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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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2
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Chong Y, Tu X, Lu Y, Gao Z, He X, Hong J, Wu J, Wu D, Xi D, Deng W. Two High-Quality Cygnus Genome Assemblies Reveal Genomic Variations Associated with Plumage Color. Int J Mol Sci 2023; 24:16953. [PMID: 38069278 PMCID: PMC10707585 DOI: 10.3390/ijms242316953] [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: 10/28/2023] [Revised: 11/26/2023] [Accepted: 11/28/2023] [Indexed: 12/18/2023] Open
Abstract
As an exemplary model for examining molecular mechanisms responsible for extreme phenotypic variations, plumage color has garnered significant interest. The Cygnus genus features two species, Cygnus olor and Cygnus atratus, that exhibit striking disparities in plumage color. However, the molecular foundation for this differentiation has remained elusive. Herein, we present two high-quality genomes for C. olor and C. atratus, procured using the Illumina and Nanopore technologies. The assembled genome of C. olor was 1.12 Gb in size with a contig N50 of 26.82 Mb, while its counterpart was 1.13 Gb in size with a contig N50 of 21.91 Mb. A comparative analysis unveiled three genes (TYR, SLC45A2, and SLC7A11) with structural variants in the melanogenic pathway. Notably, we also identified a novel gene, PWWP domain containing 2A (PWWP2A), that is related to plumage color, for the first time. Using targeted gene modification analysis, we demonstrated the potential genetic effect of the PWWP2A variant on pigment gene expression and melanin production. Finally, our findings offer insight into the intricate pattern of pigmentation and the role of polygenes in birds. Furthermore, these two high-quality genome references provide a comprehensive resource and perspective for comparative functional and genetic studies of evolution within the Cygnus genus.
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Affiliation(s)
- Yuqing Chong
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (Y.C.); (Y.L.); (Z.G.); (X.H.); (J.H.); (J.W.); (D.X.)
| | - Xiaolong Tu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China;
| | - Ying Lu
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (Y.C.); (Y.L.); (Z.G.); (X.H.); (J.H.); (J.W.); (D.X.)
| | - Zhendong Gao
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (Y.C.); (Y.L.); (Z.G.); (X.H.); (J.H.); (J.W.); (D.X.)
| | - Xiaoming He
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (Y.C.); (Y.L.); (Z.G.); (X.H.); (J.H.); (J.W.); (D.X.)
| | - Jieyun Hong
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (Y.C.); (Y.L.); (Z.G.); (X.H.); (J.H.); (J.W.); (D.X.)
| | - Jiao Wu
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (Y.C.); (Y.L.); (Z.G.); (X.H.); (J.H.); (J.W.); (D.X.)
| | - Dongdong Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China;
| | - Dongmei Xi
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (Y.C.); (Y.L.); (Z.G.); (X.H.); (J.H.); (J.W.); (D.X.)
| | - Weidong Deng
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (Y.C.); (Y.L.); (Z.G.); (X.H.); (J.H.); (J.W.); (D.X.)
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3
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Gao G, Zhang H, Ni J, Zhao X, Zhang K, Wang J, Kong X, Wang Q. Insights into genetic diversity and phenotypic variations in domestic geese through comprehensive population and pan-genome analysis. J Anim Sci Biotechnol 2023; 14:150. [PMID: 38001525 PMCID: PMC10675864 DOI: 10.1186/s40104-023-00944-y] [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: 05/23/2023] [Accepted: 10/06/2023] [Indexed: 11/26/2023] Open
Abstract
BACKGROUND Domestic goose breeds are descended from either the Swan goose (Anser cygnoides) or the Greylag goose (Anser anser), exhibiting variations in body size, reproductive performance, egg production, feather color, and other phenotypic traits. Constructing a pan-genome facilitates a thorough identification of genetic variations, thereby deepening our comprehension of the molecular mechanisms underlying genetic diversity and phenotypic variability. RESULTS To comprehensively facilitate population genomic and pan-genomic analyses in geese, we embarked on the task of 659 geese whole genome resequencing data and compiling a database of 155 RNA-seq samples. By constructing the pan-genome for geese, we generated non-reference contigs totaling 612 Mb, unveiling a collection of 2,813 novel genes and pinpointing 15,567 core genes, 1,324 softcore genes, 2,734 shell genes, and 878 cloud genes in goose genomes. Furthermore, we detected an 81.97 Mb genomic region showing signs of genome selection, encompassing the TGFBR2 gene correlated with variations in body weight among geese. Genome-wide association studies utilizing single nucleotide polymorphisms (SNPs) and presence-absence variation revealed significant genomic associations with various goose meat quality, reproductive, and body composition traits. For instance, a gene encoding the SVEP1 protein was linked to carcass oblique length, and a distinct gene-CDS haplotype of the SVEP1 gene exhibited an association with carcass oblique length. Notably, the pan-genome analysis revealed enrichment of variable genes in the "hair follicle maturation" Gene Ontology term, potentially linked to the selection of feather-related traits in geese. A gene presence-absence variation analysis suggested a reduced frequency of genes associated with "regulation of heart contraction" in domesticated geese compared to their wild counterparts. Our study provided novel insights into gene expression features and functions by integrating gene expression patterns across multiple organs and tissues in geese and analyzing population variation. CONCLUSION This accomplishment originates from the discernment of a multitude of selection signals and candidate genes associated with a wide array of traits, thereby markedly enhancing our understanding of the processes underlying domestication and breeding in geese. Moreover, assembling the pan-genome for geese has yielded a comprehensive apprehension of the goose genome, establishing it as an indispensable asset poised to offer innovative viewpoints and make substantial contributions to future geese breeding initiatives.
