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Home / Equine Research Bank / PLoS One / Ancient segmentally duplicated LCORL retrocopies in equids.
PloS one2023; 18(6); e0286861; doi: 10.1371/journal.pone.0286861

Ancient segmentally duplicated LCORL retrocopies in equids.

Abstract: LINE-1 is an active transposable element encoding proteins capable of inserting host gene retrocopies, resulting in retro-copy number variants (retroCNVs) between individuals. Here, we performed retroCNV discovery using 86 equids and identified 437 retrocopy insertions. Only 5 retroCNVs were shared between horses and other equids, indicating that the majority of retroCNVs inserted after the species diverged. A large number (17-35 copies) of segmentally duplicated Ligand Dependent Nuclear Receptor Corepressor Like (LCORL) retrocopies were present in all equids but absent from other extant perissodactyls. The majority of LCORL transcripts in horses and donkeys originate from the retrocopies. The initial LCORL retrotransposition occurred 18 million years ago (17-19 95% CI), which is coincident with the increase in body size, reduction in digit number, and changes in dentition that characterized equid evolution. Evolutionary conservation of the LCORL retrocopy segmental amplification in the Equidae family, high expression levels and the ancient timeline for LCORL retrotransposition support a functional role for this structural variant.
Copyright: © 2023 Batcher et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
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Publication Date: 2023-06-08 PubMed ID: 37289743PubMed Central: PMC10249811DOI: 10.1371/journal.pone.0286861Google Scholar: Lookup
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Summary

This research summary has been generated with artificial intelligence and may contain errors and omissions. Refer to the original study to confirm details provided. Submit correction.

The research article focuses on investigating an ancient gene duplication event in horses and related species, known as equids, and its effects on the evolution of these species. The researchers found the gene duplication of LCORL retrocopies plays a prominent role in equids’ evolution, potentially affecting their size, digit number, and dentition.

Transcription of LINE-1 and Retrocopy Variants

  • The research investigates a transposable element known as LINE-1, a part of the genome that can alter its position in the DNA sequence. LINE-1 has the ability to encode proteins that can insert host gene duplicates, known as retrocopies, into the genome.
  • Variations in the number of these retrocopies, or retroCNVs, can occur between different individuals of a species.
  • The study included 86 equids and through this, they identified 437 retrocopy insertions.

Diversity of RetroCNVs Among Equids

  • The research showed that only 5 of these retroCNVs were shared between horses and other equids. This indicates that most retroCNVs were inserted into the genome after the different equid species diverged from a common ancestor.
  • A significant number of these retrocopies were segmented duplications of a specific gene known as Ligand Dependent Nuclear Receptor Corepressor Like (LCORL).
  • These LCORL retrocopies were found in all equids but were absent in other closely related perissodactyl species.

The Role of LCORL Retrocopies in Equid Evolution

  • The majority of LCORL transcripts, the intermediate products between the DNA sequence of a gene and the protein it codes for, originate from these retrocopies in both horses and donkeys.
  • The researchers determined that the initial event where LCORL was retrotransposed (copied and inserted into another part of the genome) occurred approximately 18 million years ago.
  • This timing correlates with significant changes in the evolutionary history of equids, including an increase in body size, a reduction in the number of digits, and changes in teeth structure. These changes imply that the LCORL retrocopies may have had a significant effect on equid evolution.

Functional Role of LCORL Retrocopies

  • The conservation of the LCORL retrocopy through time, its high expression levels, and the ancient timeline of the LCORL segmental amplification in the Equidae family suggest that these structures have a functional role.
  • While the precise functionality wasn’t specified, it is implied that the structural variants may be instrumental for the functioning or development of some traits in these species.

Cite This Article

APA
Batcher K, Varney S, Raudsepp T, Jevit M, Dickinson P, Jagannathan V, Leeb T, Bannasch D. (2023). Ancient segmentally duplicated LCORL retrocopies in equids. PLoS One, 18(6), e0286861. https://doi.org/10.1371/journal.pone.0286861

Publication

PloS one
ISSN: 1932-6203
NlmUniqueID: 101285081
Country: United States
Language: English
Volume: 18
Issue: 6
Pages: e0286861
PII: e0286861

Researcher Affiliations

Batcher, Kevin
  • Department of Population Health and Reproduction, University of California Davis, Davis, CA, United States of America.
Varney, Scarlett
  • Department of Population Health and Reproduction, University of California Davis, Davis, CA, United States of America.
Raudsepp, Terje
  • Veterinary Integrative Biosciences, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, United States of America.
Jevit, Matthew
  • Veterinary Integrative Biosciences, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, United States of America.
Dickinson, Peter
  • Department of Surgical and Radiological Sciences, University of California Davis, Davis, CA, United States of America.
Jagannathan, Vidhya
  • Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland.
Leeb, Tosso
  • Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland.
Bannasch, Danika
  • Department of Population Health and Reproduction, University of California Davis, Davis, CA, United States of America.

