10.1186/s12864-023-09857-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 11/29/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND High-quality genome data of birds play a significant role in the systematic study of their origin and adaptive evolution. The Temminck's tragopan (Tragopan temminckii) (Galliformes, Phasianidae), a larger pheasant, is one of the most abundant and widely distributed species of the genus Tragopan, and was defined as class II of the list of national key protected wild animals in China. The absence of a sequenced genome has restricted previous evolutionary trait studies of this taxa. RESULTS The whole genome of the Temminck's tragopan was sequenced using Illumina and PacBio platform, and then de novo assembled and annotated. The genome size was 1.06 Gb, with a contig N50 of 4.17 Mb. A total of 117.22 Mb (11.00%) repeat sequences were identified. 16,414 genes were predicted using three methods, with 16,099 (98.08%) annotated as functional genes based on five databases. In addition, comparative genome analyses were conducted across 12 Galliformes species. The results indicated that T. temminckii was the first species to branch off from the clade containing Lophura nycthemera, Phasianus colchicus, Chrysolophus pictus, Syrmaticus mikado, Perdix hodgsoniae, and Meleagris gallopavo, with a corresponding divergence time of 31.43 million years ago (MYA). Expanded gene families associated with immune response and energy metabolism were identified. Genes and pathways associated with plumage color and feather development, immune response, and energy metabolism were found in the list of positively selected genes (PSGs). CONCLUSIONS A genome draft of the Temminck's tragopan was reported, genome feature and comparative genome analysis were described, and genes and pathways related to plumage color and feather development, immune response, and energy metabolism were identified. The genomic data of the Temminck's tragopan considerably contribute to the genome evolution and phylogeny of the genus Tragopan and the whole Galliformes species underlying ecological adaptation strategies.
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Affiliation(s)
- Xuejuan Li
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Xiaoyang Wang
- School of Biological and Environmental Engineering, Xi'an University, Xi'an, China
| | - Xiaoping Yu
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Chao Yang
- Shaanxi Institute of Zoology, Xi'an, China
| | - Liliang Lin
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Yuan Huang
- College of Life Sciences, Shaanxi Normal University, Xi'an, China.
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48
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Redlich R, Kowalczyk A, Tene M, Sestili HH, Foley K, Saputra E, Clark N, Chikina M, Meyer WK, Pfenning A. RERconverge Expansion: Using Relative Evolutionary Rates to Study Complex Categorical Trait Evolution. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.06.570425. [PMID: 38106136 PMCID: PMC10723433 DOI: 10.1101/2023.12.06.570425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Comparative genomics approaches seek to associate evolutionary genetic changes with the evolution of phenotypes across a phylogeny. Many of these methods, including our evolutionary rates based method, RERconverge, lack the capability of analyzing non-ordinal, multicategorical traits. To address this limitation, we introduce an expansion to RERconverge that associates shifts in evolutionary rates with the convergent evolution of multi-categorical traits. The categorical RERconverge expansion includes methods for performing categorical ancestral state reconstruction, statistical tests for associating relative evolutionary rates with categorical variables, and a new method for performing phylogenetic permulations on multi-categorical traits. In addition to demonstrating our new method on a three-category diet phenotype, we compare its performance to naive pairwise binary RERconverge analyses and two existing methods for comparative genomic analyses of categorical traits: phylogenetic simulations and a phylogenetic signal based method. We also present a diagnostic analysis of the new permulations approach demonstrating how the method scales with the number of species and the number of categories included in the analysis. Our results show that our new categorical method outperforms phylogenetic simulations at identifying genes and enriched pathways significantly associated with the diet phenotype and that the new ancestral reconstruction drives an improvement in our ability to capture diet-related enriched pathways. Our categorical permulations were able to account for non-uniform null distributions and correct for non-independence in gene rank during pathway enrichment analysis. The categorical expansion to RERconverge will provide a strong foundation for applying the comparative method to categorical traits on larger data sets with more species and more complex trait evolution.
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49
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Zhu F, Yin ZT, Zhao QS, Sun YX, Jie YC, Smith J, Yang YZ, Burt DW, Hincke M, Zhang ZD, Yuan MD, Kaufman J, Sun CJ, Li JY, Shao LW, Yang N, Hou ZC. A chromosome-level genome assembly for the Silkie chicken resolves complete sequences for key chicken metabolic, reproductive, and immunity genes. Commun Biol 2023; 6:1233. [PMID: 38057566 PMCID: PMC10700341 DOI: 10.1038/s42003-023-05619-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 11/21/2023] [Indexed: 12/08/2023] Open
Abstract
A set of high-quality pan-genomes would help identify important genes that are still hidden/incomplete in bird reference genomes. In an attempt to address these issues, we have assembled a de novo chromosome-level reference genome of the Silkie (Gallus gallus domesticus), which is an important avian model for unique traits, like fibromelanosis, with unclear genetic foundation. This Silkie genome includes the complete genomic sequences of well-known, but unresolved, evolutionarily, endocrinologically, and immunologically important genes, including leptin, ovocleidin-17, and tumor-necrosis factor-α. The gap-less and manually annotated MHC (major histocompatibility complex) region possesses 38 recently identified genes, with differentially regulated genes recovered in response to pathogen challenges. We also provide whole-genome methylation and genetic variation maps, and resolve a complex genetic region that may contribute to fibromelanosis in these animals. Finally, we experimentally show leptin binding to the identified leptin receptor in chicken, confirming an active leptin ligand-receptor system. The Silkie genome assembly not only provides a rich data resource for avian genome studies, but also lays a foundation for further functional validation of resolved genes.