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Affiliation(s)
- Guangliang Gao
- Chongqing Academy of Animal Science, Rongchang District, Chongqing, 402460, China
- Livestock and Poultry Multi-Omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
- Chongqing Engineering Research Center of Goose Genetic Improvement, Rongchang District, Chongqing, 402460, China
| | - Hongmei Zhang
- Department of Cardiovascular Ultrasound and Non-Invasive Cardiology, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital,University of Electronic Science and Technology of China, Chengdu, 611731, China
- Ultrasound in Cardiac Electrophysiology and Biomechanics Key Laboratory of Sichuan Province, University of Electronic Science and Technology of China, Chengdu, 611731, China
| | - Jiangping Ni
- JiguangGene Biotechnology Co., Ltd., Nanjing, 210032, China
| | - Xianzhi Zhao
- Chongqing Academy of Animal Science, Rongchang District, Chongqing, 402460, China
- Chongqing Engineering Research Center of Goose Genetic Improvement, Rongchang District, Chongqing, 402460, China
| | - Keshan Zhang
- Chongqing Academy of Animal Science, Rongchang District, Chongqing, 402460, China
- Chongqing Engineering Research Center of Goose Genetic Improvement, Rongchang District, Chongqing, 402460, China
| | - Jian Wang
- Jiangsu Agri-Animal Vocational College, Taizhou, 225300, China
| | - Xiangdong Kong
- JiguangGene Biotechnology Co., Ltd., Nanjing, 210032, China.
| | - Qigui Wang
- Chongqing Academy of Animal Science, Rongchang District, Chongqing, 402460, China.
- Chongqing Engineering Research Center of Goose Genetic Improvement, Rongchang District, Chongqing, 402460, China.
- Present Address: Poultry Science Institute, Chongqing Academy of Animal Science, No. 51 Changzhou Avenue, Rongchang District, Chongqing, 402460, P. R. China.
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Marandino A, Tomás G, Panzera Y, Leizagoyen C, Pérez R, Bassetti L, Negro R, Rodríguez S, Pérez R. Spreading of the High-Pathogenicity Avian Influenza (H5N1) Virus of Clade 2.3.4.4b into Uruguay. Viruses 2023; 15:1906. [PMID: 37766312 PMCID: PMC10536905 DOI: 10.3390/v15091906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 08/30/2023] [Accepted: 09/01/2023] [Indexed: 09/29/2023] Open
Abstract
BACKGROUND Avian influenza viruses (genus Alphainfluenzavirus, family Orthomyxoviridae) infect avian and mammal hosts. In 2022, the high pathogenicity avian influenza virus (H5N1) spread to South America, resulting in the loss of thousands of wild birds, including endangered species, and severely impacting the global poultry industry. OBJECTIVES We analyzed the complete genomes of influenza viruses obtained from wild birds and backyard poultry in Uruguay between February and May 2023. METHODS Twelve complete genomes were obtained in 2023 from cloacal swabs using Illumina sequencing. Genomes were phylogenetically analyzed with regional and global strains. FINDINGS The identified strains have multiple basic amino acids at the hemagglutinin cleavage sites, which is typical for highly pathogenic strains. The Uruguayan viruses belonged to hemagglutinin clade 2.3.4.4b of the H5N1 subtype. A reassortment in North America has resulted in some segments of South American strains being of Eurasian or North American origins. The Uruguayan viruses shared a common ancestor with South American strains from Argentina and Chile. The influenza viruses displayed a spatiotemporal divergence pattern rather than being host-specific. MAIN CONCLUSIONS The arrival of the 2.3.4.4b clade in Uruguay may have been mediated by birds that acquired the virus from Argentine and Chilean waterfowl migrating in the Pacific Flyway.