MeSH Terms

  • Animals
  • Horses / genetics
  • Long Interspersed Nucleotide Elements
  • Equidae / genetics
  • DNA Transposable Elements
  • Proteins

Conflict of Interest Statement

The authors have declared that no competing interests exist.

References

This article includes 88 references
  1. Ostertag EM, Kazazian HH Jr. Biology of mammalian L1 retrotransposons.. Annu Rev Genet 2001;35:501-38.
    pubmed: 11700292doi: 10.1146/annurev.genet.35.102401.091032google scholar: lookup
  2. Richardson SR, Salvador-Palomeque C, Faulkner GJ. Diversity through duplication: whole-genome sequencing reveals novel gene retrocopies in the human population.. Bioessays 2014 May;36(5):475-81.
    doi: 10.1002/bies.201300181pmc: PMC4314676pubmed: 24615986google scholar: lookup
  3. Luan DD, Korman MH, Jakubczak JL, Eickbush TH. Reverse transcription of R2Bm RNA is primed by a nick at the chromosomal target site: a mechanism for non-LTR retrotransposition.. Cell 1993 Feb 26;72(4):595-605.
    doi: 10.1016/0092-8674(93)90078-5pubmed: 7679954google scholar: lookup
  4. Jurka J. Sequence patterns indicate an enzymatic involvement in integration of mammalian retroposons.. Proc Natl Acad Sci U S A 1997 Mar 4;94(5):1872-7.
    doi: 10.1073/pnas.94.5.1872pmc: PMC20010pubmed: 9050872google scholar: lookup
  5. Ichiyanagi K, Okada N. Mobility pathways for vertebrate L1, L2, CR1, and RTE clade retrotransposons.. Mol Biol Evol 2008 Jun;25(6):1148-57.
    doi: 10.1093/molbev/msn061pubmed: 18343891google scholar: lookup
  6. Esnault C, Maestre J, Heidmann T. Human LINE retrotransposons generate processed pseudogenes.. Nat Genet 2000 Apr;24(4):363-7.
    doi: 10.1038/74184pubmed: 10742098google scholar: lookup
  7. Wei W, Gilbert N, Ooi SL, Lawler JF, Ostertag EM, Kazazian HH, Boeke JD, Moran JV. Human L1 retrotransposition: cis preference versus trans complementation.. Mol Cell Biol 2001 Feb;21(4):1429-39.
    doi: 10.1128/MCB.21.4.1429-1439.2001pmc: PMC99594pubmed: 11158327google scholar: lookup
  8. Vanin EF. Processed pseudogenes: characteristics and evolution.. Annu Rev Genet 1985;19:253-72.
    doi: 10.1146/annurev.ge.19.120185.001345pubmed: 3909943google scholar: lookup
  9. Rosikiewicz W, Kabza M, Kosinski JG, Ciomborowska-Basheer J, Kubiak MR, Makalowska I. RetrogeneDB-a database of plant and animal retrocopies.. Database (Oxford) 2017 Jan 1;2017.
    doi: 10.1093/database/bax038pmc: PMC5509963pubmed: 29220443google scholar: lookup
  10. Ewing AD, Ballinger TJ, Earl D, Harris CC, Ding L, Wilson RK, Haussler D. Retrotransposition of gene transcripts leads to structural variation in mammalian genomes.. Genome Biol 2013 Mar 13;14(3):R22.
    doi: 10.1186/gb-2013-14-3-r22pmc: PMC3663115pubmed: 23497673google scholar: lookup
  11. Penzkofer T, Jäger M, Figlerowicz M, Badge R, Mundlos S, Robinson PN, Zemojtel T. L1Base 2: more retrotransposition-active LINE-1s, more mammalian genomes.. Nucleic Acids Res 2017 Jan 4;45(D1):D68-D73.
    doi: 10.1093/nar/gkw925pmc: PMC5210629pubmed: 27924012google scholar: lookup
  12. Casola C, Betrán E. The Genomic Impact of Gene Retrocopies: What Have We Learned from Comparative Genomics, Population Genomics, and Transcriptomic Analyses?. Genome Biol Evol 2017 Jun 1;9(6):1351-1373.
    doi: 10.1093/gbe/evx081pmc: PMC5470649pubmed: 28605529google scholar: lookup
  13. Schrider DR, Navarro FC, Galante PA, Parmigiani RB, Camargo AA, Hahn MW, de Souza SJ. Gene copy-number polymorphism caused by retrotransposition in humans.. PLoS Genet 2013;9(1):e1003242.
    doi: 10.1371/journal.pgen.1003242pmc: PMC3554589pubmed: 23359205google scholar: lookup
  14. Zhang W, Xie C, Ullrich K, Zhang YE, Tautz D. The mutational load in natural populations is significantly affected by high primary rates of retroposition.. Proc Natl Acad Sci U S A 2021 Feb 9;118(6).
