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de Oliveira AM, Souza GM, Toma GA, Dos Santos N, Dos Santos RZ, Goes CAG, Deon GA, Setti PG, Porto-Foresti F, Utsunomia R, Gunski RJ, Del Valle Garnero A, Herculano Correa de Oliveira E, Kretschmer R, Cioffi MDB. Satellite DNAs, heterochromatin, and sex chromosomes of the wattled jacana (Charadriiformes; Jacanidae): a species with highly rearranged karyotype. Genome 2024; 67:109-118. [PMID: 38316150 DOI: 10.1139/gen-2023-0082] [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: 02/07/2024]
Abstract
Charadriiformes, which comprises shorebirds and their relatives, is one of the most diverse avian orders, with over 390 species showing a wide range of karyotypes. Here, we isolated and characterized the whole collection of satellite DNAs (satDNAs) at both molecular and cytogenetic levels of one of its representative species, named the wattled jacana (Jacana jacana), a species that contains a typical ZZ/ZW sex chromosome system and a highly rearranged karyotype. In addition, we also investigate the in situ location of telomeric and microsatellite repeats. A small catalog of 11 satDNAs was identified that typically accumulated on microchromosomes and on the W chromosome. The latter also showed a significant accumulation of telomeric signals, being (GA)10 the only microsatellite with positive hybridization signals among all the 16 tested ones. These current findings contribute to our understanding of the genomic organization of repetitive DNAs in a bird species with high degree of chromosomal reorganization contrary to the majority of bird species that have stable karyotypes.
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Affiliation(s)
- Alan Moura de Oliveira
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
| | - Guilherme Mota Souza
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
| | - Gustavo Akira Toma
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
| | | | | | | | - Geize Aparecida Deon
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
| | - Princia Grejo Setti
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
| | | | | | | | | | | | - Rafael Kretschmer
- Departamento de Ecologia, Zoologia e Genética, Instituto de Biologia, Universidade Federal de Pelotas, Pelotas, Rio Grande do Sul, Brazil
| | - Marcelo de Bello Cioffi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
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O’Connor RE, Kretschmer R, Romanov MN, Griffin DK. A Bird's-Eye View of Chromosomic Evolution in the Class Aves. Cells 2024; 13:310. [PMID: 38391923 PMCID: PMC10886771 DOI: 10.3390/cells13040310] [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: 12/05/2023] [Revised: 01/27/2024] [Accepted: 02/05/2024] [Indexed: 02/24/2024] Open
Abstract
Birds (Aves) are the most speciose of terrestrial vertebrates, displaying Class-specific characteristics yet incredible external phenotypic diversity. Critical to agriculture and as model organisms, birds have adapted to many habitats. The only extant examples of dinosaurs, birds emerged ~150 mya and >10% are currently threatened with extinction. This review is a comprehensive overview of avian genome ("chromosomic") organization research based mostly on chromosome painting and BAC-based studies. We discuss traditional and contemporary tools for reliably generating chromosome-level assemblies and analyzing multiple species at a higher resolution and wider phylogenetic distance than previously possible. These results permit more detailed investigations into inter- and intrachromosomal rearrangements, providing unique insights into evolution and speciation mechanisms. The 'signature' avian karyotype likely arose ~250 mya and remained largely unchanged in most groups including extinct dinosaurs. Exceptions include Psittaciformes, Falconiformes, Caprimulgiformes, Cuculiformes, Suliformes, occasional Passeriformes, Ciconiiformes, and Pelecaniformes. The reasons for this remarkable conservation may be the greater diploid chromosome number generating variation (the driver of natural selection) through a greater possible combination of gametes and/or an increase in recombination rate. A deeper understanding of avian genomic structure permits the exploration of fundamental biological questions pertaining to the role of evolutionary breakpoint regions and homologous synteny blocks.
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Affiliation(s)
- Rebecca E. O’Connor
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK; (R.E.O.); (M.N.R.)
| | - Rafael Kretschmer
- Departamento de Ecologia, Zoologia e Genética, Instituto de Biologia, Campus Universitário Capão do Leão, Universidade Federal de Pelotas, Pelotas 96010-900, RS, Brazil;
| | - Michael N. Romanov
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK; (R.E.O.); (M.N.R.)
- L. K. Ernst Federal Research Centre for Animal Husbandry, Dubrovitsy, 142132 Podolsk, Moscow Oblast, Russia
| | - Darren K. Griffin
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK; (R.E.O.); (M.N.R.)
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Wang Y, Yue Y, Li C, Chen Z, Cai Y, Hu C, Qu Y, Li H, Zhou K, Yan J, Li P. Insights into the adaptive evolution of chromosome and essential traits through chromosome-level genome assembly of Gekko japonicus. iScience 2024; 27:108445. [PMID: 38205241 PMCID: PMC10776941 DOI: 10.1016/j.isci.2023.108445] [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: 06/05/2023] [Revised: 09/05/2023] [Accepted: 11/09/2023] [Indexed: 01/12/2024] Open
Abstract
Gekko japonicus possesses flexible climbing and detoxification abilities under insectivorous habits. Still, the evolutionary mechanisms behind these traits remain unclarified. This study presents a chromosome-level G. japonicus genome, revealing that its evolutionary breakpoint regions were enriched with specific repetitive elements and defense response genes. Gene families unique to G. japonicus and positively selected genes are mainly enriched in immune, sensory, and nervous pathways. Expansion of bitter taste receptor type 2 primarily in insectivorous species could be associated with toxin clearance. Detox cytochrome P450 in G. japonicus has undergone more birth and death processes than biosynthesis-type P450 genes. Proline, cysteine, glycine, and serine in corneous beta proteins of G. japonicus might influence flexibility and setae adhesiveness. Certain thermosensitive transient receptor potential channels under relaxed purifying selection or positive selection in G. japonicus might enhance adaptation to climate change. This genome assembly offers insights into the adaptive evolution of gekkotans.
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Affiliation(s)
- Yinwei Wang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu 210023, P.R. China
| | - Youxia Yue
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu 210023, P.R. China
| | - Chao Li
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu 210023, P.R. China
| | - Zhiyi Chen
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu 210023, P.R. China
| | - Yao Cai
- School of Food Science, Nanjing Xiaozhuang University, Nanjing, Jiangsu 211171, P.R. China
| | - Chaochao Hu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu 210023, P.R. China
- Analytical and Testing Center, Nanjing Normal University, Nanjing, Jiangsu 210023, P.R. China
| | - Yanfu Qu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu 210023, P.R. China
| | - Hong Li
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu 210023, P.R. China
| | - Kaiya Zhou
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu 210023, P.R. China
| | - Jie Yan
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu 210023, P.R. China
| | - Peng Li
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu 210023, P.R. China
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4
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Johansen M, Saenko S, Schilthuizen M, Blaxter M, Davison A. Fine mapping of the Cepaea nemoralis shell colour and mid-banded loci using a high-density linkage map. Heredity (Edinb) 2023; 131:327-337. [PMID: 37758900 PMCID: PMC10673960 DOI: 10.1038/s41437-023-00648-z] [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: 03/31/2023] [Revised: 08/23/2023] [Accepted: 08/23/2023] [Indexed: 09/29/2023] Open
Abstract
Molluscs are a highly speciose phylum that exhibits an astonishing array of colours and patterns, yet relatively little progress has been made in identifying the underlying genes that determine phenotypic variation. One prominent example is the land snail Cepaea nemoralis for which classical genetic studies have shown that around nine loci, several physically linked and inherited together as a 'supergene', control the shell colour and banding polymorphism. As a first step towards identifying the genes involved, we used whole-genome resequencing of individuals from a laboratory cross to construct a high-density linkage map, and then trait mapping to identify 95% confidence intervals for the chromosomal region that contains the supergene, specifically the colour locus (C), and the unlinked mid-banded locus (U). The linkage map is made up of 215,593 markers, ordered into 22 linkage groups, with one large group making up ~27% of the genome. The C locus was mapped to a ~1.3 cM region on linkage group 11, and the U locus was mapped to a ~0.7 cM region on linkage group 15. The linkage map will serve as an important resource for further evolutionary and population genomic studies of C. nemoralis and related species, as well as the identification of candidate genes within the supergene and for the mid-banding phenotype.
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Affiliation(s)
- Margrethe Johansen
- School of Life Sciences, University Park, University of Nottingham, Nottingham, NG7 2RD, UK.
| | - Suzanne Saenko
- Evolutionary Ecology, Naturalis Biodiversity Center, Leiden, 2333CR, The Netherlands
- Animal Sciences, Institute of Biology Leiden, Leiden University, Leiden, 2333BE, The Netherlands
| | - Menno Schilthuizen
- Evolutionary Ecology, Naturalis Biodiversity Center, Leiden, 2333CR, The Netherlands
- Animal Sciences, Institute of Biology Leiden, Leiden University, Leiden, 2333BE, The Netherlands
| | - Mark Blaxter
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Angus Davison
- School of Life Sciences, University Park, University of Nottingham, Nottingham, NG7 2RD, UK
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5
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Seligmann ICA, Furo IDO, dos Santos MDS, Gunski RJ, Garnero ADV, Silva FAO, O´Brien P, Ferguson-Smith M, Kretschmer R, de Oliveira EHC. Comparative chromosome painting in three Pelecaniformes species (Aves): Exploring the role of macro and microchromosome fusions in karyotypic evolution. PLoS One 2023; 18:e0294776. [PMID: 38011093 PMCID: PMC10681242 DOI: 10.1371/journal.pone.0294776] [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: 07/26/2023] [Accepted: 11/08/2023] [Indexed: 11/29/2023] Open
Abstract
Pelecaniformes is an order of waterbirds that exhibit diverse and distinct morphologies. Ibis, heron, pelican, hammerkop, and shoebill are included within the order. Despite their fascinating features, the phylogenetic relationships among the families within Pelecaniformes remain uncertain and pose challenges due to their complex evolutionary history. Their karyotypic evolution is another little-known aspect. Therefore, to shed light on the chromosomal rearrangements that have occurred during the evolution of Pelecaniformes, we have used whole macrochromosome probes from Gallus gallus (GGA) to show homologies on three species with different diploid numbers, namely Cochlearius cochlearius (2n = 74), Eudocimus ruber (2n = 66), and Syrigma sibilatrix (2n = 62). A fusion between GGA6 and GGA7 was found in C. cochlearius and S. sibilatrix. In S. sibilatrix the GGA8, GGA9 and GGA10 hybridized to the long arms of biarmed macrochromosomes, indicating fusions with microchromosomes. In E. ruber the GGA7 and GGA8 hybridized to the same chromosome pair. After comparing our painting results with previously published data, we show that distinct chromosomal rearrangements have occurred in different Pelecaniformes lineages. Our study provides new insight into the evolutionary history of Pelecaniformes and the chromosomal changes involving their macrochromosomes and microchromosomes that have taken place in different species within this order.
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Affiliation(s)
- Igor Chamon Assumpção Seligmann
- Programa de Pós-graduação em Biodiversidade e Biotecnologia da Rede Bionorte, Universidade Federal do Pará, Belém, Pará, Brazil
| | - Ivanete de Oliveira Furo
- Laboratório de Reprodução Animal, LABRAC, Universidade Federal Rural da Amazônia, UFRA, Parauapebas, State of Pará, Brazil
| | - Michelly da Silva dos Santos
- Programa de Pós-graduação em Genética e Biologia Molecular, Universidade Federal do Pará, Belém, State of Pará, Brazil
| | - Ricardo José Gunski
- Programa de Pós-graduação em Ciências Biológicas, Universidade Federal do Pampa, Campus São Gabriel, São Gabriel, State of Rio Grande do Sul, Brazil
| | - Analía del Valle Garnero
- Programa de Pós-graduação em Ciências Biológicas, Universidade Federal do Pampa, Campus São Gabriel, São Gabriel, State of Rio Grande do Sul, Brazil
| | - Fabio Augusto Oliveira Silva
- Programa de Pós-graduação em Neurociência e Biologia Molecular, Universidade Federal do Pará, Belém, State of Pará, Brazil
| | - Patricia O´Brien
- Cambridge Resource Centre for Comparative Genomics, University of Cambridge, Cambridge, United Kingdom
| | - Malcolm Ferguson-Smith
- Cambridge Resource Centre for Comparative Genomics, University of Cambridge, Cambridge, United Kingdom
| | - Rafael Kretschmer
- Departamento de Ecologia, Zoologia e Genética, Universidade Federal de Pelotas, Pelotas, State of Rio Grande do Sul, Brazil
| | - Edivaldo Herculano C. de Oliveira
- Faculdade de Ciências Naturais, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belém, State of Pará, Brazil
- Laboratório de Citogenômica e Mutagênese Ambiental, SEAMB, Instituto Evandro Chagas, Ananindeua, State of Pará, Brazil
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6
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Arias-Sardá C, Quigley S, Farré M. Patterns of chromosome evolution in ruminants. Mol Ecol 2023. [PMID: 37937367 DOI: 10.1111/mec.17197] [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: 06/08/2023] [Revised: 10/20/2023] [Accepted: 10/26/2023] [Indexed: 11/09/2023]
Abstract
Studying when and where gross genomic rearrangements occurred during evolution is key to understanding changes in genome structure with functional consequences that might eventually lead to speciation. Here we identified chromosome rearrangements in ruminants, a clade characterized by large chromosome differences. Using 26 genome assemblies, we reconstructed five ancestral karyotypes and classified the rearrangement events occurring in each lineage. With these reconstructions, we then identified evolutionary breakpoints regions (EBRs) and synteny fragments. Ruminant karyotype evolution is characterized by inversions, while interchromosomal rearrangements occurred preferentially in the oldest ancestor of ruminants. We found that EBRs are depleted of protein coding genes, including housekeeping genes. Similarly, EBRs are not enriched in high GC regions, suggesting that meiotic double strand breaks might not be their origin. Overall, our results characterize at fine detail the location of chromosome rearrangements in ruminant evolution and provide new insights into the formation of EBRs.
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Affiliation(s)
| | - Sarah Quigley
- School of Biosciences, University of Kent, Canterbury, UK
| | - Marta Farré
- School of Biosciences, University of Kent, Canterbury, UK
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7
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Sales-Oliveira V, Altmanová M, Gvoždík V, Kretschmer R, Ezaz T, Liehr T, Padutsch N, Badjedjea G, Utsunomia R, Tanomtong A, Cioffi M. Cross-species chromosome painting and repetitive DNA mapping illuminate the karyotype evolution in true crocodiles (Crocodylidae). Chromosoma 2023; 132:289-303. [PMID: 37493806 DOI: 10.1007/s00412-023-00806-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 05/23/2023] [Accepted: 07/14/2023] [Indexed: 07/27/2023]
Abstract
Crocodilians have maintained very similar karyotype structures and diploid chromosome numbers for around 100 million years, with only minor variations in collinearity. Why this karyotype structure has largely stayed unaltered for so long is unclear. In this study, we analyzed the karyotypes of six species belonging to the genera Crocodylus and Osteolaemus (Crocodylidae, true crocodiles), among which the Congolian endemic O. osborni was included and investigated. We utilized various techniques (differential staining, fluorescence in situ hybridization with repetitive DNA and rDNA probes, whole chromosome painting, and comparative genomic hybridization) to better understand how crocodile chromosomes evolved. We studied representatives of three of the four main diploid chromosome numbers found in crocodiles (2n = 30/32/38). Our data provided new information about the species studied, including the identification of four major chromosomal rearrangements that occurred during the karyotype diversification process in crocodiles. These changes led to the current diploid chromosome numbers of 2n = 30 (fusion) and 2n = 38 (fissions), derived from the ancestral state of 2n = 32. The conserved cytogenetic tendency in crocodilians, where extant species keep near-ancestral state, contrasts with the more dynamic karyotype evolution seen in other major reptile groups.