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Affiliation(s)
- Ana Marandino
- Sección Genética Evolutiva, Departamento de Biología Animal, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Iguá 4225, Montevideo 11400, Uruguay; (A.M.); (G.T.); (Y.P.)
| | - Gonzalo Tomás
- Sección Genética Evolutiva, Departamento de Biología Animal, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Iguá 4225, Montevideo 11400, Uruguay; (A.M.); (G.T.); (Y.P.)
| | - Yanina Panzera
- Sección Genética Evolutiva, Departamento de Biología Animal, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Iguá 4225, Montevideo 11400, Uruguay; (A.M.); (G.T.); (Y.P.)
| | - Carmen Leizagoyen
- Dirección Nacional de Biodiversidad y Servicios Ecosistémicos (DINABISE), Ministerio de Ambiente, Juncal 1385, Montevideo 11100, Uruguay;
| | - Ramiro Pérez
- Departamento de Virología, División de Laboratorios Veterinarios “Miguel C. Rubino”, Dirección General de Servicios Ganaderos, Ministerio de Ganadería, Agricultura y Pesca, Ruta 8 “Brigadier Gral. Juan A. Lavalleja” Km 17,000, Montevideo 12100, Uruguay; (R.P.); (L.B.); (R.N.)
| | - Lucía Bassetti
- Departamento de Virología, División de Laboratorios Veterinarios “Miguel C. Rubino”, Dirección General de Servicios Ganaderos, Ministerio de Ganadería, Agricultura y Pesca, Ruta 8 “Brigadier Gral. Juan A. Lavalleja” Km 17,000, Montevideo 12100, Uruguay; (R.P.); (L.B.); (R.N.)
| | - Raúl Negro
- Departamento de Virología, División de Laboratorios Veterinarios “Miguel C. Rubino”, Dirección General de Servicios Ganaderos, Ministerio de Ganadería, Agricultura y Pesca, Ruta 8 “Brigadier Gral. Juan A. Lavalleja” Km 17,000, Montevideo 12100, Uruguay; (R.P.); (L.B.); (R.N.)
| | - Sirley Rodríguez
- Departamento de Virología, División de Laboratorios Veterinarios “Miguel C. Rubino”, Dirección General de Servicios Ganaderos, Ministerio de Ganadería, Agricultura y Pesca, Ruta 8 “Brigadier Gral. Juan A. Lavalleja” Km 17,000, Montevideo 12100, Uruguay; (R.P.); (L.B.); (R.N.)
| | - Ruben Pérez
- Sección Genética Evolutiva, Departamento de Biología Animal, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Iguá 4225, Montevideo 11400, Uruguay; (A.M.); (G.T.); (Y.P.)
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Duriez O, Sassi Y, Le Gall-Ladevèze C, Giraud L, Straughan R, Dauverné L, Terras A, Boulinier T, Choquet R, Van De Wiele A, Hirschinger J, Guérin JL, Le Loc'h G. Highly pathogenic avian influenza affects vultures' movements and breeding output. Curr Biol 2023; 33:3766-3774.e3. [PMID: 37597520 DOI: 10.1016/j.cub.2023.07.061] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 05/30/2023] [Accepted: 07/27/2023] [Indexed: 08/21/2023]
Abstract
An exceptional highly pathogenic avian influenza (HPAI) outbreak due to H5N1 virus genotypes belonging to clade 2.3.4.4.b has been affecting birds worldwide since autumn 2021.1,2,3 Mortality caused by viral infection has been well documented in poultry and more recently in wild birds, especially in seabird-breeding colonies.4,5,6 However, there is a critical lack of knowledge about how terrestrial birds deal with HPAI virus infections in terms of behavior and space use, especially during the breeding season.7,8,9 Understanding how birds move when they are infected could help evaluate the risk of spreading the virus at a distance among other populations of wild or domestic birds, this latter risk being especially important for commensal bird species. Through long-term GPS tracking, we described the changes in daily movement patterns of 31 adult griffon vultures Gyps fulvus in two French sites in 2022 compared with 3 previous years. In spring 2022, 21 vultures at both sites showed periods of immobility at the nest, during 5.6 days on average. Positive serological status of 2 individuals confirmed that they had been infected by HPAI viruses. Death was recorded for 3 of the 31 tracked individuals, whereas all others recovered and returned quickly to their foraging routine, although at least 9 birds failed breeding. Such immobility patterns and death rates were never observed in previous years and were not related to weather conditions. The high immobility behavior of infected birds could reduce the risks of transmission. The observed vulnerability to HPAI viruses questions the resistance of endangered vulture species worldwide if infected.