    doi: 10.1073/pnas.2013043118pmc: PMC8017666pubmed: 33526666google scholar: lookup
  15. Feng X, Li H. Higher Rates of Processed Pseudogene Acquisition in Humans and Three Great Apes Revealed by Long-Read Assemblies.. Mol Biol Evol 2021 Jun 25;38(7):2958-2966.
    doi: 10.1093/molbev/msab062pmc: PMC8661421pubmed: 33681998google scholar: lookup
  16. Zhang Y, Li S, Abyzov A, Gerstein MB. Landscape and variation of novel retroduplications in 26 human populations.. PLoS Comput Biol 2017 Jun;13(6):e1005567.
    doi: 10.1371/journal.pcbi.1005567pmc: PMC5510864pubmed: 28662076google scholar: lookup
  17. Batcher K, Varney S, York D, Blacksmith M, Kidd JM, Rebhun R, Dickinson P, Bannasch D. Recent, full-length gene retrocopies are common in canids.. Genome Res 2022 Aug 12;32(8):1602-11.
    doi: 10.1101/gr.276828.122pmc: PMC9435743pubmed: 35961775google scholar: lookup
  18. Tozaki T, Ohnuma A, Kikuchi M, Ishige T, Kakoi H, Hirota KI, Kusano K, Nagata SI. Identification of processed pseudogenes in the genome of Thoroughbred horses: Possibility of gene-doping detection considering the presence of pseudogenes.. Anim Genet 2022 Apr;53(2):183-192.
    doi: 10.1111/age.13174pubmed: 35077588google scholar: lookup
  19. Troskie RL, Jafrani Y, Mercer TR, Ewing AD, Faulkner GJ, Cheetham SW. Long-read cDNA sequencing identifies functional pseudogenes in the human transcriptome.. Genome Biol 2021 May 10;22(1):146.
    pmc: PMC8108447pubmed: 33971925doi: 10.1186/s13059-021-02369-0google scholar: lookup
  20. Cheetham SW, Faulkner GJ, Dinger ME. Overcoming challenges and dogmas to understand the functions of pseudogenes.. Nat Rev Genet 2020 Mar;21(3):191-201.
    doi: 10.1038/s41576-019-0196-1pubmed: 31848477google scholar: lookup
  21. Ciomborowska-Basheer J, Staszak K, Kubiak MR, Makałowska I. Not So Dead Genes-Retrocopies as Regulators of Their Disease-Related Progenitors and Hosts.. Cells 2021 Apr 15;10(4).
    doi: 10.3390/cells10040912pmc: PMC8071448pubmed: 33921034google scholar: lookup
  22. Abegglen LM, Caulin AF, Chan A, Lee K, Robinson R, Campbell MS, Kiso WK, Schmitt DL, Waddell PJ, Bhaskara S, Jensen ST, Maley CC, Schiffman JD. Potential Mechanisms for Cancer Resistance in Elephants and Comparative Cellular Response to DNA Damage in Humans.. JAMA 2015 Nov 3;314(17):1850-60.
    doi: 10.1001/jama.2015.13134pmc: PMC4858328pubmed: 26447779google scholar: lookup
  23. Sulak M, Fong L, Mika K, Chigurupati S, Yon L, Mongan NP, Emes RD, Lynch VJ. TP53 copy number expansion is associated with the evolution of increased body size and an enhanced DNA damage response in elephants.. Elife 2016 Sep 19;5.
    doi: 10.7554/eLife.11994pmc: PMC5061548pubmed: 27642012google scholar: lookup
  24. Kuzmin E, Taylor JS, Boone C. Retention of duplicated genes in evolution.. Trends Genet 2022 Jan;38(1):59-72.
    doi: 10.1016/j.tig.2021.06.016pmc: PMC8678172pubmed: 34294428google scholar: lookup
  25. Parker HG, VonHoldt BM, Quignon P, Margulies EH, Shao S, Mosher DS, Spady TC, Elkahloun A, Cargill M, Jones PG, Maslen CL, Acland GM, Sutter NB, Kuroki K, Bustamante CD, Wayne RK, Ostrander EA. An expressed fgf4 retrogene is associated with breed-defining chondrodysplasia in domestic dogs.. Science 2009 Aug 21;325(5943):995-8.
    doi: 10.1126/science.1173275pmc: PMC2748762pubmed: 19608863google scholar: lookup
  26. Brown EA, Dickinson PJ, Mansour T, Sturges BK, Aguilar M, Young AE, Korff C, Lind J, Ettinger CL, Varon S, Pollard R, Brown CT, Raudsepp T, Bannasch DL. FGF4 retrogene on CFA12 is responsible for chondrodystrophy and intervertebral disc disease in dogs.. Proc Natl Acad Sci U S A 2017 Oct 24;114(43):11476-11481.
    doi: 10.1073/pnas.1709082114pmc: PMC5664524pubmed: 29073074google scholar: lookup
  27. Orlando L. Equids.. Curr Biol 2015 Oct 19;25(20):R973-8.