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Affiliation(s)
- Vanessa Sales-Oliveira
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
| | - Marie Altmanová
- Institute of Animal Physiology and Genetics, Czech Academy of Sciences, 27721, Liběchov, Czech Republic
- Department of Ecology, Faculty of Science, Charles University, 12844, Prague, Czech Republic
| | - Václav Gvoždík
- Institute of Vertebrate Biology of the Czech Academy of Sciences, Brno, Czech Republic
- Department of Zoology, National Museum of the Czech Republic, Prague, Czech Republic
| | - Rafael Kretschmer
- Departamento de Ecologia, Zoologia e Genética, Instituto de Biologia, Universidade Federal de Pelotas, Pelotas, Rio Grande do Sul, Brazil
| | - Tariq Ezaz
- Institute for Applied Ecology, University of Canberra, Canberra, Australia
| | - Thomas Liehr
- Institute of Human Genetics, Jena University Hospital, Jena, Germany
| | - Niklas Padutsch
- Institute of Human Genetics, Jena University Hospital, Jena, Germany
| | - Gabriel Badjedjea
- Department of Aquatic Ecology, Biodiversity Monitoring Center, University of Kisangani, Kisangani, Democratic Republic of the Congo
| | | | - Alongklod Tanomtong
- Department of Biology Faculty of Science, Khon Kaen University, Muang, Khon Kaen, 40002, Thailand
| | - Marcelo Cioffi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil.
- Institute of Human Genetics, Jena University Hospital, Jena, Germany.
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8
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Foley NM, Mason VC, Harris AJ, Bredemeyer KR, Damas J, Lewin HA, Eizirik E, Gatesy J, Karlsson EK, Lindblad-Toh K, Springer MS, Murphy WJ, Andrews G, Armstrong JC, Bianchi M, Birren BW, Bredemeyer KR, Breit AM, Christmas MJ, Clawson H, Damas J, Di Palma F, Diekhans M, Dong MX, Eizirik E, Fan K, Fanter C, Foley NM, Forsberg-Nilsson K, Garcia CJ, Gatesy J, Gazal S, Genereux DP, Goodman L, Grimshaw J, Halsey MK, Harris AJ, Hickey G, Hiller M, Hindle AG, Hubley RM, Hughes GM, Johnson J, Juan D, Kaplow IM, Karlsson EK, Keough KC, Kirilenko B, Koepfli KP, Korstian JM, Kowalczyk A, Kozyrev SV, Lawler AJ, Lawless C, Lehmann T, Levesque DL, Lewin HA, Li X, Lind A, Lindblad-Toh K, Mackay-Smith A, Marinescu VD, Marques-Bonet T, Mason VC, Meadows JRS, Meyer WK, Moore JE, Moreira LR, Moreno-Santillan DD, Morrill KM, Muntané G, Murphy WJ, Navarro A, Nweeia M, Ortmann S, Osmanski A, Paten B, Paulat NS, Pfenning AR, Phan BN, Pollard KS, Pratt HE, Ray DA, Reilly SK, Rosen JR, Ruf I, Ryan L, Ryder OA, Sabeti PC, Schäffer DE, Serres A, Shapiro B, Smit AFA, Springer M, Srinivasan C, Steiner C, Storer JM, Sullivan KAM, Sullivan PF, Sundström E, Supple MA, Swofford R, Talbot JE, Teeling E, Turner-Maier J, Valenzuela A, Wagner F, Wallerman O, Wang C, Wang J, Weng Z, Wilder AP, Wirthlin ME, Xue JR, Zhang X. A genomic timescale for placental mammal evolution. Science 2023; 380:eabl8189. [PMID: 37104581 DOI: 10.1126/science.abl8189] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
The precise pattern and timing of speciation events that gave rise to all living placental mammals remain controversial. We provide a comprehensive phylogenetic analysis of genetic variation across an alignment of 241 placental mammal genome assemblies, addressing prior concerns regarding limited genomic sampling across species. We compared neutral genome-wide phylogenomic signals using concatenation and coalescent-based approaches, interrogated phylogenetic variation across chromosomes, and analyzed extensive catalogs of structural variants. Interordinal relationships exhibit relatively low rates of phylogenomic conflict across diverse datasets and analytical methods. Conversely, X-chromosome versus autosome conflicts characterize multiple independent clades that radiated during the Cenozoic. Genomic time trees reveal an accumulation of cladogenic events before and immediately after the Cretaceous-Paleogene (K-Pg) boundary, implying important roles for Cretaceous continental vicariance and the K-Pg extinction in the placental radiation.
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Affiliation(s)
- Nicole M Foley
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
| | - Victor C Mason
- Institute of Cell Biology, University of Bern, Bern, Switzerland
| | - Andrew J Harris
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
- Interdisciplinary Program in Genetics and Genomics, Texas A&M University, College Station, TX, USA
| | - Kevin R Bredemeyer
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
- Interdisciplinary Program in Genetics and Genomics, Texas A&M University, College Station, TX, USA
| | - Joana Damas
- The Genome Center, University of California, Davis, CA, USA
| | - Harris A Lewin
- The Genome Center, University of California, Davis, CA, USA
- Department of Evolution and Ecology, University of California, Davis, CA, USA
| | - Eduardo Eizirik
- School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul, Porto Alegre, Brazil
| | - John Gatesy
- Division of Vertebrate Zoology, American Museum of Natural History, New York, NY, USA
| | - Elinor K Karlsson
- Program in Bioinformatics and Integrative Biology, UMass Chan Medical School, Worcester, MA 01605, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
- Program in Molecular Medicine, University of Massachussetts Chan Medical School, Worcester, MA 01605, USA
| | - Kerstin Lindblad-Toh
- Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, 751 32 Uppsala, Sweden
| | - Mark S Springer
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, CA, USA
| | - William J Murphy
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
- Interdisciplinary Program in Genetics and Genomics, Texas A&M University, College Station, TX, USA
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Integrative comparative analysis of avian chromosome evolution by in-silico mapping of the gene ontology of homologous synteny blocks and evolutionary breakpoint regions. Genetica 2023:10.1007/s10709-023-00185-x. [PMID: 36940055 DOI: 10.1007/s10709-023-00185-x] [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: 01/04/2023] [Accepted: 03/14/2023] [Indexed: 03/21/2023]
Abstract
Avian chromosomes undergo more intra- than interchromosomal rearrangements, which either induce or are associated with genome variations among birds. Evolving from a common ancestor with a karyotype not dissimilar from modern chicken, two evolutionary elements characterize evolutionary change: homologous synteny blocks (HSBs) constitute common conserved parts at the sequence level, while evolutionary breakpoint regions (EBRs) occur between HSBs, defining the points where rearrangement occurred. Understanding the link between the structural organization and functionality of HSBs and EBRs provides insight into the mechanistic basis of chromosomal change. Previously, we identified gene ontology (GO) terms associated with both; however, here we revisit our analyses in light of newly developed bioinformatic algorithms and the chicken genome assembly galGal6. We aligned genomes available for six birds and one lizard species, identifying 630 HSBs and 19 EBRs. We demonstrate that HSBs hold vast functionality expressed by GO terms that have been largely conserved through evolution. Particularly, we found that genes within microchromosomal HSBs had specific functionalities relevant to neurons, RNA, cellular transport and embryonic development, and other associations. Our findings suggest that microchromosomes may have conserved throughout evolution due to the specificity of GO terms within their HSBs. The detected EBRs included those found in the genome of the anole lizard, meaning they were shared by all saurian descendants, with others being unique to avian lineages. Our estimate of gene richness in HSBs supported the fact that microchromosomes contain twice as many genes as macrochromosomes.
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10
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Widespread chromosomal rearrangements preceded genetic divergence in a monitor lizard, Varanus acanthurus (Varanidae). Chromosome Res 2023; 31:9. [PMID: 36745262 PMCID: PMC9902428 DOI: 10.1007/s10577-023-09715-x] [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: 09/02/2022] [Revised: 11/12/2022] [Accepted: 11/28/2022] [Indexed: 02/07/2023]
Abstract
Chromosomal rearrangements are often associated with local adaptation and speciation because they suppress recombination, and as a result, rearrangements have been implicated in disrupting gene flow. Although there is strong evidence to suggest that chromosome rearrangements are a factor in genetic isolation of divergent populations, the underlying mechanism remains elusive. Here, we applied an integrative cytogenetics and genomics approach testing whether chromosomal rearrangements are the initial process, or a consequence, of population divergence in the dwarf goanna, Varanus acanthurus. Specifically, we tested whether chromosome rearrangements are indicators of genetic barriers that can be used to identify divergent populations by looking at gene flow within and between populations with rearrangements. We found that gene flow was present between individuals with chromosome rearrangements within populations, but there was no gene flow between populations that had similar chromosome rearrangements. Moreover, we identified a correlation between reduced genetic variation in populations with a higher frequency of homozygous submetacentric individuals. These findings suggest that chromosomal rearrangements were widespread prior to divergence, and because we found populations with higher frequencies of submetacentric chromosomes were associated with lower genetic diversity, this could indicate that polymorphisms within populations are early indicators of genetic drift.
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11
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Griffin DK, Larkin DM, O’Connor RE, Romanov MN. Dinosaurs: Comparative Cytogenomics of Their Reptile Cousins and Avian Descendants. Animals (Basel) 2022; 13:ani13010106. [PMID: 36611715 PMCID: PMC9817885 DOI: 10.3390/ani13010106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/22/2022] [Accepted: 12/23/2022] [Indexed: 12/29/2022] Open
Abstract
Reptiles known as dinosaurs pervade scientific and popular culture, while interest in their genomics has increased since the 1990s. Birds (part of the crown group Reptilia) are living theropod dinosaurs. Chromosome-level genome assemblies cannot be made from long-extinct biological material, but dinosaur genome organization can be inferred through comparative genomics of related extant species. Most reptiles apart from crocodilians have both macro- and microchromosomes; comparative genomics involving molecular cytogenetics and bioinformatics has established chromosomal relationships between many species. The capacity of dinosaurs to survive multiple extinction events is now well established, and birds now have more species in comparison with any other terrestrial vertebrate. This may be due, in part, to their karyotypic features, including a distinctive karyotype of around n = 40 (~10 macro and 30 microchromosomes). Similarity in genome organization in distantly related species suggests that the common avian ancestor had a similar karyotype to e.g., the chicken/emu/zebra finch. The close karyotypic similarity to the soft-shelled turtle (n = 33) suggests that this basic pattern was mostly established before the Testudine-Archosaur divergence, ~255 MYA. That is, dinosaurs most likely had similar karyotypes and their extensive phenotypic variation may have been mediated by increased random chromosome segregation and genetic recombination, which is inherently higher in karyotypes with more and smaller chromosomes.
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Affiliation(s)
- Darren K. Griffin
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK
- Correspondence:
| | - Denis M. Larkin
- Department of Comparative Biomedical Sciences, Royal Veterinary College, University of London, London NW1 0TU, UK
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12
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Álvarez-González L, Arias-Sardá C, Montes-Espuña L, Marín-Gual L, Vara C, Lister NC, Cuartero Y, Garcia F, Deakin J, Renfree MB, Robinson TJ, Martí-Renom MA, Waters PD, Farré M, Ruiz-Herrera A. Principles of 3D chromosome folding and evolutionary genome reshuffling in mammals. Cell Rep 2022; 41:111839. [PMID: 36543130 DOI: 10.1016/j.celrep.2022.111839] [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: 06/18/2022] [Revised: 10/01/2022] [Accepted: 11/24/2022] [Indexed: 12/24/2022] Open
Abstract
Studying the similarities and differences in genomic interactions between species provides fertile grounds for determining the evolutionary dynamics underpinning genome function and speciation. Here, we describe the principles of 3D genome folding in vertebrates and show how lineage-specific patterns of genome reshuffling can result in different chromatin configurations. We (1) identified different patterns of chromosome folding in across vertebrate species (centromere clustering versus chromosomal territories); (2) reconstructed ancestral marsupial and afrotherian genomes analyzing whole-genome sequences of species representative of the major therian phylogroups; (3) detected lineage-specific chromosome rearrangements; and (4) identified the dynamics of the structural properties of genome reshuffling through therian evolution. We present evidence of chromatin configurational changes that result from ancestral inversions and fusions/fissions. We catalog the close interplay between chromatin higher-order organization and therian genome evolution and introduce an interpretative hypothesis that explains how chromatin folding influences evolutionary patterns of genome reshuffling.
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Affiliation(s)
- Lucía Álvarez-González
- Departament de Biologia Cel·lular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain; Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain
| | | | - Laia Montes-Espuña
- Departament de Biologia Cel·lular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain; Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain
| | - Laia Marín-Gual
- Departament de Biologia Cel·lular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain; Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain
| | - Covadonga Vara
- Departament de Biologia Cel·lular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain; Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain
| | - Nicholas C Lister
- School of Biotechnology and Biomolecular Sciences, Faculty of Science, UNSW Sydney, Sydney, NSW 2052, Australia
| | - Yasmina Cuartero
- CNAG-CRG, Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Baldiri Reixac 4, 08028 Barcelona, Spain
| | - Francisca Garcia
- Servei de Cultius Cel.lulars-SCAC, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain
| | - Janine Deakin
- Institute for Applied Ecology, University of Canberra, Bruce, ACT 2617, Australia
| | - Marilyn B Renfree
- School of Biosciences, The University of Melbourne, Victoria, VIC 3010, Australia
| | - Terence J Robinson
- Evolutionary Genomics Group, Department of Botany and Zoology, Faculty of Science, Stellenbosch University, Private Bag X1, Stellenbosch 7602, South Africa
| | - Marc A Martí-Renom
- CNAG-CRG, Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Baldiri Reixac 4, 08028 Barcelona, Spain; Centre for Genomic Regulation, The Barcelona Institute for Science and Technology, Carrer del Doctor Aiguader 88, 08003 Barcelona, Spain; ICREA, Pg. Lluís Companys 23, 08010 Barcelona, Spain; Universitat Pompeu Fabra (UPF), 08002 Barcelona, Spain
| | - Paul D Waters
- School of Biotechnology and Biomolecular Sciences, Faculty of Science, UNSW Sydney, Sydney, NSW 2052, Australia
| | - Marta Farré
- School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK
| | - Aurora Ruiz-Herrera
- Departament de Biologia Cel·lular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain; Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain.
