Abdelmanova AS, Dotsev AV, Romanov MN, Stanishevskaya OI, Gladyr EA, Rodionov AN, Vetokh AN, Volkova NA, Fedorova ES, Gusev IV, Griffin DK, Brem G, Zinovieva NA (2021) Unveiling comparative genomic trajectories of selection and key candidate genes in egg-type Russian White and meat-type White Cornish chickens. Biology 10:876. https://doi.org/10.3390/biology10090876

Article  CAS  PubMed  PubMed Central  Google Scholar 

Alföldi J, Di Palma F, Grabherr M, Williams C, Kong L, Mauceli E, Russell P, Lowe CB, Glor RE, Jaffe JD, Ray DA, Boissinot S, Shedlock AM, Botka C, Castoe TA, Colbourne JK, Fujita MK, Moreno RG, ten Hallers BF, Haussler D, Heger A, Heiman D, Janes DE, Johnson J, de Jong PJ, Koriabine MY, Lara M, Novick PA, Organ CL, Peach SE, Poe S, Pollock DD, de Queiroz K, Sanger T, Searle S, Smith JD, Smith Z, Swofford R, Turner-Maier J, Wade J, Young S, Zadissa A, Edwards SV, Glenn TC, Schneider CJ, Losos JB, Lander ES, Breen M, Ponting CP, Lindblad-Toh K (2011) The genome of the green anole lizard and a comparative analysis with birds and mammals. Nature 477:587–591. https://doi.org/10.1038/nature10390

Article  CAS  PubMed  PubMed Central  Google Scholar 

Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25:25–29. https://doi.org/10.1038/75556

Article  CAS  PubMed  PubMed Central  Google Scholar 

Dalloul RA, Long JA, Zimin AV, Aslam L, Beal K, Ann BL, Bouffard P, Burt DW, Crasta O, Crooijmans RP, Cooper K, Coulombe RA, De S, Delany ME, Dodgson JB, Dong JJ, Evans C, Frederickson KM, Flicek P, Florea L, Folkerts O, Groenen MA, Harkins TT, Herrero J, Hoffmann S, Megens HJ, Jiang A, de Jong P, Kaiser P, Kim H, Kim KW, Kim S, Langenberger D, Lee MK, Lee T, Mane S, Marcais G, Marz M, McElroy AP, Modise T, Nefedov M, Notredame C, Paton IR, Payne WS, Pertea G, Prickett D, Puiu D, Qioa D, Raineri E, Ruffier M, Salzberg SL, Schatz MC, Scheuring C, Schmidt CJ, Schroeder S, Searle SM, Smith EJ, Smith J, Sonstegard TS, Stadler PF, Tafer H, Tu ZJ, Van Tassell CP, Vilella AJ, Williams KP, Yorke JA, Zhang L, Zhang HB, Zhang X, Zhang Y, Reed KM (2010) Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo): genome assembly and analysis. PLoS Biol Sep 8:e1000475. https://doi.org/10.1371/journal.pbio.1000475

Article  CAS  Google Scholar 

Damas J, Kim J, Farré M, Griffin DK, Larkin DM (2018) Reconstruction of avian ancestral karyotypes reveals differences in the evolutionary history of macro- and microchromosomes. Genome Biol 19:155. https://doi.org/10.1186/s13059-018-1544-8

Article  CAS  PubMed  PubMed Central  Google Scholar 

Farré M, Narayan J, Slavov GT, Damas J, Auvil L, Li C, Jarvis ED, Burt DW, Griffin DK, Larkin DM (2016) Novel insights into chromosome evolution in birds, archosaurs, and reptiles. Genome Biol Evol 8:2442–2451. https://doi.org/10.1093/gbe/evw166

Article  PubMed  PubMed Central  Google Scholar 

GRCg6a (2018) Genome Reference Consortium Chicken Build 6a. In: National Library of Medicine, National Center for Biotechnology Information. https://www.ncbi.nlm.nih.gov/assembly/GCF_000002315.6. Accessed on 2 August 2022

Griffin DK, Farré M, Lithgow P, O’Connor R, Fowler K, Romanov MN, Larkin D (2015) Avian chromonomics goes functional. Chromosome Res 23(2):367. https://doi.org/10.1007/s10577-014-9447-3

Article  CAS  Google Scholar 

Hardison RC (2003) Comparative genomics. PLoS Biol 1:E58. https://doi.org/10.1371/journal.pbio.0000058

Article  CAS  PubMed  PubMed Central  Google Scholar 

Hinrichs AS, Karolchik D, Baertsch R, Barber GP, Bejerano G, Clawson H, Diekhans M, Furey TS, Harte RA, Hsu F, Hillman-Jackson J, Kuhn RM, Pedersen JS, Pohl A, Raney BJ, Rosenbloom KR, Siepel A, Smith KE, Sugnet CW, Sultan-Qurraie A, Thomas DJ, Trumbower H, Weber RJ, Weirauch M, Zweig AS, Haussler D, Kent WJ (2006) The UCSC Genome Browser Database: update 2006. Nucleic Acids Res 34(Database issue):D590–598. https://doi.org/10.1093/nar/gkj144