    doi: 10.1016/j.cub.2015.09.005pubmed: 26485367google scholar: lookup
  28. MacFadden BJ, Hulbert RC. Explosive speciation at the base of the adaptive radiation of Miocene grazing horses. Nature 1988;336:466–8.
  29. Orlando L, Ginolhac A, Zhang G, Froese D, Albrechtsen A, Stiller M, Schubert M, Cappellini E, Petersen B, Moltke I, Johnson PL, Fumagalli M, Vilstrup JT, Raghavan M, Korneliussen T, Malaspinas AS, Vogt J, Szklarczyk D, Kelstrup CD, Vinther J, Dolocan A, Stenderup J, Velazquez AM, Cahill J, Rasmussen M, Wang X, Min J, Zazula GD, Seguin-Orlando A, Mortensen C, Magnussen K, Thompson JF, Weinstock J, Gregersen K, Røed KH, Eisenmann V, Rubin CJ, Miller DC, Antczak DF, Bertelsen MF, Brunak S, Al-Rasheid KA, Ryder O, Andersson L, Mundy J, Krogh A, Gilbert MT, Kjær K, Sicheritz-Ponten T, Jensen LJ, Olsen JV, Hofreiter M, Nielsen R, Shapiro B, Wang J, Willerslev E. Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse.. Nature 2013 Jul 4;499(7456):74-8.
    doi: 10.1038/nature12323pubmed: 23803765google scholar: lookup
  30. Librado P, Orlando L. Genomics and the Evolutionary History of Equids.. Annu Rev Anim Biosci 2021 Feb 16;9:81-101.
    doi: 10.1146/annurev-animal-061220-023118pubmed: 33197207google scholar: lookup
  31. Pertea G, Pertea M. GFF Utilities: GffRead and GffCompare.. F1000Res 2020;9.
    doi: 10.12688/f1000research.23297.2pmc: PMC7222033pubmed: 32489650google scholar: lookup
  32. Marcais G, Kingsford C. Jellyfish: A fast k-mer counter. Tutorialis e Manuais 2012;1:1–8.
  33. Hach F, Sarrafi I, Hormozdiari F, Alkan C, Eichler EE, Sahinalp SC. mrsFAST-Ultra: a compact, SNP-aware mapper for high performance sequencing applications.. Nucleic Acids Res 2014 Jul;42(Web Server issue):W494-500.
    doi: 10.1093/nar/gku370pmc: PMC4086126pubmed: 24810850google scholar: lookup
  34. Leinonen R, Sugawara H, Shumway M. The sequence read archive.. Nucleic Acids Res 2011 Jan;39(Database issue):D19-21.
    doi: 10.1093/nar/gkq1019pmc: PMC3013647pubmed: 21062823google scholar: lookup
  35. Kalbfleisch TS, Rice ES, DePriest MS Jr, Walenz BP, Hestand MS, Vermeesch JR, O Connell BL, Fiddes IT, Vershinina AO, Saremi NF, Petersen JL, Finno CJ, Bellone RR, McCue ME, Brooks SA, Bailey E, Orlando L, Green RE, Miller DC, Antczak DF, MacLeod JN. Improved reference genome for the domestic horse increases assembly contiguity and composition.. Commun Biol 2018;1:197.
    doi: 10.1038/s42003-018-0199-zpmc: PMC6240028pubmed: 30456315google scholar: lookup
  36. Li H. Minimap2: pairwise alignment for nucleotide sequences.. Bioinformatics 2018 Sep 15;34(18):3094-3100.
    doi: 10.1093/bioinformatics/bty191pmc: PMC6137996pubmed: 29750242google scholar: lookup
  37. Danecek P, Bonfield JK, Liddle J, Marshall J, Ohan V, Pollard MO, Whitwham A, Keane T, McCarthy SA, Davies RM, Li H. Twelve years of SAMtools and BCFtools.. Gigascience 2021 Feb 16;10(2).
    doi: 10.1093/gigascience/giab008pmc: PMC7931819pubmed: 33590861google scholar: lookup
  38. Carreira PE, Ewing AD, Li G, Schauer SN, Upton KR, Fagg AC, Morell S, Kindlova M, Gerdes P, Richardson SR, Li B, Gerhardt DJ, Wang J, Brennan PM, Faulkner GJ. Evidence for L1-associated DNA rearrangements and negligible L1 retrotransposition in glioblastoma multiforme.. Mob DNA 2016;7:21.
    doi: 10.1186/s13100-016-0076-6pmc: PMC5105311pubmed: 27843499google scholar: lookup
  39. Thorvaldsdóttir H, Robinson JT, Mesirov JP. Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration.. Brief Bioinform 2013 Mar;14(2):178-92.
    doi: 10.1093/bib/bbs017pmc: PMC3603213pubmed: 22517427google scholar: lookup