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13
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Can changes in 3D genome architecture create new regulatory landscapes that contribute to phenotypic evolution? Essays Biochem 2022; 66:745-752. [PMID: 36250960 DOI: 10.1042/ebc20220057] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 09/20/2022] [Accepted: 09/23/2022] [Indexed: 12/13/2022]
Abstract
Animal genomes are compartmentalized into insulated regulatory units named topology-associated domains (TADs). TADs insulate gene promoters from enhancers that occupy neighboring TADs. Chromosomal rearrangements that disrupt TAD structure can generate new regulatory interactions between enhancers and promoters that were once separated into different TADs, which might lead to new gene expression patterns. On the one hand, TAD rearrangements are known to cause deleterious phenotypes, but, on the other hand, rearrangements can also create novel expression patterns that may be selected during evolution because they generate advantageous phenotypes. Here, we review recent studies that explore the effects of chromosomal rearrangements and genetic perturbations on TAD structure and gene regulation in the context of development and evolution. We discuss the possible contribution of evolutionary breakpoints (EBRs) that affect TAD structure to the evolution of gene regulation and the phenotype.
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14
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Abstract
Computational reconstruction of ancestral mammalian karyotypes revealed a comprehensive picture of the chromosome rearrangements that occurred over the evolutionary history of mammals. Ancient gene order, in some cases extending to full chromosomes, was found conserved for more than 300 My, demonstrating strong evolutionary constraint against rearrangements in some regions. Conserved segments of chromosomes are enriched for genes that control developmental processes. Therefore, Darwinian selection likely maintains ancient gene combinations while allowing for genomic innovations within or near chromosomal sites that break and rearrange over evolutionary time. The revealed relationship between the three-dimensional structure of chromosomes and the evolutionary stability of chromosome segments provides additional insights into the mechanisms of chromosome evolution and diseases associated with genome rearrangements. Decrypting the rearrangements that drive mammalian chromosome evolution is critical to understanding the molecular bases of speciation, adaptation, and disease susceptibility. Using 8 scaffolded and 26 chromosome-scale genome assemblies representing 23/26 mammal orders, we computationally reconstructed ancestral karyotypes and syntenic relationships at 16 nodes along the mammalian phylogeny. Three different reference genomes (human, sloth, and cattle) representing phylogenetically distinct mammalian superorders were used to assess reference bias in the reconstructed ancestral karyotypes and to expand the number of clades with reconstructed genomes. The mammalian ancestor likely had 19 pairs of autosomes, with nine of the smallest chromosomes shared with the common ancestor of all amniotes (three still conserved in extant mammals), demonstrating a striking conservation of synteny for ∼320 My of vertebrate evolution. The numbers and types of chromosome rearrangements were classified for transitions between the ancestral mammalian karyotype, descendent ancestors, and extant species. For example, 94 inversions, 16 fissions, and 14 fusions that occurred over 53 My differentiated the therian from the descendent eutherian ancestor. The highest breakpoint rate was observed between the mammalian and therian ancestors (3.9 breakpoints/My). Reconstructed mammalian ancestor chromosomes were found to have distinct evolutionary histories reflected in their rates and types of rearrangements. The distributions of genes, repetitive elements, topologically associating domains, and actively transcribed regions in multispecies homologous synteny blocks and evolutionary breakpoint regions indicate that purifying selection acted over millions of years of vertebrate evolution to maintain syntenic relationships of developmentally important genes and regulatory landscapes of gene-dense chromosomes.
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15
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Yan C, Wu W, Dong W, Zhu B, Chang J, Lv Y, Yang S, Li JT. Temperature acclimation in hot-spring snakes and the convergence of cold response. Innovation (N Y) 2022; 3:100295. [PMID: 36032194 PMCID: PMC9405097 DOI: 10.1016/j.xinn.2022.100295] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Accepted: 07/28/2022] [Indexed: 11/05/2022] Open
Abstract
Animals have evolved sophisticated temperature-sensing systems and mechanisms to detect and respond to ambient temperature changes. As a relict species endemic to the Qinghai-Tibet Plateau, hot-spring snake (Thermophis baileyi) survived the dramatic changes in climate that occurred during plateau uplift and ice ages, providing an excellent opportunity to explore the evolution of temperature sensation in ectotherms. Based on distributional information and behavioral experiments, we found that T. baileyi prefer hot-spring habitats and respond more quickly to warmth than other two snakes, suggesting that T. baileyi may evolve an efficient thermal-sensing system. Using high-quality chromosome-level assembly and comparative genomic analysis, we identified cold acclimation genes experiencing convergent acceleration in high-altitude lineages. We also discovered significant evolutionary changes in thermosensation- and thermoregulation-related genes, including the transient receptor potential (TRP) channels. Among these genes, TRPA1 exhibited three species-specific amino acid replacements, which differed from those found in infrared imaging snakes, implying different temperature-sensing molecular strategies. Based on laser-heating experiments, the T. baileyi-specific mutations in TRPA1 resulted in an increase in heat-induced opening probability and thermal sensitivity of the ion channels under the same degree of temperature stimulation, which may help the organism respond to temperature changes more quickly. These results provide insight into the genetic mechanisms underpinning the evolution of temperature-sensing strategies in ectotherms as well as genetic evidence of temperature acclimation in this group. Hot-spring snakes prefer hot-spring habitats on the Qinghai-Tibet Plateau Genetic variation in the snakes contribute to the temperature acclimation Unique mutations in TRPA1 increase thermal sensitivity of the ion channel Different temperature-sensing strategies existed across snakes
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16
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Hubley R, Wheeler TJ, Smit AFA. Accuracy of multiple sequence alignment methods in the reconstruction of transposable element families. NAR Genom Bioinform 2022; 4:lqac040. [PMID: 35591887 PMCID: PMC9112768 DOI: 10.1093/nargab/lqac040] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 03/29/2022] [Accepted: 04/29/2022] [Indexed: 02/06/2023] Open
Abstract
The construction of a high-quality multiple sequence alignment (MSA) from copies of a transposable element (TE) is a critical step in the characterization of a new TE family. Most studies of MSA accuracy have been conducted on protein or RNA sequence families, where structural features and strong signals of selection may assist with alignment. Less attention has been given to the quality of sequence alignments involving neutrally evolving DNA sequences such as those resulting from TE replication. Transposable element sequences are challenging to align due to their wide divergence ranges, fragmentation, and predominantly-neutral mutation patterns. To gain insight into the effects of these properties on MSA accuracy, we developed a simulator of TE sequence evolution, and used it to generate a benchmark with which we evaluated the MSA predictions produced by several popular aligners, along with Refiner, a method we developed in the context of our RepeatModeler software. We find that MAFFT and Refiner generally outperform other aligners for low to medium divergence simulated sequences, while Refiner is uniquely effective when tasked with aligning high-divergent and fragmented instances of a family.
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Affiliation(s)
- Robert Hubley
- Institute for Systems Biology, Seattle, WA 98109, USA
| | - Travis J Wheeler
- Department of Computer Science, University of Montana, Missoula, MT 59801, USA
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17
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3D chromatin remodelling in the germ line modulates genome evolutionary plasticity. Nat Commun 2022; 13:2608. [PMID: 35546158 PMCID: PMC9095871 DOI: 10.1038/s41467-022-30296-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 04/21/2022] [Indexed: 11/09/2022] Open
Abstract
Chromosome folding has profound impacts on gene regulation, whose evolutionary consequences are far from being understood. Here we explore the relationship between 3D chromatin remodelling in mouse germ cells and evolutionary changes in genome structure. Using a comprehensive integrative computational analysis, we (i) reconstruct seven ancestral rodent genomes analysing whole-genome sequences of 14 species representatives of the major phylogroups, (ii) detect lineage-specific chromosome rearrangements and (iii) identify the dynamics of the structural and epigenetic properties of evolutionary breakpoint regions (EBRs) throughout mouse spermatogenesis. Our results show that EBRs are devoid of programmed meiotic DNA double-strand breaks (DSBs) and meiotic cohesins in primary spermatocytes, but are associated in post-meiotic cells with sites of DNA damage and functional long-range interaction regions that recapitulate ancestral chromosomal configurations. Overall, we propose a model that integrates evolutionary genome reshuffling with DNA damage response mechanisms and the dynamic spatial genome organisation of germ cells. The role of genome folding in the heritability and evolvability of structural variations is not well understood. Here the authors investigate the impact of the three-dimensional genome topology of germ cells in the formation and transmission of gross structural genomic changes detected from comparing whole-genome sequences of 14 rodent species.
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18
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Recurrent erosion of COA1/MITRAC15 exemplifies conditional gene dispensability in oxidative phosphorylation. Sci Rep 2021; 11:24437. [PMID: 34952909 PMCID: PMC8709867 DOI: 10.1038/s41598-021-04077-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 12/15/2021] [Indexed: 11/08/2022] Open
Abstract
Skeletal muscle fibers rely upon either oxidative phosphorylation or the glycolytic pathway with much less reliance on oxidative phosphorylation to achieve muscular contractions that power mechanical movements. Species with energy-intensive adaptive traits that require sudden bursts of energy have a greater dependency on glycolytic fibers. Glycolytic fibers have decreased reliance on OXPHOS and lower mitochondrial content compared to oxidative fibers. Hence, we hypothesized that gene loss might have occurred within the OXPHOS pathway in lineages that largely depend on glycolytic fibers. The protein encoded by the COA1/MITRAC15 gene with conserved orthologs found in budding yeast to humans promotes mitochondrial translation. We show that gene disrupting mutations have accumulated within the COA1 gene in the cheetah, several species of galliform birds, and rodents. The genomic region containing COA1 is a well-established evolutionary breakpoint region in mammals. Careful inspection of genome assemblies of closely related species of rodents and marsupials suggests two independent COA1 gene loss events co-occurring with chromosomal rearrangements. Besides recurrent gene loss events, we document changes in COA1 exon structure in primates and felids. The detailed evolutionary history presented in this study reveals the intricate link between skeletal muscle fiber composition and the occasional dispensability of the chaperone-like role of the COA1 gene.
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19
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Galbraith JD, Kortschak RD, Suh A, Adelson DL. Genome Stability Is in the Eye of the Beholder: CR1 Retrotransposon Activity Varies Significantly across Avian Diversity. Genome Biol Evol 2021; 13:6433158. [PMID: 34894225 PMCID: PMC8665684 DOI: 10.1093/gbe/evab259] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/12/2021] [Indexed: 12/20/2022] Open
Abstract
Since the sequencing of the zebra finch genome it has become clear that avian genomes, while largely stable in terms of chromosome number and gene synteny, are more dynamic at an intrachromosomal level. A multitude of intrachromosomal rearrangements and significant variation in transposable element (TE) content have been noted across the avian tree. TEs are a source of genome plasticity, because their high similarity enables chromosomal rearrangements through nonallelic homologous recombination, and they have potential for exaptation as regulatory and coding sequences. Previous studies have investigated the activity of the dominant TE in birds, chicken repeat 1 (CR1) retrotransposons, either focusing on their expansion within single orders, or comparing passerines with nonpasserines. Here, we comprehensively investigate and compare the activity of CR1 expansion across orders of birds, finding levels of CR1 activity vary significantly both between and within orders. We describe high levels of TE expansion in genera which have speciated in the last 10 Myr including kiwis, geese, and Amazon parrots; low levels of TE expansion in songbirds across their diversification, and near inactivity of TEs in the cassowary and emu for millions of years. CR1s have remained active over long periods of time across most orders of neognaths, with activity at any one time dominated by one or two families of CR1s. Our findings of higher TE activity in species-rich clades and dominant families of TEs within lineages mirror past findings in mammals and indicate that genome evolution in amniotes relies on universal TE-driven processes.
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Affiliation(s)
- James D Galbraith
- School of Biological Sciences, The University of Adelaide, South Australia, Australia
| | | | - Alexander Suh
- School of Biological Sciences, University of East Anglia, Norwich, United Kingdom.,Department of Organismal Biology, Evolutionary Biology Centre (EBC), Science for Life Laboratory, Uppsala University, Sweden
| | - David L Adelson
- School of Biological Sciences, The University of Adelaide, South Australia, Australia
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20
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Bravo GA, Schmitt CJ, Edwards SV. What Have We Learned from the First 500 Avian Genomes? ANNUAL REVIEW OF ECOLOGY, EVOLUTION, AND SYSTEMATICS 2021. [DOI: 10.1146/annurev-ecolsys-012121-085928] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The increased capacity of DNA sequencing has significantly advanced our understanding of the phylogeny of birds and the proximate and ultimate mechanisms molding their genomic diversity. In less than a decade, the number of available avian reference genomes has increased to over 500—approximately 5% of bird diversity—placing birds in a privileged position to advance the fields of phylogenomics and comparative, functional, and population genomics. Whole-genome sequence data, as well as indels and rare genomic changes, are further resolving the avian tree of life. The accumulation of bird genomes, increasingly with long-read sequence data, greatly improves the resolution of genomic features such as germline-restricted chromosomes and the W chromosome, and is facilitating the comparative integration of genotypes and phenotypes. Community-based initiatives such as the Bird 10,000 Genomes Project and Vertebrate Genome Project are playing a fundamental role in amplifying and coalescing a vibrant international program in avian comparative genomics.
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Affiliation(s)
- Gustavo A. Bravo
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts 02138, USA;, ,
| | - C. Jonathan Schmitt
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts 02138, USA;, ,
| | - Scott V. Edwards
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts 02138, USA;, ,
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21
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Kretschmer R, Franz I, de Souza MS, Garnero ADV, Gunski RJ, de Oliveira EHC, O’Connor RE, Griffin DK, de Freitas TRO. Cytogenetic Evidence Clarifies the Phylogeny of the Family Rhynchocyclidae (Aves: Passeriformes). Cells 2021; 10:2650. [PMID: 34685630 PMCID: PMC8534115 DOI: 10.3390/cells10102650] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 09/27/2021] [Accepted: 09/30/2021] [Indexed: 11/16/2022] Open
Abstract
The phylogenetic position and taxonomic status of Rhynchocyclidae (Aves: Passeriformes) have been the subject of debate since their first description. In most models, Rhynchocyclidae represents a subfamily-level taxon placed within the Tyrant Flycatchers (Tyrannidae). Considering that this classification does not include cytotaxonomic characters, we tested the hypothesis that the chromosome organization of Rhynchocyclidae members differs from that of Tyrannidae. Hence, we selected two species, Tolmomyias sulphurescens, and Pitangus sulphuratus, representing Rhynchocyclidae and Tyrannidae, respectively. Results revealed a diploid number (2n) of 60 in T. sulphurescens and 2n = 80 in P. sulphuratus, indicating significant chromosomal differences. Chromosome mapping of Gallus gallus (GGA) and Taeniopygia guttata bacterial artificial chromosome (BAC) corresponding to chromosomes GGA1-28 (except 16) revealed that the genome evolution of T. sulphurescens involved extensive chromosome fusions of macrochromosomes and microchromosomes. On the other hand, P. sulphuratus retained the ancestral pattern of organization of macrochromosomes (except the centric fission involving GGA1) and microchromosomes. In conclusion, comparing our results with previous studies in Tyrant Flycatchers and allies indicates that P. sulphuratus has similar karyotypes to other Tyrannidae members. However, T. sulphurescens does not resemble the Tyrannidae family, reinforcing family status to the clade named Rhynchocyclidae.