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Affiliation(s)
- Olivier Duriez
- CEFE, University of Montpellier, CNRS, EPHE, IRD, 1919 Route de Mende, 34293 Montpellier, France.
| | - Yohan Sassi
- CEFE, University of Montpellier, CNRS, EPHE, IRD, 1919 Route de Mende, 34293 Montpellier, France
| | - Chloé Le Gall-Ladevèze
- IHAP, ENVT, INRAE, Université de Toulouse, 23 chemin des Capelles, BP 87614, 31076 Toulouse Cedex 3, France
| | - Léa Giraud
- LPO France - site Grands Causses, Le Bourg, 12720 Peyreleau, France
| | - Robert Straughan
- LPO France - site Grands Causses, Le Bourg, 12720 Peyreleau, France
| | - Lise Dauverné
- LPO Occitanie DT Aude, Ecluse de Mandirac, 11100 Narbonne, France
| | - Anna Terras
- LPO Occitanie DT Aude, Ecluse de Mandirac, 11100 Narbonne, France
| | - Thierry Boulinier
- CEFE, University of Montpellier, CNRS, EPHE, IRD, 1919 Route de Mende, 34293 Montpellier, France
| | - Rémi Choquet
- CEFE, University of Montpellier, CNRS, EPHE, IRD, 1919 Route de Mende, 34293 Montpellier, France
| | | | - Julien Hirschinger
- IHAP, ENVT, INRAE, Université de Toulouse, 23 chemin des Capelles, BP 87614, 31076 Toulouse Cedex 3, France
| | - Jean-Luc Guérin
- IHAP, ENVT, INRAE, Université de Toulouse, 23 chemin des Capelles, BP 87614, 31076 Toulouse Cedex 3, France
| | - Guillaume Le Loc'h
- IHAP, ENVT, INRAE, Université de Toulouse, 23 chemin des Capelles, BP 87614, 31076 Toulouse Cedex 3, France
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Bertram H, Wilhelmi S, Rajavel A, Boelhauve M, Wittmann M, Ramzan F, Schmitt AO, Gültas M. Comparative Investigation of Coincident Single Nucleotide Polymorphisms Underlying Avian Influenza Viruses in Chickens and Ducks. BIOLOGY 2023; 12:969. [PMID: 37508399 PMCID: PMC10375970 DOI: 10.3390/biology12070969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 06/26/2023] [Accepted: 07/04/2023] [Indexed: 07/30/2023]
Abstract
Avian influenza is a severe viral infection that has the potential to cause human pandemics. In particular, chickens are susceptible to many highly pathogenic strains of the virus, resulting in significant losses. In contrast, ducks have been reported to exhibit rapid and effective innate immune responses to most avian influenza virus (AIV) infections. To explore the distinct genetic programs that potentially distinguish the susceptibility/resistance of both species to AIV, the investigation of coincident SNPs (coSNPs) and their differing causal effects on gene functions in both species is important to gain novel insight into the varying immune-related responses of chickens and ducks. By conducting a pairwise genome alignment between these species, we identified coSNPs and their respective effect on AIV-related differentially expressed genes (DEGs) in this study. The examination of these genes (e.g., CD74, RUBCN, and SHTN1 for chickens and ABCA3, MAP2K6, and VIPR2 for ducks) reveals their high relevance to AIV. Further analysis of these genes provides promising effector molecules (such as IκBα, STAT1/STAT3, GSK-3β, or p53) and related key signaling pathways (such as NF-κB, JAK/STAT, or Wnt) to elucidate the complex mechanisms of immune responses to AIV infections in both chickens and ducks.