  40. Janečka JE, Davis BW, Ghosh S, Paria N, Das PJ, Orlando L, Schubert M, Nielsen MK, Stout TAE, Brashear W, Li G, Johnson CD, Metz RP, Zadjali AMA, Love CC, Varner DD, Bellott DW, Murphy WJ, Chowdhary BP, Raudsepp T. Horse Y chromosome assembly displays unique evolutionary features and putative stallion fertility genes.. Nat Commun 2018 Jul 27;9(1):2945.
    pmc: PMC6063916pubmed: 30054462doi: 10.1038/s41467-018-05290-6google scholar: lookup
  41. Madden T. The BLAST sequence analysis tool. The NCBI handbook 2013;2:425–36.
  42. Rausch T, Zichner T, Schlattl A, Stütz AM, Benes V, Korbel JO. DELLY: structural variant discovery by integrated paired-end and split-read analysis.. Bioinformatics 2012 Sep 15;28(18):i333-i339.
    doi: 10.1093/bioinformatics/bts378pmc: PMC3436805pubmed: 22962449google scholar: lookup
  43. Burns EN, Bordbari MH, Mienaltowski MJ, Affolter VK, Barro MV, Gianino F, Gianino G, Giulotto E, Kalbfleisch TS, Katzman SA, Lassaline M, Leeb T, Mack M, Müller EJ, MacLeod JN, Ming-Whitfield B, Alanis CR, Raudsepp T, Scott E, Vig S, Zhou H, Petersen JL, Bellone RR, Finno CJ. Generation of an equine biobank to be used for Functional Annotation of Animal Genomes project.. Anim Genet 2018 Dec;49(6):564-570.
    doi: 10.1111/age.12717pmc: PMC6264908pubmed: 30311254google scholar: lookup
  44. Kim D, Paggi JM, Park C, Bennett C, Salzberg SL. Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype.. Nat Biotechnol 2019 Aug;37(8):907-915.
    doi: 10.1038/s41587-019-0201-4pmc: PMC7605509pubmed: 31375807google scholar: lookup
  45. Krueger F, Andrews SR. SNPsplit: Allele-specific splitting of alignments between genomes with known SNP genotypes.. F1000Res 2016;5:1479.
    doi: 10.12688/f1000research.9037.2pmc: PMC4934512pubmed: 27429743google scholar: lookup
  46. Bray NL, Pimentel H, Melsted P, Pachter L. Near-optimal probabilistic RNA-seq quantification.. Nat Biotechnol 2016 May;34(5):525-7.
    doi: 10.1038/nbt.3519pubmed: 27043002google scholar: lookup
  47. Wang C, Li H, Guo Y, Huang J, Sun Y, Min J, Wang J, Fang X, Zhao Z, Wang S, Zhang Y, Liu Q, Jiang Q, Wang X, Guo Y, Yang C, Wang Y, Tian F, Zhuang G, Fan Y, Gao Q, Li Y, Ju Z, Li J, Li R, Hou M, Yang G, Liu G, Liu W, Guo J, Pan S, Fan G, Zhang W, Zhang R, Yu J, Zhang X, Yin Q, Ji C, Jin Y, Yue G, Liu M, Xu J, Liu S, Jordana J, Noce A, Amills M, Wu DD, Li S, Zhou X, Zhong J. Donkey genomes provide new insights into domestication and selection for coat color.. Nat Commun 2020 Dec 8;11(1):6014.
    pmc: PMC7723042pubmed: 33293529doi: 10.1038/s41467-020-19813-7google scholar: lookup
  48. Uhlén M, Fagerberg L, Hallström BM, Lindskog C, Oksvold P, Mardinoglu A, Sivertsson Å, Kampf C, Sjöstedt E, Asplund A, Olsson I, Edlund K, Lundberg E, Navani S, Szigyarto CA, Odeberg J, Djureinovic D, Takanen JO, Hober S, Alm T, Edqvist PH, Berling H, Tegel H, Mulder J, Rockberg J, Nilsson P, Schwenk JM, Hamsten M, von Feilitzen K, Forsberg M, Persson L, Johansson F, Zwahlen M, von Heijne G, Nielsen J, Pontén F. Proteomics. Tissue-based map of the human proteome.. Science 2015 Jan 23;347(6220):1260419.
    pubmed: 25613900doi: 10.1126/science.1260419google scholar: lookup
  49. Peng S, Dahlgren AR, Hales EN, Barber AM, Kalbefleich T, Petersen JL. Long-read RNA Sequencing Improves the Annotation of the Equine Transcriptome. bioRxiv 2022.
  50. Raudsepp T, Chowdhary BP. FISH for mapping single copy genes.. Methods Mol Biol 2008;422:31-49.
    pubmed: 18629659doi: 10.1007/978-1-59745-581-7_3google scholar: lookup
  51. Staiger EA, Al Abri MA, Pflug KM, Kalla SE, Ainsworth DM, Miller D, Raudsepp T, Sutter NB, Brooks SA. Skeletal variation in Tennessee Walking Horses maps to the LCORL/NCAPG gene region.. Physiol Genomics 2016 May;48(5):325-35.
    doi: 10.1152/physiolgenomics.00100.2015pubmed: 26931356google scholar: lookup