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Affiliation(s)
- Rafael Kretschmer
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK; (R.K.); (R.E.O.)
- Laboratório de Citogenética e Evolução, Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre 91509-900, RS, Brazil;
| | - Ismael Franz
- Departamento de Zoologia, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre 91509-900, RS, Brazil;
| | - Marcelo Santos de Souza
- Laboratório de Diversidade Genética Animal, Universidade Federal do Pampa, São Gabriel 97300-162, RS, Brazil; (M.S.d.S.); (A.D.V.G.); (R.J.G.)
| | - Analía Del Valle Garnero
- Laboratório de Diversidade Genética Animal, Universidade Federal do Pampa, São Gabriel 97300-162, RS, Brazil; (M.S.d.S.); (A.D.V.G.); (R.J.G.)
| | - Ricardo José Gunski
- Laboratório de Diversidade Genética Animal, Universidade Federal do Pampa, São Gabriel 97300-162, RS, Brazil; (M.S.d.S.); (A.D.V.G.); (R.J.G.)
| | - Edivaldo Herculano Corrêa de Oliveira
- Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belém 66075-110, PA, Brazil;
- Laboratório de Cultura de Tecidos e Citogenética, SAMAM, Instituto Evandro Chagas, Ananindeua 67030-000, PA, Brazil
| | - Rebecca E. O’Connor
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK; (R.K.); (R.E.O.)
| | - Darren K. Griffin
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK; (R.K.); (R.E.O.)
| | - Thales Renato Ochotorena de Freitas
- Laboratório de Citogenética e Evolução, Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre 91509-900, RS, Brazil;
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22
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Bergero R, Ellis P, Haerty W, Larcombe L, Macaulay I, Mehta T, Mogensen M, Murray D, Nash W, Neale MJ, O'Connor R, Ottolini C, Peel N, Ramsey L, Skinner B, Suh A, Summers M, Sun Y, Tidy A, Rahbari R, Rathje C, Immler S. Meiosis and beyond - understanding the mechanistic and evolutionary processes shaping the germline genome. Biol Rev Camb Philos Soc 2021; 96:822-841. [PMID: 33615674 PMCID: PMC8246768 DOI: 10.1111/brv.12680] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 12/15/2020] [Accepted: 12/15/2020] [Indexed: 12/11/2022]
Abstract
The separation of germ cell populations from the soma is part of the evolutionary transition to multicellularity. Only genetic information present in the germ cells will be inherited by future generations, and any molecular processes affecting the germline genome are therefore likely to be passed on. Despite its prevalence across taxonomic kingdoms, we are only starting to understand details of the underlying micro-evolutionary processes occurring at the germline genome level. These include segregation, recombination, mutation and selection and can occur at any stage during germline differentiation and mitotic germline proliferation to meiosis and post-meiotic gamete maturation. Selection acting on germ cells at any stage from the diploid germ cell to the haploid gametes may cause significant deviations from Mendelian inheritance and may be more widespread than previously assumed. The mechanisms that affect and potentially alter the genomic sequence and allele frequencies in the germline are pivotal to our understanding of heritability. With the rise of new sequencing technologies, we are now able to address some of these unanswered questions. In this review, we comment on the most recent developments in this field and identify current gaps in our knowledge.
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Affiliation(s)
- Roberta Bergero
- Institute of Evolutionary BiologyUniversity of EdinburghEdinburghEH9 3JTU.K.
| | - Peter Ellis
- School of BiosciencesUniversity of KentCanterburyCT2 7NJU.K.
| | | | - Lee Larcombe
- Applied Exomics LtdStevenage Bioscience CatalystStevenageSG1 2FXU.K.
| | - Iain Macaulay
- Earlham InstituteNorwich Research ParkNorwichNR4 7UZU.K.
| | - Tarang Mehta
- Earlham InstituteNorwich Research ParkNorwichNR4 7UZU.K.
| | - Mette Mogensen
- School of Biological SciencesUniversity of East AngliaNorwich Research ParkNorwichNR4 7TJU.K.
| | - David Murray
- School of Biological SciencesUniversity of East AngliaNorwich Research ParkNorwichNR4 7TJU.K.
| | - Will Nash
- Earlham InstituteNorwich Research ParkNorwichNR4 7UZU.K.
| | - Matthew J. Neale
- Genome Damage and Stability Centre, School of Life SciencesUniversity of SussexBrightonBN1 9RHU.K.
| | | | | | - Ned Peel
- Earlham InstituteNorwich Research ParkNorwichNR4 7UZU.K.
| | - Luke Ramsey
- The James Hutton InstituteInvergowrieDundeeDD2 5DAU.K.
| | - Ben Skinner
- School of Life SciencesUniversity of EssexColchesterCO4 3SQU.K.
| | - Alexander Suh
- School of Biological SciencesUniversity of East AngliaNorwich Research ParkNorwichNR4 7TJU.K.
- Department of Organismal BiologyUppsala UniversityNorbyvägen 18DUppsala752 36Sweden
| | - Michael Summers
- School of BiosciencesUniversity of KentCanterburyCT2 7NJU.K.
- The Bridge Centre1 St Thomas Street, London BridgeLondonSE1 9RYU.K.
| | - Yu Sun
- Norwich Medical SchoolUniversity of East AngliaNorwich Research Park, Colney LnNorwichNR4 7UGU.K.
| | - Alison Tidy
- School of BiosciencesUniversity of Nottingham, Plant Science, Sutton Bonington CampusSutton BoningtonLE12 5RDU.K.
| | | | - Claudia Rathje
- School of BiosciencesUniversity of KentCanterburyCT2 7NJU.K.
| | - Simone Immler
- School of Biological SciencesUniversity of East AngliaNorwich Research ParkNorwichNR4 7TJU.K.
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23
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Kretschmer R, de Souza MS, Furo IDO, Romanov MN, Gunski RJ, Garnero ADV, de Freitas TRO, de Oliveira EHC, O’Connor RE, Griffin DK. Interspecies Chromosome Mapping in Caprimulgiformes, Piciformes, Suliformes, and Trogoniformes (Aves): Cytogenomic Insight into Microchromosome Organization and Karyotype Evolution in Birds. Cells 2021; 10:cells10040826. [PMID: 33916942 PMCID: PMC8067558 DOI: 10.3390/cells10040826] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 04/02/2021] [Accepted: 04/05/2021] [Indexed: 01/18/2023] Open
Abstract
Interchromosomal rearrangements involving microchromosomes are rare events in birds. To date, they have been found mostly in Psittaciformes, Falconiformes, and Cuculiformes, although only a few orders have been analyzed. Hence, cytogenomic studies focusing on microchromosomes in species belonging to different bird orders are essential to shed more light on the avian chromosome and karyotype evolution. Based on this, we performed a comparative chromosome mapping for chicken microchromosomes 10 to 28 using interspecies BAC-based FISH hybridization in five species, representing four Neoaves orders (Caprimulgiformes, Piciformes, Suliformes, and Trogoniformes). Our results suggest that the ancestral microchromosomal syntenies are conserved in Pteroglossus inscriptus (Piciformes), Ramphastos tucanus tucanus (Piciformes), and Trogon surrucura surrucura (Trogoniformes). On the other hand, chromosome reorganization in Phalacrocorax brasilianus (Suliformes) and Hydropsalis torquata (Caprimulgiformes) included fusions involving both macro- and microchromosomes. Fissions in macrochromosomes were observed in P. brasilianus and H. torquata. Relevant hypothetical Neognathae and Neoaves ancestral karyotypes were reconstructed to trace these rearrangements. We found no interchromosomal rearrangement involving microchromosomes to be shared between avian orders where rearrangements were detected. Our findings suggest that convergent evolution involving microchromosomal change is a rare event in birds and may be appropriate in cytotaxonomic inferences in orders where these rearrangements occurred.
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Affiliation(s)
- Rafael Kretschmer
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK; (R.K.); (M.N.R.); (R.E.O.)
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, 91509-900 Rio Grande do Sul, Brazil;
| | - Marcelo Santos de Souza
- Laboratório de Diversidade Genética Animal, Universidade Federal do Pampa, São Gabriel, 97300-162 Rio Grande do Sul, Brazil; (M.S.d.S.); (R.J.G.); (A.d.V.G.)
| | - Ivanete de Oliveira Furo
- Laboratório de Reprodução Animal, LABRAC, Universidade Federal Rural da Amazônia, UFRA, Parauapebas, 68515-000 Pará, Brazil;
| | - Michael N. Romanov
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK; (R.K.); (M.N.R.); (R.E.O.)
| | - Ricardo José Gunski
- Laboratório de Diversidade Genética Animal, Universidade Federal do Pampa, São Gabriel, 97300-162 Rio Grande do Sul, Brazil; (M.S.d.S.); (R.J.G.); (A.d.V.G.)
| | - Analía del Valle Garnero
- Laboratório de Diversidade Genética Animal, Universidade Federal do Pampa, São Gabriel, 97300-162 Rio Grande do Sul, Brazil; (M.S.d.S.); (R.J.G.); (A.d.V.G.)
| | | | - Edivaldo Herculano Corrêa de Oliveira
- Laboratório de Cultura de Tecidos e Citogenética, SAMAM, Instituto Evandro Chagas, Ananindeua, 67030-000 Pará, Brazil;
- Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belém, 66075-110 Pará, Brazil
| | - Rebecca E. O’Connor
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK; (R.K.); (M.N.R.); (R.E.O.)
| | - Darren K. Griffin
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK; (R.K.); (M.N.R.); (R.E.O.)
- Correspondence: ; Tel.: +44-1227-823022
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24
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Rhie A, McCarthy SA, Fedrigo O, Damas J, Formenti G, Koren S, Uliano-Silva M, Chow W, Fungtammasan A, Kim J, Lee C, Ko BJ, Chaisson M, Gedman GL, Cantin LJ, Thibaud-Nissen F, Haggerty L, Bista I, Smith M, Haase B, Mountcastle J, Winkler S, Paez S, Howard J, Vernes SC, Lama TM, Grutzner F, Warren WC, Balakrishnan CN, Burt D, George JM, Biegler MT, Iorns D, Digby A, Eason D, Robertson B, Edwards T, Wilkinson M, Turner G, Meyer A, Kautt AF, Franchini P, Detrich HW, Svardal H, Wagner M, Naylor GJP, Pippel M, Malinsky M, Mooney M, Simbirsky M, Hannigan BT, Pesout T, Houck M, Misuraca A, Kingan SB, Hall R, Kronenberg Z, Sović I, Dunn C, Ning Z, Hastie A, Lee J, Selvaraj S, Green RE, Putnam NH, Gut I, Ghurye J, Garrison E, Sims Y, Collins J, Pelan S, Torrance J, Tracey A, Wood J, Dagnew RE, Guan D, London SE, Clayton DF, Mello CV, Friedrich SR, Lovell PV, Osipova E, Al-Ajli FO, Secomandi S, Kim H, Theofanopoulou C, Hiller M, Zhou Y, Harris RS, Makova KD, Medvedev P, Hoffman J, Masterson P, Clark K, Martin F, Howe K, Flicek P, Walenz BP, Kwak W, Clawson H, Diekhans M, Nassar L, Paten B, Kraus RHS, Crawford AJ, Gilbert MTP, Zhang G, Venkatesh B, Murphy RW, Koepfli KP, Shapiro B, Johnson WE, Di Palma F, Marques-Bonet T, Teeling EC, Warnow T, Graves JM, Ryder OA, Haussler D, O'Brien SJ, Korlach J, Lewin HA, Howe K, Myers EW, Durbin R, Phillippy AM, Jarvis ED. Towards complete and error-free genome assemblies of all vertebrate species. Nature 2021; 592:737-746. [PMID: 33911273 PMCID: PMC8081667 DOI: 10.1038/s41586-021-03451-0] [Citation(s) in RCA: 804] [Impact Index Per Article: 268.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 03/12/2021] [Indexed: 02/02/2023]
Abstract
High-quality and complete reference genome assemblies are fundamental for the application of genomics to biology, disease, and biodiversity conservation. However, such assemblies are available for only a few non-microbial species1-4. To address this issue, the international Genome 10K (G10K) consortium5,6 has worked over a five-year period to evaluate and develop cost-effective methods for assembling highly accurate and nearly complete reference genomes. Here we present lessons learned from generating assemblies for 16 species that represent six major vertebrate lineages. We confirm that long-read sequencing technologies are essential for maximizing genome quality, and that unresolved complex repeats and haplotype heterozygosity are major sources of assembly error when not handled correctly. Our assemblies correct substantial errors, add missing sequence in some of the best historical reference genomes, and reveal biological discoveries. These include the identification of many false gene duplications, increases in gene sizes, chromosome rearrangements that are specific to lineages, a repeated independent chromosome breakpoint in bat genomes, and a canonical GC-rich pattern in protein-coding genes and their regulatory regions. Adopting these lessons, we have embarked on the Vertebrate Genomes Project (VGP), an international effort to generate high-quality, complete reference genomes for all of the roughly 70,000 extant vertebrate species and to help to enable a new era of discovery across the life sciences.