Article  CAS  PubMed  Google Scholar 

Huang DW, Sherman BT, Lempicki RA (2009a) Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res 37:1–13. https://doi.org/10.1093/nar/gkn923

Article  CAS  PubMed  Google Scholar 

Huang DW, Sherman BT, Lempicki RA (2009b) Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 4:44–57. https://doi.org/10.1038/nprot.2008.211

Article  CAS  PubMed  Google Scholar 

Huang Y, Li Y, Burt DW, Chen H, Zhang Y, Qian W, Kim H, Gan S, Zhao Y, Li J, Yi K, Feng H, Zhu P, Li B, Liu Q, Fairley S, Magor KE, Du Z, Hu X, Goodman L, Tafer H, Vignal A, Lee T, Kim KW, Sheng Z, An Y, Searle S, Herrero J, Groenen MAM, Crooijmans RPMA, Faraut T, Cai Q, Webster RG, Aldridge JR, Warren WC, Bartschat S, Kehr S, Marz M, Stadler PF, Smith J, Kraus RHS, Zhao Y, Ren L, Fei J, Morisson M, Kaiser P, Griffin DK, Rao M, Pitel F, Wang J, Li N (2013) The duck genome and transcriptome provide insight into an avian influenza virus reservoir species. Nat Genet 45:776–783. https://doi.org/10.1038/ng.2657

Article  CAS  PubMed  PubMed Central  Google Scholar 

International Chicken Genome Sequencing Consortium (2004) Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature 432:695–716. https://doi.org/10.1038/nature03154

Article  CAS  Google Scholar 

Itan Y, Gerbault P, Pines G (2016) Evolutionary genomics. Evol Bioinform Online 11(Suppl 2):53–55. https://doi.org/10.4137/EBO.S39729

Article  PubMed  PubMed Central  Google Scholar 

Jarvis ED, Mirarab S, Aberer AJ, Li B, Houde P, Li C, Ho SY, Faircloth BC, Nabholz B, Howard JT, Suh A, Weber CC, da Fonseca RR, Li J, Zhang F, Li H, Zhou L, Narula N, Liu L, Ganapathy G, Boussau B, Bayzid MS, Zavidovych V, Subramanian S, Gabaldón T, Capella-Gutiérrez S, Huerta-Cepas J, Rekepalli B, Munch K, Schierup M, Lindow B, Warren WC, Ray D, Green RE, Bruford MW, Zhan X, Dixon A, Li S, Li N, Huang Y, Derryberry EP, Bertelsen MF, Sheldon FH, Brumfield RT, Mello CV, Lovell PV, Wirthlin M, Schneider MP, Prosdocimi F, Samaniego JA, Vargas Velazquez AM, Alfaro-Núñez A, Campos PF, Petersen B, Sicheritz-Ponten T, Pas A, Bailey T, Scofield P, Bunce M, Lambert DM, Zhou Q, Perelman P, Driskell AC, Shapiro B, Xiong Z, Zeng Y, Liu S, Li Z, Liu B, Wu K, Xiao J, Yinqi X, Zheng Q, Zhang Y, Yang H, Wang J, Smeds L, Rheindt FE, Braun M, Fjeldsa J, Orlando L, Barker FK, Jønsson KA, Johnson W, Koepfli KP, O’Brien S, Haussler D, Ryder OA, Rahbek C, Willerslev E, Graves GR, Glenn TC, McCormack J, Burt D, Ellegren H, Alström P, Edwards SV, Stamatakis A, Mindell DP, Cracraft J, Braun EL, Warnow T, Jun W, Gilbert MT, Zhang G (2014) Whole-genome analyses resolve early branches in the tree of life of modern birds. Science 346:1320–1331. https://doi.org/10.1126/science.1253451

Article  CAS  PubMed  PubMed Central  Google Scholar 

Kasprzyk A (2011) BioMart: driving a paradigm change in biological data management. Database 2011:bar049. https://doi.org/10.1093/database/bar049

Kiazim LG, O’Connor RE, Larkin DM, Romanov MN, Narushin VG, Brazhnik EA, Griffin DK (2021) Comparative mapping of the macrochromosomes of eight avian species provides further insight into their phylogenetic relationships and avian karyotype evolution. Cells 10:362. https://doi.org/10.3390/cells10020362

Article  CAS  PubMed  PubMed Central  Google Scholar 

Kretschmer R, de Souza MS, Furo IO, Romanov MN, Gunski RJ, Garnero ADV, de Freitas TRO, de Oliveira EHC, O’Connor RE, Griffin DK (2021) Interspecies chromosome mapping in Caprimulgiformes, Piciformes, Suliformes, and Trogoniformes (Aves): cytogenomic insight into microchromosome organization and karyotype evolution in birds. Cells 10:826. https://doi.org/10.3390/cells10040826