  52. Bowling AT, Breen M, Chowdhary BP, Hirota K, Lear T, Millon LV, Ponce de Leon FA, Raudsepp T, Stranzinger G. International system for cytogenetic nomenclature of the domestic horse. Report of the Third International Committee for the Standardization of the domestic horse karyotype, Davis, CA, USA, 1996.. Chromosome Res 1997 Nov;5(7):433-43.
    pubmed: 9421259doi: 10.1023/a:1018408811881google scholar: lookup
  53. Raudsepp T, Christensen K, Chowdhar BP. Cytogenetics of donkey chromosomes: nomenclature proposal based on GTG-banded chromosomes and depiction of NORs and telomeric sites.. Chromosome Res 2000;8(8):659-70.
    doi: 10.1023/a:1026707002538pubmed: 11196129google scholar: lookup
  54. . Atlas of Mammalian Chromosomes 2nd Edition. Wiley-Blackwell; 2020.
  55. Cappelletti E, Piras FM, Sola L, Santagostino M, Abdelgadir WA, Raimondi E, Lescai F, Nergadze SG, Giulotto E. Robertsonian Fusion and Centromere Repositioning Contributed to the Formation of Satellite-free Centromeres During the Evolution of Zebras.. Mol Biol Evol 2022 Aug 3;39(8).
    pmc: PMC9356731pubmed: 35881460doi: 10.1093/molbev/msac162google scholar: lookup
  56. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput.. Nucleic Acids Res 2004;32(5):1792-7.
    doi: 10.1093/nar/gkh340pmc: PMC390337pubmed: 15034147google scholar: lookup
  57. Page AJ, Taylor B, Delaney AJ, Soares J, Seemann T, Keane JA, Harris SR. SNP-sites: rapid efficient extraction of SNPs from multi-FASTA alignments.. Microb Genom 2016 Apr;2(4):e000056.
    doi: 10.1099/mgen.0.000056pmc: PMC5320690pubmed: 28348851google scholar: lookup
  58. Vershinina AO, Heintzman PD, Froese DG, Zazula G, Cassatt-Johnstone M, Dalén L, Der Sarkissian C, Dunn SG, Ermini L, Gamba C, Groves P, Kapp JD, Mann DH, Seguin-Orlando A, Southon J, Stiller M, Wooller MJ, Baryshnikov G, Gimranov D, Scott E, Hall E, Hewitson S, Kirillova I, Kosintsev P, Shidlovsky F, Tong HW, Tiunov MP, Vartanyan S, Orlando L, Corbett-Detig R, MacPhee RD, Shapiro B. Ancient horse genomes reveal the timing and extent of dispersals across the Bering Land Bridge.. Mol Ecol 2021 Dec;30(23):6144-6161.
    doi: 10.1111/mec.15977pubmed: 33971056google scholar: lookup
  59. Dudchenko O, Batra SS, Omer AD, Nyquist SK, Hoeger M, Durand NC, Shamim MS, Machol I, Lander ES, Aiden AP, Aiden EL. De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds.. Science 2017 Apr 7;356(6333):92-95.
    doi: 10.1126/science.aal3327pmc: PMC5635820pubmed: 28336562google scholar: lookup
  60. Suzuki R, Shimodaira H. Pvclust: an R package for assessing the uncertainty in hierarchical clustering.. Bioinformatics 2006 Jun 15;22(12):1540-2.
    doi: 10.1093/bioinformatics/btl117pubmed: 16595560google scholar: lookup
  61. MacFadden BJ. Fossil horses from “Eohippus”(Hyracotherium) to Equus: scaling, Cope’s Law, and the evolution of body size. Paleobiology 1986;12(4):355–69.
  62. Janis CM, Bernor RL. The evolution of equid monodactyly: a review including a new hypothesis. Frontiers in Ecology and Evolution 2019;7:119.
  63. Cantalapiedra JL, Prado JL, Hernández Fernández M, Alberdi MT. Decoupled ecomorphological evolution and diversification in Neogene-Quaternary horses.. Science 2017 Feb 10;355(6325):627-630.
    doi: 10.1126/science.aag1772pubmed: 28183978google scholar: lookup
  64. Jónsson H, Schubert M, Seguin-Orlando A, Ginolhac A, Petersen L, Fumagalli M, Albrechtsen A, Petersen B, Korneliussen TS, Vilstrup JT, Lear T, Myka JL, Lundquist J, Miller DC, Alfarhan AH, Alquraishi SA, Al-Rasheid KA, Stagegaard J, Strauss G, Bertelsen MF, Sicheritz-Ponten T, Antczak DF, Bailey E, Nielsen R, Willerslev E, Orlando L. Speciation with gene flow in equids despite extensive chromosomal plasticity.. Proc Natl Acad Sci U S A 2014 Dec 30;111(52):18655-60.
    doi: 10.1073/pnas.1412627111pmc: PMC4284605pubmed: 25453089google scholar: lookup
  65. Metzger J, Schrimpf R, Philipp U, Distl O. Expression levels of LCORL are associated with body size in horses.. PLoS One 2013;8(2):e56497.