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Affiliation(s)
- Arang Rhie
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Shane A McCarthy
- Department of Genetics, University of Cambridge, Cambridge, UK
- Wellcome Sanger Institute, Cambridge, UK
| | - Olivier Fedrigo
- Vertebrate Genome Lab, The Rockefeller University, New York, NY, USA
| | - Joana Damas
- The Genome Center, University of California Davis, Davis, CA, USA
| | - Giulio Formenti
- Vertebrate Genome Lab, The Rockefeller University, New York, NY, USA
- Laboratory of Neurogenetics of Language, The Rockefeller University, New York, NY, USA
| | - Sergey Koren
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Marcela Uliano-Silva
- Leibniz Institute for Zoo and Wildlife Research, Department of Evolutionary Genetics, Berlin, Germany
- Berlin Center for Genomics in Biodiversity Research, Berlin, Germany
| | | | | | - Juwan Kim
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea
| | - Chul Lee
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea
| | - Byung June Ko
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Mark Chaisson
- University of Southern California, Los Angeles, CA, USA
| | - Gregory L Gedman
- Laboratory of Neurogenetics of Language, The Rockefeller University, New York, NY, USA
| | - Lindsey J Cantin
- Laboratory of Neurogenetics of Language, The Rockefeller University, New York, NY, USA
| | - Francoise Thibaud-Nissen
- National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD, USA
| | - Leanne Haggerty
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Iliana Bista
- Department of Genetics, University of Cambridge, Cambridge, UK
- Wellcome Sanger Institute, Cambridge, UK
| | | | - Bettina Haase
- Vertebrate Genome Lab, The Rockefeller University, New York, NY, USA
| | | | - Sylke Winkler
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- DRESDEN-concept Genome Center, Dresden, Germany
| | - Sadye Paez
- Vertebrate Genome Lab, The Rockefeller University, New York, NY, USA
- Laboratory of Neurogenetics of Language, The Rockefeller University, New York, NY, USA
| | | | - Sonja C Vernes
- Neurogenetics of Vocal Communication Group, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands
- School of Biology, University of St Andrews, St Andrews, UK
| | - Tanya M Lama
- University of Massachusetts Cooperative Fish and Wildlife Research Unit, Amherst, MA, USA
| | - Frank Grutzner
- School of Biological Science, The Environment Institute, University of Adelaide, Adelaide, South Australia, Australia
| | - Wesley C Warren
- Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
| | | | - Dave Burt
- UQ Genomics, University of Queensland, Brisbane, Queensland, Australia
| | - Julia M George
- Department of Biological Sciences, Clemson University, Clemson, SC, USA
| | - Matthew T Biegler
- Laboratory of Neurogenetics of Language, The Rockefeller University, New York, NY, USA
| | - David Iorns
- The Genetic Rescue Foundation, Wellington, New Zealand
| | - Andrew Digby
- Kākāpō Recovery, Department of Conservation, Invercargill, New Zealand
| | - Daryl Eason
- Kākāpō Recovery, Department of Conservation, Invercargill, New Zealand
| | - Bruce Robertson
- Department of Zoology, University of Otago, Dunedin, New Zealand
| | | | - Mark Wilkinson
- Department of Life Sciences, Natural History Museum, London, UK
| | - George Turner
- School of Natural Sciences, Bangor University, Gwynedd, UK
| | - Axel Meyer
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Andreas F Kautt
- Department of Biology, University of Konstanz, Konstanz, Germany
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Paolo Franchini
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - H William Detrich
- Department of Marine and Environmental Sciences, Northeastern University Marine Science Center, Nahant, MA, USA
| | - Hannes Svardal
- Department of Biology, University of Antwerp, Antwerp, Belgium
- Naturalis Biodiversity Center, Leiden, The Netherlands
| | - Maximilian Wagner
- Institute of Biology, Karl-Franzens University of Graz, Graz, Austria
| | - Gavin J P Naylor
- Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
| | - Martin Pippel
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- Center for Systems Biology, Dresden, Germany
| | - Milan Malinsky
- Wellcome Sanger Institute, Cambridge, UK
- Zoological Institute, University of Basel, Basel, Switzerland
| | | | | | | | - Trevor Pesout
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA
| | | | | | | | | | | | - Ivan Sović
- Pacific Biosciences, Menlo Park, CA, USA
- Digital BioLogic, Ivanić-Grad, Croatia
| | | | - Zemin Ning
- Wellcome Sanger Institute, Cambridge, UK
| | | | - Joyce Lee
- Bionano Genomics, San Diego, CA, USA
| | | | - Richard E Green
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA
- Dovetail Genomics, Santa Cruz, CA, USA
| | | | - Ivo Gut
- CNAG-CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
| | - Jay Ghurye
- Dovetail Genomics, Santa Cruz, CA, USA
- Department of Computer Science, University of Maryland College Park, College Park, MD, USA
| | - Erik Garrison
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA
| | - Ying Sims
- Wellcome Sanger Institute, Cambridge, UK
| | | | | | | | | | | | | | - Dengfeng Guan
- Department of Genetics, University of Cambridge, Cambridge, UK
- School of Computer Science and Technology, Center for Bioinformatics, Harbin Institute of Technology, Harbin, China
| | - Sarah E London
- Department of Psychology, Institute for Mind and Biology, University of Chicago, Chicago, IL, USA
| | - David F Clayton
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC, USA
| | - Claudio V Mello
- Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, OR, USA
| | - Samantha R Friedrich
- Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, OR, USA
| | - Peter V Lovell
- Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, OR, USA
| | - Ekaterina Osipova
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- Center for Systems Biology, Dresden, Germany
- Max Planck Institute for the Physics of Complex Systems, Dresden, Germany
| | - Farooq O Al-Ajli
- Monash University Malaysia Genomics Facility, School of Science, Selangor Darul Ehsan, Malaysia
- Tropical Medicine and Biology Multidisciplinary Platform, Monash University Malaysia, Selangor Darul Ehsan, Malaysia
- Qatar Falcon Genome Project, Doha, Qatar
| | | | - Heebal Kim
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
- eGnome, Inc., Seoul, Republic of Korea
| | | | - Michael Hiller
- LOEWE Centre for Translational Biodiversity Genomics, Frankfurt, Germany
- Senckenberg Research Institute, Frankfurt, Germany
- Goethe-University, Faculty of Biosciences, Frankfurt, Germany
| | | | - Robert S Harris
- Department of Biology, Pennsylvania State University, University Park, PA, USA
| | - Kateryna D Makova
- Department of Biology, Pennsylvania State University, University Park, PA, USA
- Center for Medical Genomics, Pennsylvania State University, University Park, PA, USA
- Center for Computational Biology and Bioinformatics, Pennsylvania State University, University Park, PA, USA
| | - Paul Medvedev
- Center for Medical Genomics, Pennsylvania State University, University Park, PA, USA
- Center for Computational Biology and Bioinformatics, Pennsylvania State University, University Park, PA, USA
- Department of Computer Science and Engineering, Pennsylvania State University, University Park, PA, USA
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA
| | - Jinna Hoffman
- National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD, USA
| | - Patrick Masterson
- National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD, USA
| | - Karen Clark
- National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD, USA
| | - Fergal Martin
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Kevin Howe
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Brian P Walenz
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Woori Kwak
- eGnome, Inc., Seoul, Republic of Korea
- Hoonygen, Seoul, Korea
| | - Hiram Clawson
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA
| | - Mark Diekhans
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA
| | - Luis Nassar
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA
| | - Benedict Paten
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA
| | - Robert H S Kraus
- Department of Biology, University of Konstanz, Konstanz, Germany
- Department of Migration, Max Planck Institute of Animal Behavior, Radolfzell, Germany
| | - Andrew J Crawford
- Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
| | - M Thomas P Gilbert
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
- University Museum, NTNU, Trondheim, Norway
| | - Guojie Zhang
- China National Genebank, BGI-Shenzhen, Shenzhen, China
- Villum Center for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| | - Byrappa Venkatesh
- Institute of Molecular and Cell Biology, A*STAR, Biopolis, Singapore, Singapore
| | - Robert W Murphy
- Centre for Biodiversity, Royal Ontario Museum, Toronto, Ontario, Canada
| | - Klaus-Peter Koepfli
- Smithsonian Conservation Biology Institute, Center for Species Survival, National Zoological Park, Washington, DC, USA
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Warren E Johnson
- Smithsonian Conservation Biology Institute, Center for Species Survival, National Zoological Park, Washington, DC, USA
- The Walter Reed Biosystematics Unit, Museum Support Center MRC-534, Smithsonian Institution, Suitland, MD, USA
- Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Federica Di Palma
- Department of Biological Sciences, Earlham Institute, University of East Anglia, Norwich, UK
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Barcelona, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), Barcelona, Spain
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Emma C Teeling
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - Tandy Warnow
- Department of Computer Science, The University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | | | - Oliver A Ryder
- San Diego Zoo Global, Escondido, CA, USA
- Department of Evolution, Behavior, and Ecology, University of California San Diego, La Jolla, CA, USA
| | - David Haussler
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Stephen J O'Brien
- Laboratory of Genomics Diversity-Center for Computer Technologies, ITMO University, St. Petersburg, Russian Federation
- Guy Harvey Oceanographic Center, Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, Fort Lauderdale, FL, USA
| | | | - Harris A Lewin
- The Genome Center, University of California Davis, Davis, CA, USA
- Department of Evolution and Ecology, University of California Davis, Davis, CA, USA
- John Muir Institute for the Environment, University of California Davis, Davis, CA, USA
| | | | - Eugene W Myers
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.
- Center for Systems Biology, Dresden, Germany.
- Faculty of Computer Science, Technical University Dresden, Dresden, Germany.
| | - Richard Durbin
- Department of Genetics, University of Cambridge, Cambridge, UK.
- Wellcome Sanger Institute, Cambridge, UK.
| | - Adam M Phillippy
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
| | - 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.
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25
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Comparative Mapping of the Macrochromosomes of Eight Avian Species Provides Further Insight into Their Phylogenetic Relationships and Avian Karyotype Evolution. Cells 2021; 10:cells10020362. [PMID: 33572408 PMCID: PMC7916199 DOI: 10.3390/cells10020362] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 01/30/2021] [Accepted: 02/02/2021] [Indexed: 11/17/2022] Open
Abstract
Avian genomes typically consist of ~10 pairs of macro- and ~30 pairs of microchromosomes. While inter-chromosomally, a pattern emerges of very little change (with notable exceptions) throughout evolution, intrachromosomal changes remain relatively poorly studied. To rectify this, here we use a pan-avian universally hybridising set of 74 chicken bacterial artificial chromosome (BAC) probes on the macrochromosomes of eight bird species: common blackbird, Atlantic canary, Eurasian woodcock, helmeted guinea fowl, houbara bustard, mallard duck, and rock dove. A combination of molecular cytogenetic, bioinformatics, and mathematical analyses allowed the building of comparative cytogenetic maps, reconstruction of a putative Neognathae ancestor, and assessment of chromosome rearrangement patterns and phylogenetic relationships in the studied neognath lineages. We observe that, as with our previous studies, chicken appears to have the karyotype most similar to the ancestor; however, previous reports of an increased rate of intrachromosomal change in Passeriformes (songbirds) appear not to be the case in our dataset. The use of this universally hybridizing probe set is applicable not only for the re-tracing of avian karyotype evolution but, potentially, for reconstructing genome assemblies.
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26
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Abstract
The study of chromosome evolution is undergoing a resurgence of interest owing to advances in DNA sequencing technology that facilitate the production of chromosome-scale whole-genome assemblies de novo. This review focuses on the history, methods, discoveries, and current challenges facing the field, with an emphasis on vertebrate genomes. A detailed examination of the literature on the biology of chromosome rearrangements is presented, specifically the relationship between chromosome rearrangements and phenotypic evolution, adaptation, and speciation. A critical review of the methods for identifying, characterizing, and visualizing chromosome rearrangements and computationally reconstructing ancestral karyotypes is presented. We conclude by looking to the future, identifying the enormous technical and scientific challenges presented by the accumulation of hundreds and eventually thousands of chromosome-scale assemblies.
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Affiliation(s)
- Joana Damas
- The Genome Center, University of California, Davis, California 95616, USA; , ,
| | - Marco Corbo
- The Genome Center, University of California, Davis, California 95616, USA; , ,
| | - Harris A Lewin
- The Genome Center, University of California, Davis, California 95616, USA; , , .,Department of Evolution and Ecology, College of Biological Sciences, University of California, Davis, California 95616, USA
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27
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Ahmad SF, Singchat W, Jehangir M, Panthum T, Srikulnath K. Consequence of Paradigm Shift with Repeat Landscapes in Reptiles: Powerful Facilitators of Chromosomal Rearrangements for Diversity and Evolution. Genes (Basel) 2020; 11:E827. [PMID: 32708239 PMCID: PMC7397244 DOI: 10.3390/genes11070827] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 07/16/2020] [Accepted: 07/17/2020] [Indexed: 12/24/2022] Open
Abstract
Reptiles are notable for the extensive genomic diversity and species richness among amniote classes, but there is nevertheless a need for detailed genome-scale studies. Although the monophyletic amniotes have recently been a focus of attention through an increasing number of genome sequencing projects, the abundant repetitive portion of the genome, termed the "repeatome", remains poorly understood across different lineages. Consisting predominantly of transposable elements or mobile and satellite sequences, these repeat elements are considered crucial in causing chromosomal rearrangements that lead to genomic diversity and evolution. Here, we propose major repeat landscapes in representative reptilian species, highlighting their evolutionary dynamics and role in mediating chromosomal rearrangements. Distinct karyotype variability, which is typically a conspicuous feature of reptile genomes, is discussed, with a particular focus on rearrangements correlated with evolutionary reorganization of micro- and macrochromosomes and sex chromosomes. The exceptional karyotype variation and extreme genomic diversity of reptiles are used to test several hypotheses concerning genomic structure, function, and evolution.
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Affiliation(s)
- Syed Farhan Ahmad
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (S.F.A.); (W.S.); (M.J.); (T.P.)
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Worapong Singchat
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (S.F.A.); (W.S.); (M.J.); (T.P.)
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Maryam Jehangir
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (S.F.A.); (W.S.); (M.J.); (T.P.)
- Integrative Genomics Lab-LGI, Department of Structural and Functional Biology, Institute of Bioscience at Botucatu, São Paulo State University (UNESP), Botucatu 18618-689, Brazil
| | - Thitipong Panthum
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (S.F.A.); (W.S.); (M.J.); (T.P.)
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Kornsorn Srikulnath
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (S.F.A.); (W.S.); (M.J.); (T.P.)
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
- Center for Advanced Studies in Tropical Natural Resources, National Research University-Kasetsart University, Kasetsart University, Bangkok 10900, Thailand
- Center of Excellence on Agricultural Biotechnology (AG-BIO/PERDO-CHE), Bangkok 10900, Thailand
- Omics Center for Agriculture, Bioresources, Food and Health, Kasetsart University (OmiKU), Bangkok 10900, Thailand
- Amphibian Research Center, Hiroshima University, 1-3-1, Kagamiyama, Higashihiroshima 739-8526, Japan
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28
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Kretschmer R, Furo IDO, Gomes AJB, Kiazim LG, Gunski RJ, Garnero ADV, Pereira JC, Ferguson-Smith MA, de Oliveira EHC, Griffin DK, de Freitas TRO, O’Connor RE. A Comprehensive Cytogenetic Analysis of Several Members of the Family Columbidae (Aves, Columbiformes). Genes (Basel) 2020; 11:genes11060632. [PMID: 32521831 PMCID: PMC7349364 DOI: 10.3390/genes11060632] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 06/05/2020] [Accepted: 06/05/2020] [Indexed: 11/18/2022] Open
Abstract
The Columbidae species (Aves, Columbiformes) show considerable variation in their diploid numbers (2n = 68-86), but there is limited understanding of the events that shaped the extant karyotypes. Hence, we performed whole chromosome painting (wcp) for paints GGA1-10 and bacterial artificial chromosome (BAC) probes for chromosomes GGA11-28 for Columbina passerina, Columbina talpacoti, Patagioenas cayennensis, Geotrygon violacea and Geotrygon montana. Streptopelia decaocto was only investigated with paints because BACs for GGA10-28 had been previously analyzed. We also performed phylogenetic analyses in order to trace the evolutionary history of this family in light of chromosomal changes using our wcp data with chicken probes and from Zenaida auriculata, Columbina picui, Columba livia and Leptotila verreauxi, previously published. G-banding was performed on all these species. Comparative chromosome paint and G-banding results suggested that at least one interchromosomal and many intrachromosomal rearrangements had occurred in the diversification of Columbidae species. On the other hand, a high degree of conservation of microchromosome organization was observed in these species. Our cladistic analysis, considering all the chromosome rearrangements detected, provided strong support for L. verreauxi and P. cayennensis, G. montana and G. violacea, C. passerina and C. talpacoti having sister taxa relationships, as well as for all Columbidae species analyzed herein. Additionally, the chromosome characters were mapped in a consensus phylogenetic topology previously proposed, revealing a pericentric inversion in the chromosome homologous to GGA4 in a chromosomal signature unique to small New World ground doves.