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Affiliation(s)
- Hendrik Bertram
- Faculty of Agriculture, South Westphalia University of Applied Sciences, Lübecker Ring 2, 59494 Soest, Germany; (H.B.)
- Breeding Informatics Group, Department of Animal Sciences, Georg-August University, Margarethe von Wrangell-Weg 7, 37075 Göttingen, Germany
| | - Selina Wilhelmi
- Breeding Informatics Group, Department of Animal Sciences, Georg-August University, Margarethe von Wrangell-Weg 7, 37075 Göttingen, Germany
- Center for Integrated Breeding Research (CiBreed), Albrecht-Thaer-Weg 3, Georg-August University, 37075 Göttingen, Germany
| | - Abirami Rajavel
- Breeding Informatics Group, Department of Animal Sciences, Georg-August University, Margarethe von Wrangell-Weg 7, 37075 Göttingen, Germany
- Center for Integrated Breeding Research (CiBreed), Albrecht-Thaer-Weg 3, Georg-August University, 37075 Göttingen, Germany
| | - Marc Boelhauve
- Faculty of Agriculture, South Westphalia University of Applied Sciences, Lübecker Ring 2, 59494 Soest, Germany; (H.B.)
| | - Margareta Wittmann
- Faculty of Agriculture, South Westphalia University of Applied Sciences, Lübecker Ring 2, 59494 Soest, Germany; (H.B.)
| | - Faisal Ramzan
- Institute of Animal and Dairy Sciences, University of Agriculture, Faisalabad 38000, Pakistan
| | - Armin Otto Schmitt
- Breeding Informatics Group, Department of Animal Sciences, Georg-August University, Margarethe von Wrangell-Weg 7, 37075 Göttingen, Germany
- Center for Integrated Breeding Research (CiBreed), Albrecht-Thaer-Weg 3, Georg-August University, 37075 Göttingen, Germany
| | - Mehmet Gültas
- Faculty of Agriculture, South Westphalia University of Applied Sciences, Lübecker Ring 2, 59494 Soest, Germany; (H.B.)
- Center for Integrated Breeding Research (CiBreed), Albrecht-Thaer-Weg 3, Georg-August University, 37075 Göttingen, Germany
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Pinto BJ, Gamble T, Smith CH, Wilson MA. A lizard is never late: squamate genomics as a recent catalyst for understanding sex chromosome and microchromosome evolution. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.20.524006. [PMID: 37034614 PMCID: PMC10081179 DOI: 10.1101/2023.01.20.524006] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
In 2011, the first high-quality genome assembly of a squamate reptile (lizard or snake) was published for the green anole. Dozens of genome assemblies were subsequently published over the next decade, yet these assemblies were largely inadequate for answering fundamental questions regarding genome evolution in squamates due to their lack of contiguity or annotation. As the "genomics age" was beginning to hit its stride in many organismal study systems, progress in squamates was largely stagnant following the publication of the green anole genome. In fact, zero high-quality (chromosome-level) squamate genomes were published between the years 2012-2017. However, since 2018, an exponential increase in high-quality genome assemblies has materialized with 24 additional high-quality genomes published for species across the squamate tree of life. As the field of squamate genomics is rapidly evolving, we provide a systematic review from an evolutionary genomics perspective. We collated a near-complete list of publicly available squamate genome assemblies from more than half-a-dozen international and third-party repositories and systematically evaluated them with regard to their overall quality, phylogenetic breadth, and usefulness for continuing to provide accurate and efficient insights into genome evolution across squamate reptiles. This review both highlights and catalogs the currently available genomic resources in squamates and their ability to address broader questions in vertebrates, specifically sex chromosome and microchromosome evolution, while addressing why squamates may have received less historical focus and has caused their progress in genomics to lag behind peer taxa.
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Affiliation(s)
- Brendan J Pinto
- School of Life Sciences, Arizona State University, Tempe, AZ USA
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ USA
- Department of Zoology, Milwaukee Public Museum, Milwaukee, WI USA
| | - Tony Gamble
- Department of Zoology, Milwaukee Public Museum, Milwaukee, WI USA
- Department of Biological Sciences, Marquette University, Milwaukee WI USA
- Bell Museum of Natural History, University of Minnesota, St Paul, MN USA
| | - Chase H Smith
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - Melissa A Wilson
- School of Life Sciences, Arizona State University, Tempe, AZ USA
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ USA
- Center for Mechanisms of Evolution, Biodesign Institute, Tempe, AZ USA
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