    doi: 10.1371/journal.pone.0056497pmc: PMC3572084pubmed: 23418579google scholar: lookup
  66. Tetens J, Widmann P, Kühn C, Thaller G. A genome-wide association study indicates LCORL/NCAPG as a candidate locus for withers height in German Warmblood horses.. Anim Genet 2013 Aug;44(4):467-71.
    doi: 10.1111/age.12031pubmed: 23418885google scholar: lookup
  67. Soranzo N, Rivadeneira F, Chinappen-Horsley U, Malkina I, Richards JB, Hammond N, Stolk L, Nica A, Inouye M, Hofman A, Stephens J, Wheeler E, Arp P, Gwilliam R, Jhamai PM, Potter S, Chaney A, Ghori MJ, Ravindrarajah R, Ermakov S, Estrada K, Pols HA, Williams FM, McArdle WL, van Meurs JB, Loos RJ, Dermitzakis ET, Ahmadi KR, Hart DJ, Ouwehand WH, Wareham NJ, Barroso I, Sandhu MS, Strachan DP, Livshits G, Spector TD, Uitterlinden AG, Deloukas P. Meta-analysis of genome-wide scans for human adult stature identifies novel Loci and associations with measures of skeletal frame size.. PLoS Genet 2009 Apr;5(4):e1000445.
    doi: 10.1371/journal.pgen.1000445pmc: PMC2661236pubmed: 19343178google scholar: lookup
  68. Lindholm-Perry AK, Kuehn LA, Oliver WT, Sexten AK, Miles JR, Rempel LA, Cushman RA, Freetly HC. Adipose and muscle tissue gene expression of two genes (NCAPG and LCORL) located in a chromosomal region associated with cattle feed intake and gain.. PLoS One 2013;8(11):e80882.
    doi: 10.1371/journal.pone.0080882pmc: PMC3835320pubmed: 24278337google scholar: lookup
  69. Saif R, Henkel J, Jagannathan V, Drögemüller C, Flury C, Leeb T. The LCORL Locus is under Selection in Large-Sized Pakistani Goat Breeds.. Genes (Basel) 2020 Feb 5;11(2).
    doi: 10.3390/genes11020168pmc: PMC7074466pubmed: 32033434google scholar: lookup
  70. Takasuga A. PLAG1 and NCAPG-LCORL in livestock.. Anim Sci J 2016 Feb;87(2):159-67.
    doi: 10.1111/asj.12417pmc: PMC5042058pubmed: 26260584google scholar: lookup
  71. Plassais J, Kim J, Davis BW, Karyadi DM, Hogan AN, Harris AC, Decker B, Parker HG, Ostrander EA. Whole genome sequencing of canids reveals genomic regions under selection and variants influencing morphology.. Nat Commun 2019 Apr 2;10(1):1489.
    pmc: PMC6445083pubmed: 30940804doi: 10.1038/s41467-019-09373-wgoogle scholar: lookup
  72. Halo JV, Pendleton AL, Shen F, Doucet AJ, Derrien T, Hitte C, Kirby LE, Myers B, Sliwerska E, Emery S, Moran JV, Boyko AR, Kidd JM. Long-read assembly of a Great Dane genome highlights the contribution of GC-rich sequence and mobile elements to canine genomes.. Proc Natl Acad Sci U S A 2021 Mar 16;118(11).
    doi: 10.1073/pnas.2016274118pmc: PMC7980453pubmed: 33836575google scholar: lookup
  73. Wang W, Kirkness EF. Short interspersed elements (SINEs) are a major source of canine genomic diversity.. Genome Res 2005 Dec;15(12):1798-808.
    doi: 10.1101/gr.3765505pmc: PMC1356118pubmed: 16339378google scholar: lookup
  74. Abyzov A, Iskow R, Gokcumen O, Radke DW, Balasubramanian S, Pei B, Habegger L, Lee C, Gerstein M. Analysis of variable retroduplications in human populations suggests coupling of retrotransposition to cell division.. Genome Res 2013 Dec;23(12):2042-52.
    doi: 10.1101/gr.154625.113pmc: PMC3847774pubmed: 24026178google scholar: lookup
  75. Gonçalves I, Duret L, Mouchiroud D. Nature and structure of human genes that generate retropseudogenes.. Genome Res 2000 May;10(5):672-8.
    doi: 10.1101/gr.10.5.672pmc: PMC310883pubmed: 10810090google scholar: lookup
  76. Zhang Z, Harrison PM, Liu Y, Gerstein M. Millions of years of evolution preserved: a comprehensive catalog of the processed pseudogenes in the human genome.. Genome Res 2003 Dec;13(12):2541-58.
    doi: 10.1101/gr.1429003pmc: PMC403796pubmed: 14656962google scholar: lookup