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Affiliation(s)
- Rafael Kretschmer
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK; (L.G.K.); (D.K.G.);
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre 91509-900, Brazil;
- Correspondence:
| | - Ivanete de Oliveira Furo
- Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém 66075-110, Brazil;
- Laboratório de Cultura de Tecidos e Citogenética, SAMAM, Instituto Evandro Chagas, Ananindeua 67030-000, Brazil;
| | | | - Lucas G. Kiazim
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK; (L.G.K.); (D.K.G.);
| | - Ricardo José Gunski
- Laboratório de Diversidade Genética Animal, Universidade Federal do Pampa, São Gabriel 97300-162, Brazil; (R.J.G.); (A.d.V.G.)
| | - Analía del Valle Garnero
- Laboratório de Diversidade Genética Animal, Universidade Federal do Pampa, São Gabriel 97300-162, Brazil; (R.J.G.); (A.d.V.G.)
| | - Jorge C. Pereira
- Animal and Veterinary Research Centre (CECAV), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal;
| | - Malcolm A. Ferguson-Smith
- Cambridge Resource Centre for Comparative Genomics, University of Cambridge Department of Veterinary Medicine, Cambridge CB3 0ES, UK;
| | - Edivaldo Herculano Corrêa de Oliveira
- Laboratório de Cultura de Tecidos e Citogenética, SAMAM, Instituto Evandro Chagas, Ananindeua 67030-000, Brazil;
- Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belém 66075-110, Brazil
| | - Darren K. Griffin
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK; (L.G.K.); (D.K.G.);
| | | | - Rebecca E. O’Connor
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK; (L.G.K.); (D.K.G.);
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29
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Fishman V, Battulin N, Nuriddinov M, Maslova A, Zlotina A, Strunov A, Chervyakova D, Korablev A, Serov O, Krasikova A. 3D organization of chicken genome demonstrates evolutionary conservation of topologically associated domains and highlights unique architecture of erythrocytes' chromatin. Nucleic Acids Res 2019; 47:648-665. [PMID: 30418618 PMCID: PMC6344868 DOI: 10.1093/nar/gky1103] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 10/24/2018] [Indexed: 12/25/2022] Open
Abstract
How chromosomes are folded, spatially organized and regulated in three dimensions inside the cell nucleus are among the longest standing questions in cell biology. Genome-wide chromosome conformation capture (Hi-C) technique allowed identifying and characterizing spatial chromatin compartments in several mammalian species. Here, we present the first genome-wide analysis of chromatin interactions in chicken embryonic fibroblasts (CEF) and adult erythrocytes. We showed that genome of CEF is partitioned into topologically associated domains (TADs), distributed in accordance with gene density, transcriptional activity and CTCF-binding sites. In contrast to mammals, where all examined somatic cell types display relatively similar spatial organization of genome, chicken erythrocytes strongly differ from fibroblasts, showing pronounced A- and B- compartments, absence of typical TADs and formation of long-range chromatin interactions previously observed on mitotic chromosomes. Comparing mammalian and chicken genome architectures, we provide evidence highlighting evolutionary role of chicken TADs and their significance in genome activity and regulation.
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Affiliation(s)
- Veniamin Fishman
- Department of molecular mechanisms of ontogenesis, Institute of Cytology and Genetics, Novosibirsk 630099, Russia.,Department of Natural Science, Novosibirsk State University, Novosibirsk 630099, Russia
| | - Nariman Battulin
- Department of molecular mechanisms of ontogenesis, Institute of Cytology and Genetics, Novosibirsk 630099, Russia.,Department of Natural Science, Novosibirsk State University, Novosibirsk 630099, Russia
| | - Miroslav Nuriddinov
- Department of molecular mechanisms of ontogenesis, Institute of Cytology and Genetics, Novosibirsk 630099, Russia
| | - Antonina Maslova
- Saint-Petersburg State University, Saint-Petersburg 199034, Russia
| | - Anna Zlotina
- Saint-Petersburg State University, Saint-Petersburg 199034, Russia
| | - Anton Strunov
- Department of cell biology, Institute of Cytology and Genetics, Novosibirsk 630099, Russia
| | | | - Alexey Korablev
- Department of molecular mechanisms of ontogenesis, Institute of Cytology and Genetics, Novosibirsk 630099, Russia
| | - Oleg Serov
- Department of molecular mechanisms of ontogenesis, Institute of Cytology and Genetics, Novosibirsk 630099, Russia.,Department of Natural Science, Novosibirsk State University, Novosibirsk 630099, Russia
| | - Alla Krasikova
- Saint-Petersburg State University, Saint-Petersburg 199034, Russia
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30
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Boman J, Frankl-Vilches C, da Silva Dos Santos M, de Oliveira EHC, Gahr M, Suh A. The Genome of Blue-Capped Cordon-Bleu Uncovers Hidden Diversity of LTR Retrotransposons in Zebra Finch. Genes (Basel) 2019; 10:E301. [PMID: 31013951 PMCID: PMC6523648 DOI: 10.3390/genes10040301] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 04/05/2019] [Accepted: 04/05/2019] [Indexed: 02/02/2023] Open
Abstract
Avian genomes have perplexed researchers by being conservative in both size and rearrangements, while simultaneously holding the blueprints for a massive species radiation during the last 65 million years (My). Transposable elements (TEs) in bird genomes are relatively scarce but have been implicated as important hotspots for chromosomal inversions. In zebra finch (Taeniopygia guttata), long terminal repeat (LTR) retrotransposons have proliferated and are positively associated with chromosomal breakpoint regions. Here, we present the genome, karyotype and transposons of blue-capped cordon-bleu (Uraeginthus cyanocephalus), an African songbird that diverged from zebra finch at the root of estrildid finches 10 million years ago (Mya). This constitutes the third linked-read sequenced genome assembly and fourth in-depth curated TE library of any bird. Exploration of TE diversity on this brief evolutionary timescale constitutes a considerable increase in resolution for avian TE biology and allowed us to uncover 4.5 Mb more LTR retrotransposons in the zebra finch genome. In blue-capped cordon-bleu, we likewise observed a recent LTR accumulation indicating that this is a shared feature of Estrildidae. Curiously, we discovered 25 new endogenous retrovirus-like LTR retrotransposon families of which at least 21 are present in zebra finch but were previously undiscovered. This highlights the importance of studying close relatives of model organisms.
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Affiliation(s)
- Jesper Boman
- Department of Evolutionary Biology, Evolutionary Biology Centre (EBC), Science for Life Laboratory, Uppsala University, SE-752 36 Uppsala, Sweden.
| | - Carolina Frankl-Vilches
- Department of Behavioral Neurobiology, Max Planck Institute for Ornithology, 82319 Seewiesen, Germany.
| | - Michelly da Silva Dos Santos
- Laboratório de Cultura de Tecidos e Citogenética, SAMAM, Instituto Evandro Chagas, Ananindeua, Pará, and Faculdade de Ciências Naturais (ICEN), Universidade Federal do Pará, Belém 66075-110, Brazil.
| | - Edivaldo H C de Oliveira
- Laboratório de Cultura de Tecidos e Citogenética, SAMAM, Instituto Evandro Chagas, Ananindeua, Pará, and Faculdade de Ciências Naturais (ICEN), Universidade Federal do Pará, Belém 66075-110, Brazil.
| | - Manfred Gahr
- Department of Behavioral Neurobiology, Max Planck Institute for Ornithology, 82319 Seewiesen, Germany.
| | - Alexander Suh
- Department of Evolutionary Biology, Evolutionary Biology Centre (EBC), Science for Life Laboratory, Uppsala University, SE-752 36 Uppsala, Sweden.
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31
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Griffin DK, Larkin DM, O'Connor RE. Time lapse: A glimpse into prehistoric genomics. Eur J Med Genet 2019; 63:103640. [PMID: 30922926 PMCID: PMC7026692 DOI: 10.1016/j.ejmg.2019.03.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 03/10/2019] [Indexed: 11/28/2022]
Abstract
For the purpose of this review, ‘time-lapse’ refers to the reconstruction of ancestral (in this case dinosaur) karyotypes using genome assemblies of extant species. Such reconstructions are only usually possible when genomes are assembled to ‘chromosome level’ i.e. a complete representation of all the sequences, correctly ordered contiguously on each of the chromosomes. Recent paleontological evidence is very clear that birds are living dinosaurs, the latest example of dinosaurs emerging from a catastrophic extinction event. Non-avian dinosaurs (ever present in the public imagination through art, and broadcast media) emerged some 240 million years ago and have displayed incredible phenotypic diversity. Here we report on our recent studies to infer the overall karyotype of the Theropod dinosaur lineage from extant avian chromosome level genome assemblies. Our work first focused on determining the likely karyotype of the avian ancestor (most likely a chicken-sized, two-legged, feathered, land dinosaur from the Jurassic period) finding karyotypic similarity to the chicken. We then took the work further to determine the likely karyotype of the bird-lizard ancestor and the chromosomal changes (chiefly translocations and inversions) that occurred between then and modern birds. A combination of bioinformatics and cross-species fluorescence in situ hybridization (zoo-FISH) uncovered a considerable number of translocations and fissions from a ‘lizard-like’ genome structure of 2n = 36–46 to one similar to that of soft-shelled turtles (2n = 66) from 275 to 255 million years ago (mya). Remarkable karyotypic similarities between some soft-shelled turtles and chicken suggests that there were few translocations from the bird-turtle ancestor (plus ∼7 fissions) through the dawn of the dinosaurs and pterosaurs, through the theropod linage and on to most to modern birds. In other words, an avian-like karyotype was in place about 240mya when the dinosaurs and pterosaurs first emerged. We mapped 49 chromosome inversions from then to the present day, uncovering some gene ontology enrichment in evolutionary breakpoint regions. This avian-like karyotype with its many (micro)chromosomes provides the basis for variation (the driver of natural selection) through increased random segregation and recombination. It may therefore contribute to the ability of dinosaurs to survive multiple extinction events, emerging each time as speciose and diverse.
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Affiliation(s)
- Darren K Griffin
- School of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK.
| | - Denis M Larkin
- Department of Comparative Biomedical Sciences, Royal Veterinary College, University of London, London, NW1 0TU, UK.
| | - Rebecca E O'Connor
- School of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK. R.O'
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32
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Farré M, Kim J, Proskuryakova AA, Zhang Y, Kulemzina AI, Li Q, Zhou Y, Xiong Y, Johnson JL, Perelman PL, Johnson WE, Warren WC, Kukekova AV, Zhang G, O'Brien SJ, Ryder OA, Graphodatsky AS, Ma J, Lewin HA, Larkin DM. Evolution of gene regulation in ruminants differs between evolutionary breakpoint regions and homologous synteny blocks. Genome Res 2019; 29:576-589. [PMID: 30760546 PMCID: PMC6442394 DOI: 10.1101/gr.239863.118] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 02/08/2019] [Indexed: 02/02/2023]
Abstract
The role of chromosome rearrangements in driving evolution has been a long-standing question of evolutionary biology. Here we focused on ruminants as a model to assess how rearrangements may have contributed to the evolution of gene regulation. Using reconstructed ancestral karyotypes of Cetartiodactyls, Ruminants, Pecorans, and Bovids, we traced patterns of gross chromosome changes. We found that the lineage leading to the ruminant ancestor after the split from other cetartiodactyls was characterized by mostly intrachromosomal changes, whereas the lineage leading to the pecoran ancestor (including all livestock ruminants) included multiple interchromosomal changes. We observed that the liver cell putative enhancers in the ruminant evolutionary breakpoint regions are highly enriched for DNA sequences under selective constraint acting on lineage-specific transposable elements (TEs) and a set of 25 specific transcription factor (TF) binding motifs associated with recently active TEs. Coupled with gene expression data, we found that genes near ruminant breakpoint regions exhibit more divergent expression profiles among species, particularly in cattle, which is consistent with the phylogenetic origin of these breakpoint regions. This divergence was significantly greater in genes with enhancers that contain at least one of the 25 specific TF binding motifs and located near bovidae-to-cattle lineage breakpoint regions. Taken together, by combining ancestral karyotype reconstructions with analysis of cis regulatory element and gene expression evolution, our work demonstrated that lineage-specific regulatory elements colocalized with gross chromosome rearrangements may have provided valuable functional modifications that helped to shape ruminant evolution.