Article  CAS  PubMed  PubMed Central  Google Scholar 

Larkin DM, Pape G, Donthu R, Auvil L, Welge M, Lewin HA (2009) Breakpoint regions and homologous synteny blocks in chromosomes have different evolutionary histories. Genome Res 19:770–777. https://doi.org/10.1101/gr.086546.108

Article  CAS  PubMed  PubMed Central  Google Scholar 

Lithgow PE, O’Connor R, Smith D, Fonseka G, Rathje C, Frodsham R, O’Brien PC, Ferguson-Smith MA, Skinner BM, Griffin DK, Romanov MN (2014) Novel tools for characterising inter- and intra-chromosomal rearrangements in avian microchromosomes. In: 2014 Meeting on Avian Model Systems (March 5–8, 2014). Cold Spring Harbor, NY, USA, p 56

Maddison DR, Schulz K-S (eds) (eds) (2007) The Tree of Life Web Project. http://tolweb.org. Accessed on 2 August 2022

Modi WS, Romanov M, Green ED, Ryder O (2009) Molecular cytogenetics of the California condor: evolutionary and conservation implications. Cytogenet Genome Res 127:26–32. https://doi.org/10.1159/000272458

Article  CAS  PubMed  PubMed Central  Google Scholar 

Murphy WJ, Larkin DM, Everts-van der Wind A, Bourque G, Tesler G, Auvil L, Beever JE, Chowdhary BP, Galibert F, Gatzke L, Hitte C, Meyers SN, Milan D, Ostrander EA, Pape G, Parker HG, Raudsepp T, Rogatcheva MB, Schook LB, Skow LC, Welge M, Womack JE, O’Brien SJ, Pevzner PA, Lewin HA (2005) Dynamics of mammalian chromosome evolution inferred from multispecies comparative maps. Science 309:613–617. https://doi.org/10.1126/science.1111387

Article  CAS  PubMed  Google Scholar 

O’Connor RE, Romanov MN, Kiazim LG, Barrett PM, Farré M, Damas J, Ferguson-Smith M, Valenzuela N, Larkin DM, Griffin DK (2018a) Reconstruction of the diapsid ancestral genome permits chromosome evolution tracing in avian and non-avian dinosaurs. Nat Commun 9:1883. https://doi.org/10.1038/s41467-018-04267-9

Article  CAS  PubMed  PubMed Central  Google Scholar 

O’Connor RE, Farré M, Joseph S, Damas J, Kiazim L, Jennings R, Bennett S, Slack EA, Allanson E, Larkin DM, Griffin DK (2018b) Chromosome-level assembly reveals extensive rearrangement in saker falcon and budgerigar, but not ostrich, genomes. Genome Biol 19:171. https://doi.org/10.1186/s13059-018-1550-x

Article  CAS  PubMed  PubMed Central  Google Scholar 

Robinson O, Dylus D, Dessimoz C (2016) Phylo.io: interactive viewing and comparison of large phylogenetic trees on the web. Mol Biol Evol 33:2163–2166. https://doi.org/10.1093/molbev/msw080

Article  CAS  PubMed  PubMed Central  Google Scholar 

Rogers RL (2015) Chromosomal rearrangements as barriers to genetic homogenization between archaic and modern humans. Mol Biol Evol 32:3064–3078. https://doi.org/10.1093/molbev/msv204

Article  CAS  PubMed  PubMed Central  Google Scholar 

Romanov MN, Daniels LM, Dodgson JB, Delany ME (2005) Integration of the cytogenetic and physical maps of chicken chromosome 17. Chromosome Res 13:215–222. https://doi.org/10.1007/s10577-005-1506-3

Article  CAS  PubMed  Google Scholar 

Romanov MN, Farré-Belmonte M, Lithgow PE, O’Connor B, Fowler KE, Larkin DM, Griffin DK (2014a) In silico reconstruction of chromosomal rearrangements and an avian ancestral karyotype. In: International Plant and Animal Genome XXII Conference (January 11–15, 2014). San Diego, CA, USA, Abstract P1106

Romanov MN, Farré M, Lithgow PE, Fowler KE, Skinner BM, O’Connor R, Fonseka G, Backström N, Matsuda Y, Nishida C, Houde P, Jarvis ED, Ellegren H, Burt DW, Larkin DM, Griffin DK (2014b) Reconstruction of gross avian genome structure, organization and evolution suggests that the chicken lineage most closely resembles the dinosaur avian ancestor. BMC Genomics 15:1060. https://doi.org/10.1186/1471-2164-15-1060

Article  PubMed  PubMed Central  Google Scholar 

Sankoff D (2009) The where and wheref