  77. Vollger MR, Guitart X, Dishuck PC, Mercuri L, Harvey WT, Gershman A, Diekhans M, Sulovari A, Munson KM, Lewis AP, Hoekzema K, Porubsky D, Li R, Nurk S, Koren S, Miga KH, Phillippy AM, Timp W, Ventura M, Eichler EE. Segmental duplications and their variation in a complete human genome.. Science 2022 Apr;376(6588):eabj6965.
    doi: 10.1126/science.abj6965pmc: PMC8979283pubmed: 35357917google scholar: lookup
  78. Makvandi-Nejad S, Hoffman GE, Allen JJ, Chu E, Gu E, Chandler AM, Loredo AI, Bellone RR, Mezey JG, Brooks SA, Sutter NB. Four loci explain 83% of size variation in the horse.. PLoS One 2012;7(7):e39929.
    doi: 10.1371/journal.pone.0039929pmc: PMC3394777pubmed: 22808074google scholar: lookup
  79. Kunieda T, Park JM, Takeuchi H, Kubo T. Identification and characterization of Mlr1,2: two mouse homologues of Mblk-1, a transcription factor from the honeybee brain(1).. FEBS Lett 2003 Jan 30;535(1-3):61-5.
    pubmed: 12560079doi: 10.1016/s0014-5793(02)03858-9google scholar: lookup
  80. Conway E, Jerman E, Healy E, Ito S, Holoch D, Oliviero G, Deevy O, Glancy E, Fitzpatrick DJ, Mucha M, Watson A, Rice AM, Chammas P, Huang C, Pratt-Kelly I, Koseki Y, Nakayama M, Ishikura T, Streubel G, Wynne K, Hokamp K, McLysaght A, Ciferri C, Di Croce L, Cagney G, Margueron R, Koseki H, Bracken AP. A Family of Vertebrate-Specific Polycombs Encoded by the LCOR/LCORL Genes Balance PRC2 Subtype Activities.. Mol Cell 2018 May 3;70(3):408-421.e8.
    doi: 10.1016/j.molcel.2018.03.005pubmed: 29628311google scholar: lookup
  81. Srikanth K, Kim NY, Park W, Kim JM, Kim KD, Lee KT, Son JH, Chai HH, Choi JW, Jang GW, Kim H, Ryu YC, Nam JW, Park JE, Kim JM, Lim D. Comprehensive genome and transcriptome analyses reveal genetic relationship, selection signature, and transcriptome landscape of small-sized Korean native Jeju horse.. Sci Rep 2019 Nov 13;9(1):16672.
    pmc: PMC6853925pubmed: 31723199doi: 10.1038/s41598-019-53102-8google scholar: lookup
  82. Sotgia F, Fiorillo M, Lisanti MP. Mitochondrial markers predict recurrence, metastasis and tamoxifen-resistance in breast cancer patients: Early detection of treatment failure with companion diagnostics.. Oncotarget 2017 Sep 15;8(40):68730-68745.
    doi: 10.18632/oncotarget.19612pmc: PMC5620292pubmed: 28978152google scholar: lookup
  83. Deng F, Shen L, Wang H, Zhang L. Classify multicategory outcome in patients with lung adenocarcinoma using clinical, transcriptomic and clinico-transcriptomic data: machine learning versus multinomial models.. Am J Cancer Res 2020;10(12):4624-4639.
    pmc: PMC7783755pubmed: 33415023
  84. Zeng Y, Shi Y, Xu L, Zeng Y, Cui X, Wang Y, Yang N, Zhou F, Zhou Y. Prognostic Value and Related Regulatory Networks of MRPL15 in Non-Small-Cell Lung Cancer.. Front Oncol 2021;11:656172.
    doi: 10.3389/fonc.2021.656172pmc: PMC8138120pubmed: 34026630google scholar: lookup
  85. McHorse BK, Biewener AA, Pierce SE. The Evolution of a Single Toe in Horses: Causes, Consequences, and the Way Forward.. Integr Comp Biol 2019 Sep 1;59(3):638-655.
    doi: 10.1093/icb/icz050pubmed: 31127281google scholar: lookup
  86. Elder JF Jr, Turner BJ. Concerted evolution of repetitive DNA sequences in eukaryotes.. Q Rev Biol 1995 Sep;70(3):297-320.
    doi: 10.1086/419073pubmed: 7568673google scholar: lookup
  87. Nunney L. Cancer suppression and the evolution of multiple retrogene copies of TP53 in elephants: A re-evaluation.. Evol Appl 2022 May;15(5):891-901.
    doi: 10.1111/eva.13383pmc: PMC9108310pubmed: 35603034google scholar: lookup
  88. Yang L, Emerman M, Malik HS, McLaughlin RN Jnr. Retrocopying expands the functional repertoire of APOBEC3 antiviral proteins in primates.. Elife 2020 Jun 1;9.
    doi: 10.7554/eLife.58436pmc: PMC7263822pubmed: 32479260google scholar: lookup

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