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Affiliation(s)
- Marta Farré
- Royal Veterinary College, University of London, London NW1 0TU, United Kingdom
| | - Jaebum Kim
- Department of Biomedical Science and Engineering, Konkuk University, Seoul 05029, Korea
| | - Anastasia A Proskuryakova
- Institute of Molecular and Cellular Biology, SB RAS, Novosibirsk 630090, Russia.,Synthetic Biology Unit, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Yang Zhang
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
| | | | - Qiye Li
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Yang Zhou
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Yingqi Xiong
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Jennifer L Johnson
- Department of Animal Sciences, College of Agricultural, Consumer and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Polina L Perelman
- Institute of Molecular and Cellular Biology, SB RAS, Novosibirsk 630090, Russia.,Synthetic Biology Unit, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Warren E Johnson
- Smithsonian Conservation Biology Institute, National Zoological Park, Front Royal, Virginia 22630, USA.,Walter Reed Biosystematics Unit, Museum Support Center, Smithsonian Institution, Suitland, Maryland 20746, USA
| | - Wesley C Warren
- Bond Life Sciences Center, University of Missouri, Columbia, Missouri 63201, USA
| | - Anna V Kukekova
- Department of Animal Sciences, College of Agricultural, Consumer and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Guojie Zhang
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China.,State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.,Centre for Social Evolution, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Stephen J O'Brien
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg 199004, Russia.,Guy Harvey Oceanographic Center, Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, Fort Lauderdale, Florida 33004, USA
| | - Oliver A Ryder
- Institute for Conservation Research, San Diego Zoo, Escondido, California 92027, USA
| | - Alexander S Graphodatsky
- Institute of Molecular and Cellular Biology, SB RAS, Novosibirsk 630090, Russia.,Synthetic Biology Unit, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Jian Ma
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
| | - Harris A Lewin
- Department of Evolution and Ecology and the UC Davis Genome Center, University of California, Davis, California 95616, USA
| | - Denis M Larkin
- Royal Veterinary College, University of London, London NW1 0TU, United Kingdom.,The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), Novosibirsk 630090, Russia
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33
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Ruvinskiy D, Larkin DM, Farré M. A Near Chromosome Assembly of the Dromedary Camel Genome. Front Genet 2019; 10:32. [PMID: 30804979 PMCID: PMC6371769 DOI: 10.3389/fgene.2019.00032] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 01/17/2019] [Indexed: 01/11/2023] Open
Abstract
The dromedary camel is an economically and socially important species of livestock in many parts of the world, being used for transport and the production of milk and meat. Much like cattle and horses, the camel may be found in industrial farming conditions as well as used in sporting. Camel racing is a multi-million dollar industry, with some specimens being valued at upward of 9.5 million USD. Despite its apparent value to humans, the dromedary camel is a neglected species in genomics. While cattle and other domesticated species have had much attention in terms of genome assembly, the camel has only been assembled to scaffold level, which does not give a clear indication of the order or chromosomal location of sequenced fragments. In this study, the Reference Assistant Chromosome Assembly (RACA) algorithm was implemented to use read-pair information of camel scaffolds, aligned with the cattle and human genomes in order to organize and orient these scaffolds in a near-chromosome level assembly. This method generated 72 large size fragments (N50 54.36 Mb). These predicted chromosome fragments (PCFs) were then compared with comparative maps of camel and cytogenetic map of alpaca chromosomes, allowing us to further upgrade the assembly. This dromedary camel assembly will be an invaluable tool to verify future camel assemblies generated with chromatin conformation or/and long read technologies. This study provides the first near-chromosome assembly of the dromedary camel, thus adding this economically important species to a growing pool of knowledge regarding the genome structure of domesticated livestock.
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Affiliation(s)
- Daniil Ruvinskiy
- Comparative Biomedical Sciences, Royal Veterinary College, University of London, London, United Kingdom
| | - Denis M Larkin
- Comparative Biomedical Sciences, Royal Veterinary College, University of London, London, United Kingdom.,The Federal Research Center, Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Marta Farré
- Comparative Biomedical Sciences, Royal Veterinary College, University of London, London, United Kingdom.,School of Biosciences, University of Kent, Canterbury, United Kingdom
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34
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O'Connor RE, Kiazim L, Skinner B, Fonseka G, Joseph S, Jennings R, Larkin DM, Griffin DK. Patterns of microchromosome organization remain highly conserved throughout avian evolution. Chromosoma 2018; 128:21-29. [PMID: 30448925 PMCID: PMC6394684 DOI: 10.1007/s00412-018-0685-6] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 10/31/2018] [Accepted: 11/05/2018] [Indexed: 01/08/2023]
Abstract
The structure and organization of a species genome at a karyotypic level, and in interphase nuclei, have broad functional significance. Although regular sized chromosomes are studied extensively in this regard, microchromosomes, which are present in many terrestrial vertebrates, remain poorly explored. Birds have more cytologically indistinguishable microchromosomes (~ 30 pairs) than other vertebrates; however, the degree to which genome organization patterns at a karyotypic and interphase level differ between species is unknown. In species where microchromosomes have fused to other chromosomes, they retain genomic features such as gene density and GC content; however, the extent to which they retain a central nuclear position has not been investigated. In studying 22 avian species from 10 orders, we established that, other than in species where microchromosomal fusion is obvious (Falconiformes and Psittaciformes), there was no evidence of microchromosomal rearrangement, suggesting an evolutionarily stable avian genome (karyotypic) organization. Moreover, in species where microchromosomal fusion has occurred, they retain a central nuclear location, suggesting that the nuclear position of microchromosomes is a function of their genomic features rather than their physical size.
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Affiliation(s)
- Rebecca E O'Connor
- School of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK. r.o'
| | - Lucas Kiazim
- School of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK
| | - Ben Skinner
- Department of Pathology, Cambridge University, Cambridge, CB2 1QP, UK
| | - Gothami Fonseka
- Cytocell Ltd, 3-4 Technopark Newmarket Road Cambridge, Cambridge, CB5 8PB, UK
| | - Sunitha Joseph
- School of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK
| | - Rebecca Jennings
- School of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK
| | - Denis M Larkin
- Department of Comparative Biomedical Sciences, Royal Veterinary College, University of London, London, NW1 0TU, UK
| | - Darren K Griffin
- School of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK
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35
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O’Connor RE, Farré M, Joseph S, Damas J, Kiazim L, Jennings R, Bennett S, Slack EA, Allanson E, Larkin DM, Griffin DK. Chromosome-level assembly reveals extensive rearrangement in saker falcon and budgerigar, but not ostrich, genomes. Genome Biol 2018; 19:171. [PMID: 30355328 PMCID: PMC6201548 DOI: 10.1186/s13059-018-1550-x] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 09/24/2018] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND The number of de novo genome sequence assemblies is increasing exponentially; however, relatively few contain one scaffold/contig per chromosome. Such assemblies are essential for studies of genotype-to-phenotype association, gross genomic evolution, and speciation. Inter-species differences can arise from chromosomal changes fixed during evolution, and we previously hypothesized that a higher fraction of elements under negative selection contributed to avian-specific phenotypes and avian genome organization stability. The objective of this study is to generate chromosome-level assemblies of three avian species (saker falcon, budgerigar, and ostrich) previously reported as karyotypically rearranged compared to most birds. We also test the hypothesis that the density of conserved non-coding elements is associated with the positions of evolutionary breakpoint regions. RESULTS We used reference-assisted chromosome assembly, PCR, and lab-based molecular approaches, to generate chromosome-level assemblies of the three species. We mapped inter- and intrachromosomal changes from the avian ancestor, finding no interchromosomal rearrangements in the ostrich genome, despite it being previously described as chromosomally rearranged. We found that the average density of conserved non-coding elements in evolutionary breakpoint regions is significantly reduced. Fission evolutionary breakpoint regions have the lowest conserved non-coding element density, and intrachromomosomal evolutionary breakpoint regions have the highest. CONCLUSIONS The tools used here can generate inexpensive, efficient chromosome-level assemblies, with > 80% assigned to chromosomes, which is comparable to genomes assembled using high-density physical or genetic mapping. Moreover, conserved non-coding elements are important factors in defining where rearrangements, especially interchromosomal, are fixed during evolution without deleterious effects.
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Affiliation(s)
| | - Marta Farré
- Department of Comparative Biomedical Sciences, Royal Veterinary College, University of London, London, UK
| | - Sunitha Joseph
- School of Biosciences, University of Kent, Canterbury, UK
| | - Joana Damas
- Department of Comparative Biomedical Sciences, Royal Veterinary College, University of London, London, UK
| | - Lucas Kiazim
- School of Biosciences, University of Kent, Canterbury, UK
| | | | - Sophie Bennett
- School of Biosciences, University of Kent, Canterbury, UK
| | - Eden A Slack
- Department of Comparative Biomedical Sciences, Royal Veterinary College, University of London, London, UK
| | - Emily Allanson
- Department of Comparative Biomedical Sciences, Royal Veterinary College, University of London, London, UK
| | - Denis M Larkin
- Department of Comparative Biomedical Sciences, Royal Veterinary College, University of London, London, UK
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36
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Chromosome Level Genome Assembly and Comparative Genomics between Three Falcon Species Reveals an Unusual Pattern of Genome Organisation. DIVERSITY-BASEL 2018. [DOI: 10.3390/d10040113] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Whole genome assemblies are crucial for understanding a wide range of aspects of falcon biology, including morphology, ecology, and physiology, and are thus essential for their care and conservation. A key aspect of the genome of any species is its karyotype, which can then be linked to the whole genome sequence to generate a so-called chromosome-level assembly. Chromosome-level assemblies are essential for marker assisted selection and genotype-phenotype correlations in breeding regimes, as well as determining patterns of gross genomic evolution. To date, only two falcon species have been sequenced and neither initially were assembled to the chromosome level. Falcons have atypical avian karyotypes with fewer chromosomes than other birds, presumably brought about by wholesale fusion. To date, however, published chromosome preparations are of poor quality, few chromosomes have been distinguished and standard ideograms have not been made. The purposes of this study were to generate analyzable karyotypes and ideograms of peregrine, saker, and gyr falcons, report on our recent generation of chromosome level sequence assemblies of peregrine and saker falcons, and for the first time, sequence the gyr falcon genome. Finally, we aimed to generate comparative genomic data between all three species and the reference chicken genome. Results revealed a diploid number of 2n = 50 for peregrine falcon and 2n = 52 for saker and gyr through high quality banded chromosomes. Standard ideograms that are generated here helped to map predicted chromosomal fragments (PCFs) from the genome sequences directly to chromosomes and thus generate chromosome level sequence assemblies for peregrine and saker falcons. Whole genome sequencing was successful in gyr falcon, but read depth and coverage was not sufficient to generate a chromosome level assembly. Nonetheless, comparative genomics revealed no differences in genome organization between gyr and saker falcons. When compared to peregrine falcon, saker/gyr differed by one interchromosomal and seven intrachromosomal rearrangements (a fusion plus seven inversions), whereas peregrine and saker/gyr differ from the reference chicken genome by 14/13 fusions (11 microchromosomal) and six fissions. The chromosomal differences between the species could potentially provide the basis of a screening test for hybrid animals.
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Damas J, Kim J, Farré M, Griffin DK, Larkin DM. Reconstruction of avian ancestral karyotypes reveals differences in the evolutionary history of macro- and microchromosomes. Genome Biol 2018; 19:155. [PMID: 30290830 PMCID: PMC6173868 DOI: 10.1186/s13059-018-1544-8] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 09/18/2018] [Indexed: 11/29/2022] Open
Abstract
Background Reconstruction of ancestral karyotypes is critical for our understanding of genome evolution, allowing for the identification of the gross changes that shaped extant genomes. The identification of such changes and their time of occurrence can shed light on the biology of each species, clade and their evolutionary history. However, this is impeded by both the fragmented nature of the majority of genome assemblies and the limitations of the available software to work with them. These limitations are particularly apparent in birds, with only 10 chromosome-level assemblies reported thus far. Algorithmic approaches applied to fragmented genome assemblies can nonetheless help define patterns of chromosomal change in defined taxonomic groups. Results Here, we make use of the DESCHRAMBLER algorithm to perform the first large-scale study of ancestral chromosome structure and evolution in birds. This algorithm allows us to reconstruct the overall genome structure of 14 key nodes of avian evolution from the Avian ancestor to the ancestor of the Estrildidae, Thraupidae and Fringillidae families. Conclusions Analysis of these reconstructions provides important insights into the variability of rearrangement rates during avian evolution and allows the detection of patterns related to the chromosome distribution of evolutionary breakpoint regions. Moreover, the inclusion of microchromosomes in our reconstructions allows us to provide novel insights into the evolution of these avian chromosomes, specifically. Electronic supplementary material The online version of this article (10.1186/s13059-018-1544-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Joana Damas
- Department of Comparative Biomedical Sciences, Royal Veterinary College, University of London, London, NW1 0TU, UK
| | - Jaebum Kim
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029, South Korea
| | - Marta Farré
- Department of Comparative Biomedical Sciences, Royal Veterinary College, University of London, London, NW1 0TU, UK
| | - Darren K Griffin
- School of Biosciences, University of Kent, Canterbury, CT2 7NY, UK
| | - Denis M Larkin
- Department of Comparative Biomedical Sciences, Royal Veterinary College, University of London, London, NW1 0TU, UK.
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O'Connor RE, Romanov MN, Kiazim LG, Barrett PM, Farré M, Damas J, Ferguson-Smith M, Valenzuela N, Larkin DM, Griffin DK. Reconstruction of the diapsid ancestral genome permits chromosome evolution tracing in avian and non-avian dinosaurs. Nat Commun 2018; 9:1883. [PMID: 29784931 PMCID: PMC5962605 DOI: 10.1038/s41467-018-04267-9] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 04/12/2018] [Indexed: 01/07/2023] Open
Abstract
Genomic organisation of extinct lineages can be inferred from extant chromosome-level genome assemblies. Here, we apply bioinformatic and molecular cytogenetic approaches to determine the genomic structure of the diapsid common ancestor. We then infer the events that likely occurred along this lineage from theropod dinosaurs through to modern birds. Our results suggest that most elements of a typical ‘avian-like’ karyotype (40 chromosome pairs, including 30 microchromosomes) were in place before the divergence of turtles from birds ~255 mya. This genome organisation therefore predates the emergence of early dinosaurs and pterosaurs and the evolution of flight. Remaining largely unchanged interchromosomally through the dinosaur–theropod route that led to modern birds, intrachromosomal changes nonetheless reveal evolutionary breakpoint regions enriched for genes with ontology terms related to chromatin organisation and transcription. This genomic structure therefore appears highly stable yet contributes to a large degree of phenotypic diversity, as well as underpinning adaptive responses to major environmental disruptions via intrachromosomal repatterning. Ancient diapsids diverged into the lineages leading to turtles and birds over 250 million years ago. Here, the authors use genomic and molecular cytogenetic analyses of modern species to infer the genome structure of the diapsid common ancestor (DCA) and the changes occurring along the lineage to birds through theropod dinosaurs.
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Affiliation(s)
- Rebecca E O'Connor
- School of Biosciences, University of Kent, Canterbury, Kent, CT2 7NJ, UK
| | - Michael N Romanov
- School of Biosciences, University of Kent, Canterbury, Kent, CT2 7NJ, UK
| | - Lucas G Kiazim
- School of Biosciences, University of Kent, Canterbury, Kent, CT2 7NJ, UK
| | - Paul M Barrett
- Department of Earth Sciences, Natural History Museum, Cromwell Road, London, SW7 5BD, UK
| | - Marta Farré
- Department of Comparative Biomedical Sciences, Royal Veterinary College, University of London, London, NW1 0TU, UK
| | - Joana Damas
- Department of Comparative Biomedical Sciences, Royal Veterinary College, University of London, London, NW1 0TU, UK
| | | | - Nicole Valenzuela
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Iowa, IA, 50011, USA
| | - Denis M Larkin
- Department of Comparative Biomedical Sciences, Royal Veterinary College, University of London, London, NW1 0TU, UK
| | - Darren K Griffin
- School of Biosciences, University of Kent, Canterbury, Kent, CT2 7NJ, UK.