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Affiliation(s)
- Feng Zhu
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA; College of Animal Science and Technology, China Agricultural University, No. 2 Yuanmingyuan West Rd, 100193, Beijing, China
| | - Zhong-Tao Yin
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA; College of Animal Science and Technology, China Agricultural University, No. 2 Yuanmingyuan West Rd, 100193, Beijing, China
| | - Qiang-Sen Zhao
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA; College of Animal Science and Technology, China Agricultural University, No. 2 Yuanmingyuan West Rd, 100193, Beijing, China
| | - Yun-Xiao Sun
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA; College of Animal Science and Technology, China Agricultural University, No. 2 Yuanmingyuan West Rd, 100193, Beijing, China
| | - Yu-Chen Jie
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA; College of Animal Science and Technology, China Agricultural University, No. 2 Yuanmingyuan West Rd, 100193, Beijing, China
| | - Jacqueline Smith
- The Roslin Institute & R(D)SVS, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - Yu-Ze Yang
- Beijing General Station of Animal Husbandry, 100101, Beijing, China
| | - David W Burt
- The Roslin Institute & R(D)SVS, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
- The University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Maxwell Hincke
- Department of Cellular and Molecular Medicine, Department of Innovation in Medical Education, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, KIH 8M5, Canada
| | - Zi-Ding Zhang
- College of Biological Sciences, China Agricultural University, 100193, Beijing, China
| | - Meng-Di Yuan
- College of Biological Sciences, China Agricultural University, 100193, Beijing, China
| | - Jim Kaufman
- Institute for Immunology and Infection Research, University of Edinburgh, Edinburgh, EH9 3FL, UK
- Department of Pathology, University of Cambridge, Cambridge, CB2 1QP, UK
| | - Cong-Jiao Sun
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA; College of Animal Science and Technology, China Agricultural University, No. 2 Yuanmingyuan West Rd, 100193, Beijing, China
| | - Jun-Ying Li
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA; College of Animal Science and Technology, China Agricultural University, No. 2 Yuanmingyuan West Rd, 100193, Beijing, China
| | - Li-Wa Shao
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA; College of Animal Science and Technology, China Agricultural University, No. 2 Yuanmingyuan West Rd, 100193, Beijing, China.
| | - Ning Yang
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA; College of Animal Science and Technology, China Agricultural University, No. 2 Yuanmingyuan West Rd, 100193, Beijing, China.
| | - Zhuo-Cheng Hou
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA; College of Animal Science and Technology, China Agricultural University, No. 2 Yuanmingyuan West Rd, 100193, Beijing, China.
- Sanya Institute of China Agricultural University, Beijing, China.
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50
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Hill J, Enbody ED, Bi H, Lamichhaney S, Lei W, Chen J, Wei C, Liu Y, Schwochow D, Younis S, Widemo F, Andersson L. Low Mutation Load in a Supergene Underpinning Alternative Male Mating Strategies in Ruff (Calidris pugnax). Mol Biol Evol 2023; 40:msad224. [PMID: 37804117 DOI: 10.1093/molbev/msad224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 09/23/2023] [Accepted: 09/28/2023] [Indexed: 10/08/2023] Open
Abstract
A paradox in evolutionary biology is how supergenes can maintain high fitness despite reduced effective population size, the suppression of recombination, and the expected accumulation of mutational load. The ruff supergene involves 2 rare inversion haplotypes (satellite and faeder). These are recessive lethals but with dominant effects on male mating strategies, plumage, and body size. Sequence divergence to the wild-type (independent) haplotype indicates that the inversion could be as old as 4 million years. Here, we have constructed a highly contiguous genome assembly of the inversion region for both the independent and satellite haplotypes. Based on the new data, we estimate that the recombination event(s) creating the satellite haplotype occurred only about 70,000 yr ago. Contrary to expectations for supergenes, we find no substantial expansion of repeats and only a modest mutation load on the satellite and faeder haplotypes despite high sequence divergence to the non-inverted haplotype (1.46%). The essential centromere protein N (CENPN) gene is disrupted by the inversion and is as well conserved on the inversion haplotypes as on the noninversion haplotype. These results suggest that the inversion may be much younger than previously thought. The low mutation load, despite recessive lethality, may be explained by the introgression of the inversion from a now extinct lineage.
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Affiliation(s)
- Jason Hill
- Department of Medical Biochemistry and Microbiology, Uppsala University, SE-75123 Uppsala, Sweden
| | - Erik D Enbody
- Department of Medical Biochemistry and Microbiology, Uppsala University, SE-75123 Uppsala, Sweden
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95060, USA
| | - Huijuan Bi
- Department of Medical Biochemistry and Microbiology, Uppsala University, SE-75123 Uppsala, Sweden
| | - Sangeet Lamichhaney
- Department of Medical Biochemistry and Microbiology, Uppsala University, SE-75123 Uppsala, Sweden
- Department of Biological Sciences, Kent State University, Kent, OH 44241, USA
| | - Weipan Lei
- Key Laboratory for Biodiversity Science and Ecological Engineering, National Demonstration Center for Experimental Life Sciences and Biotechnology Education, College of Life Sciences, Beijing Normal University, 100875 Beijing, China
| | - Juexin Chen
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, 510275 Guangzhou, China
| | - Chentao Wei
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, 510275 Guangzhou, China
| | - Yang Liu
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, 510275 Guangzhou, China
| | - Doreen Schwochow
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, SE-75007 Uppsala, Sweden
| | - Shady Younis
- Department of Medical Biochemistry and Microbiology, Uppsala University, SE-75123 Uppsala, Sweden
- Division of Immunology and Rheumatology, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Fredrik Widemo
- Department of Wildlife, Fish and Environmental Studies, Swedish University of Agricultural Sciences, SE-901 83 Umeå, Sweden
| | - Leif Andersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, SE-75123 Uppsala, Sweden
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843, USA
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