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Capilla L, Sánchez-Guillén RA, Farré M, Paytuví-Gallart A, Malinverni R, Ventura J, Larkin DM, Ruiz-Herrera A. Mammalian Comparative Genomics Reveals Genetic and Epigenetic Features Associated with Genome Reshuffling in Rodentia. Genome Biol Evol 2018; 8:3703-3717. [PMID: 28175287 PMCID: PMC5521730 DOI: 10.1093/gbe/evw276] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/08/2016] [Indexed: 12/16/2022] Open
Abstract
Understanding how mammalian genomes have been reshuffled through structural changes is fundamental to the dynamics of its composition, evolutionary relationships between species and, in the long run, speciation. In this work, we reveal the evolutionary genomic landscape in Rodentia, the most diverse and speciose mammalian order, by whole-genome comparisons of six rodent species and six representative outgroup mammalian species. The reconstruction of the evolutionary breakpoint regions across rodent phylogeny shows an increased rate of genome reshuffling that is approximately two orders of magnitude greater than in other mammalian species here considered. We identified novel lineage and clade-specific breakpoint regions within Rodentia and analyzed their gene content, recombination rates and their relationship with constitutive lamina genomic associated domains, DNase I hypersensitivity sites and chromatin modifications. We detected an accumulation of protein-coding genes in evolutionary breakpoint regions, especially genes implicated in reproduction and pheromone detection and mating. Moreover, we found an association of the evolutionary breakpoint regions with active chromatin state landscapes, most probably related to gene enrichment. Our results have two important implications for understanding the mechanisms that govern and constrain mammalian genome evolution. The first is that the presence of genes related to species-specific phenotypes in evolutionary breakpoint regions reinforces the adaptive value of genome reshuffling. Second, that chromatin conformation, an aspect that has been often overlooked in comparative genomic studies, might play a role in modeling the genomic distribution of evolutionary breakpoints.
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Affiliation(s)
- Laia Capilla
- Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina (IBB), Universitat Autònoma de Barcelona (UAB), Barcelona, Spain.,Departament de Biologia Animal, Biologia Vegetal i Ecologia, Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
| | - Rosa Ana Sánchez-Guillén
- Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina (IBB), Universitat Autònoma de Barcelona (UAB), Barcelona, Spain.,Biología Evolutiva, Instituto de Ecología A.C, Xalapa, Veracruz, Apartado, Mexico
| | - Marta Farré
- Biología Evolutiva, Instituto de Ecología A.C, Xalapa, Veracruz, Apartado, Mexico
| | - Andreu Paytuví-Gallart
- Department of Comparative Biomedical Sciences, The Royal Veterinary College, London, UK.,Sequentia Biotech S.L. Calle Comte d'Urgell, Barcelona, Spain
| | - Roberto Malinverni
- Departament de Biologia Cel·lular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
| | - Jacint Ventura
- Departament de Biologia Animal, Biologia Vegetal i Ecologia, Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
| | - Denis M Larkin
- Biología Evolutiva, Instituto de Ecología A.C, Xalapa, Veracruz, Apartado, Mexico
| | - Aurora Ruiz-Herrera
- Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina (IBB), Universitat Autònoma de Barcelona (UAB), Barcelona, Spain.,Sequentia Biotech S.L. Calle Comte d'Urgell, Barcelona, Spain
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40
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Suh A, Smeds L, Ellegren H. Abundant recent activity of retrovirus-like retrotransposons within and among flycatcher species implies a rich source of structural variation in songbird genomes. Mol Ecol 2017; 27:99-111. [DOI: 10.1111/mec.14439] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 11/01/2017] [Accepted: 11/06/2017] [Indexed: 01/01/2023]
Affiliation(s)
- Alexander Suh
- Department of Evolutionary Biology; Evolutionary Biology Centre (EBC); Uppsala University; Uppsala Sweden
| | - Linnéa Smeds
- Department of Evolutionary Biology; Evolutionary Biology Centre (EBC); Uppsala University; Uppsala Sweden
| | - Hans Ellegren
- Department of Evolutionary Biology; Evolutionary Biology Centre (EBC); Uppsala University; Uppsala Sweden
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41
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Zlotina A, Dedukh D, Krasikova A. Amphibian and Avian Karyotype Evolution: Insights from Lampbrush Chromosome Studies. Genes (Basel) 2017; 8:genes8110311. [PMID: 29117127 PMCID: PMC5704224 DOI: 10.3390/genes8110311] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 10/29/2017] [Accepted: 10/31/2017] [Indexed: 01/04/2023] Open
Abstract
Amphibian and bird karyotypes typically have a complex organization, which makes them difficult for standard cytogenetic analysis. That is, amphibian chromosomes are generally large, enriched with repetitive elements, and characterized by the absence of informative banding patterns. The majority of avian karyotypes comprise a small number of relatively large macrochromosomes and numerous tiny morphologically undistinguishable microchromosomes. A good progress in investigation of amphibian and avian chromosome evolution became possible with the usage of giant lampbrush chromosomes typical for growing oocytes. Due to the giant size, peculiarities of organization and enrichment with cytological markers, lampbrush chromosomes can serve as an opportune model for comprehensive high-resolution cytogenetic and cytological investigations. Here, we review the main findings on chromosome evolution in amphibians and birds that were obtained using lampbrush chromosomes. In particular, we discuss the data on evolutionary chromosomal rearrangements, accumulation of polymorphisms, evolution of sex chromosomes as well as chromosomal changes during clonal reproduction of interspecies hybrids.
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Affiliation(s)
- Anna Zlotina
- Saint-Petersburg State University, Saint-Petersburg 199034, Russia.
| | - Dmitry Dedukh
- Saint-Petersburg State University, Saint-Petersburg 199034, Russia.
| | - Alla Krasikova
- Saint-Petersburg State University, Saint-Petersburg 199034, Russia.
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42
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Abstract
Whole-genome assemblies of 19 placental mammals and two outgroup species were used to reconstruct the order and orientation of syntenic fragments in chromosomes of the eutherian ancestor and six other descendant ancestors leading to human. For ancestral chromosome reconstructions, we developed an algorithm (DESCHRAMBLER) that probabilistically determines the adjacencies of syntenic fragments using chromosome-scale and fragmented genome assemblies. The reconstructed chromosomes of the eutherian, boreoeutherian, and euarchontoglires ancestor each included >80% of the entire length of the human genome, whereas reconstructed chromosomes of the most recent common ancestor of simians, catarrhini, great apes, and humans and chimpanzees included >90% of human genome sequence. These high-coverage reconstructions permitted reliable identification of chromosomal rearrangements over ∼105 My of eutherian evolution. Orangutan was found to have eight chromosomes that were completely conserved in homologous sequence order and orientation with the eutherian ancestor, the largest number for any species. Ruminant artiodactyls had the highest frequency of intrachromosomal rearrangements, and interchromosomal rearrangements dominated in murid rodents. A total of 162 chromosomal breakpoints in evolution of the eutherian ancestral genome to the human genome were identified; however, the rate of rearrangements was significantly lower (0.80/My) during the first ∼60 My of eutherian evolution, then increased to greater than 2.0/My along the five primate lineages studied. Our results significantly expand knowledge of eutherian genome evolution and will facilitate greater understanding of the role of chromosome rearrangements in adaptation, speciation, and the etiology of inherited and spontaneously occurring diseases.
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43
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dos Santos MDS, Kretschmer R, Frankl-Vilches C, Bakker A, Gahr M, O´Brien PCM, Ferguson-Smith MA, de Oliveira EHC. Comparative Cytogenetics between Two Important Songbird, Models: The Zebra Finch and the Canary. PLoS One 2017; 12:e0170997. [PMID: 28129381 PMCID: PMC5271350 DOI: 10.1371/journal.pone.0170997] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 01/14/2017] [Indexed: 11/18/2022] Open
Abstract
Songbird species (order Passeriformes, suborder Oscines) are important models in various experimental fields spanning behavioural genomics to neurobiology. Although the genomes of some songbird species were sequenced recently, the chromosomal organization of these species is mostly unknown. Here we focused on the two most studied songbird species in neuroscience, the zebra finch (Taeniopygia guttata) and the canary (Serinus canaria). In order to clarify these issues and also to integrate chromosome data with their assembled genomes, we used classical and molecular cytogenetics in both zebra finch and canary to define their chromosomal homology, localization of heterochromatic blocks and distribution of rDNA clusters. We confirmed the same diploid number (2n = 80) in both species, as previously reported. FISH experiments confirmed the occurrence of multiple paracentric and pericentric inversions previously found in other species of Passeriformes, providing a cytogenetic signature for this order, and corroborating data from in silico analyses. Additionally, compared to other Passeriformes, we detected differences in the zebra finch karyotype concerning the morphology of some chromosomes, in the distribution of 5S rDNA clusters, and an inversion in chromosome 1.
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Affiliation(s)
| | - Rafael Kretschmer
- Programa de Pós-Graduação em Genética e Biologia Molecular, UFRGS, Porto Alegre, RS, Brazil
| | - Carolina Frankl-Vilches
- Department of Behavioral Neurobiology, Max Planck Institute for Ornithology, Seewiesen, Germany
| | - Antje Bakker
- Department of Behavioral Neurobiology, Max Planck Institute for Ornithology, Seewiesen, Germany
| | - Manfred Gahr
- Department of Behavioral Neurobiology, Max Planck Institute for Ornithology, Seewiesen, Germany
| | - Patricia C. M. O´Brien
- Cambridge Resource Centre for Comparative Genomics, University of Cambridge Department of Veterinary Medicine, Cambridge, United Kingdom
| | - Malcolm A. Ferguson-Smith
- Cambridge Resource Centre for Comparative Genomics, University of Cambridge Department of Veterinary Medicine, Cambridge, United Kingdom
| | - Edivaldo H. C. de Oliveira
- Laboratório de Cultura de Tecidos e Citogenética, SAMAM, Instituto Evandro Chagas, Ananindeua, PA, Brazil
- Faculdade de Ciências Naturais, ICEN, Universidade Federal do Pará, Belém, Brazil
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44
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Matsunaga S, Nakaya A. Computational Synteny Analysis Promotes a Better Understanding of Chromosome Evolution. CYTOLOGIA 2017. [DOI: 10.1508/cytologia.82.101] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Sachihiro Matsunaga
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science
| | - Akihiro Nakaya
- Department of Genome Informatics, Graduate School of Medicine, Osaka University
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45
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Kapusta A, Suh A. Evolution of bird genomes-a transposon's-eye view. Ann N Y Acad Sci 2016; 1389:164-185. [DOI: 10.1111/nyas.13295] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Revised: 10/06/2016] [Accepted: 10/11/2016] [Indexed: 02/06/2023]
Affiliation(s)
- Aurélie Kapusta
- Department of Human Genetics; University of Utah School of Medicine; Salt Lake City Utah
| | - Alexander Suh
- Department of Evolutionary Biology (EBC); Uppsala University; Uppsala Sweden
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46
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Damas J, O'Connor R, Farré M, Lenis VPE, Martell HJ, Mandawala A, Fowler K, Joseph S, Swain MT, Griffin DK, Larkin DM. Upgrading short-read animal genome assemblies to chromosome level using comparative genomics and a universal probe set. Genome Res 2016; 27:875-884. [PMID: 27903645 PMCID: PMC5411781 DOI: 10.1101/gr.213660.116] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 11/16/2016] [Indexed: 02/07/2023]
Abstract
Most recent initiatives to sequence and assemble new species’ genomes de novo fail to achieve the ultimate endpoint to produce contigs, each representing one whole chromosome. Even the best-assembled genomes (using contemporary technologies) consist of subchromosomal-sized scaffolds. To circumvent this problem, we developed a novel approach that combines computational algorithms to merge scaffolds into chromosomal fragments, PCR-based scaffold verification, and physical mapping to chromosomes. Multigenome-alignment-guided probe selection led to the development of a set of universal avian BAC clones that permit rapid anchoring of multiple scaffolds to chromosomes on all avian genomes. As proof of principle, we assembled genomes of the pigeon (Columbia livia) and peregrine falcon (Falco peregrinus) to chromosome levels comparable, in continuity, to avian reference genomes. Both species are of interest for breeding, cultural, food, and/or environmental reasons. Pigeon has a typical avian karyotype (2n = 80), while falcon (2n = 50) is highly rearranged compared to the avian ancestor. By using chromosome breakpoint data, we established that avian interchromosomal breakpoints appear in the regions of low density of conserved noncoding elements (CNEs) and that the chromosomal fission sites are further limited to long CNE “deserts.” This corresponds with fission being the rarest type of rearrangement in avian genome evolution. High-throughput multiple hybridization and rapid capture strategies using the current BAC set provide the basis for assembling numerous avian (and possibly other reptilian) species, while the overall strategy for scaffold assembly and mapping provides the basis for an approach that (provided metaphases can be generated) could be applied to any animal genome.
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Affiliation(s)
- Joana Damas
- Department of Comparative Biomedical Sciences, Royal Veterinary College, University of London, London, NW1 0TU, United Kingdom
| | - Rebecca O'Connor
- School of Biosciences, University of Kent, Canterbury, CT2 7NY, United Kingdom
| | - Marta Farré
- Department of Comparative Biomedical Sciences, Royal Veterinary College, University of London, London, NW1 0TU, United Kingdom
| | - Vasileios Panagiotis E Lenis
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, SY23 3DA, United Kingdom
| | - Henry J Martell
- School of Biosciences, University of Kent, Canterbury, CT2 7NY, United Kingdom
| | - Anjali Mandawala
- School of Biosciences, University of Kent, Canterbury, CT2 7NY, United Kingdom.,School of Human and Life Sciences, Canterbury Christ Church University, Canterbury, CT1 1QU, United Kingdom
| | - Katie Fowler
- School of Human and Life Sciences, Canterbury Christ Church University, Canterbury, CT1 1QU, United Kingdom
| | - Sunitha Joseph
- School of Biosciences, University of Kent, Canterbury, CT2 7NY, United Kingdom
| | - Martin T Swain
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, SY23 3DA, United Kingdom
| | - Darren K Griffin
- School of Biosciences, University of Kent, Canterbury, CT2 7NY, United Kingdom
| | - Denis M Larkin
- Department of Comparative Biomedical Sciences, Royal Veterinary College, University of London, London, NW1 0TU, United Kingdom
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Duplication of chicken defensin7 gene generated by gene conversion and homologous recombination. Proc Natl Acad Sci U S A 2016; 113:13815-13820. [PMID: 27849592 DOI: 10.1073/pnas.1616948113] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Defensins constitute an evolutionary conserved family of cationic antimicrobial peptides that play a key role in host innate immune responses to infection. Defensin genes generally reside in complex genomic regions that are prone to structural variation, and defensin genes exhibit extensive copy number variation in humans and in other species. Copy number variation of defensin genes was examined in inbred lines of Leghorn and Fayoumi chickens, and a duplication of defensin7 was discovered in the Fayoumi breed. Analysis of junction sequences confirmed the occurrence of a simple tandem duplication of defensin7 with sequence identity at the junction, suggesting nonallelic homologous recombination between defensin7 and defensin6 The duplication event generated two chimeric promoters that are best explained by gene conversion followed by homologous recombination. Expression of defensin7 was not elevated in animals with two genes despite both genes being transcribed in the tissues examined. Computational prediction of promoter regions revealed the presence of several putative transcription factor binding sites generated by the duplication event. These data provide insight into the evolution and possible function of large gene families and specifically, the defensins.
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