Ancient segmentally duplicated LCORL retrocopies in equids.
Journal
PloS one
ISSN: 1932-6203
Titre abrégé: PLoS One
Pays: United States
ID NLM: 101285081
Informations de publication
Date de publication:
2023
2023
Historique:
received:
17
04
2023
accepted:
25
05
2023
medline:
12
6
2023
pubmed:
8
6
2023
entrez:
8
6
2023
Statut:
epublish
Résumé
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.
Identifiants
pubmed: 37289743
doi: 10.1371/journal.pone.0286861
pii: PONE-D-23-11627
pmc: PMC10249811
doi:
Substances chimiques
DNA Transposable Elements
0
Proteins
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
e0286861Informations de copyright
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.
Déclaration de conflit d'intérêts
The authors have declared that no competing interests exist.
Références
Bioinformatics. 2012 Sep 15;28(18):i333-i339
pubmed: 22962449
Cell. 1993 Feb 26;72(4):595-605
pubmed: 7679954
Anim Genet. 2018 Dec;49(6):564-570
pubmed: 30311254
PLoS Comput Biol. 2017 Jun 29;13(6):e1005567
pubmed: 28662076
Science. 2022 Apr;376(6588):eabj6965
pubmed: 35357917
Database (Oxford). 2017 Jan 1;2017:
pubmed: 29220443
Elife. 2016 Sep 19;5:
pubmed: 27642012
Nat Commun. 2018 Jul 27;9(1):2945
pubmed: 30054462
Proc Natl Acad Sci U S A. 2017 Oct 24;114(43):11476-11481
pubmed: 29073074
Nat Commun. 2020 Dec 8;11(1):6014
pubmed: 33293529
Q Rev Biol. 1995 Sep;70(3):297-320
pubmed: 7568673
Science. 2015 Jan 23;347(6220):1260419
pubmed: 25613900
Nat Rev Genet. 2020 Mar;21(3):191-201
pubmed: 31848477
Anim Genet. 2022 Apr;53(2):183-192
pubmed: 35077588
PLoS Genet. 2009 Apr;5(4):e1000445
pubmed: 19343178
Genome Res. 2003 Dec;13(12):2541-58
pubmed: 14656962
Elife. 2020 Jun 01;9:
pubmed: 32479260
Science. 2017 Apr 7;356(6333):92-95
pubmed: 28336562
Science. 2009 Aug 21;325(5943):995-8
pubmed: 19608863
Mol Biol Evol. 2022 Aug 3;39(8):
pubmed: 35881460
Nat Biotechnol. 2016 May;34(5):525-7
pubmed: 27043002
Nucleic Acids Res. 2017 Jan 4;45(D1):D68-D73
pubmed: 27924012
Genome Res. 2005 Dec;15(12):1798-808
pubmed: 16339378
Microb Genom. 2016 Apr 29;2(4):e000056
pubmed: 28348851
Nat Biotechnol. 2019 Aug;37(8):907-915
pubmed: 31375807
JAMA. 2015 Nov 3;314(17):1850-60
pubmed: 26447779
Anim Genet. 2013 Aug;44(4):467-71
pubmed: 23418885
PLoS One. 2013 Nov 20;8(11):e80882
pubmed: 24278337
Genome Res. 2022 Aug 12;:
pubmed: 35961775
Oncotarget. 2017 Jul 27;8(40):68730-68745
pubmed: 28978152
Integr Comp Biol. 2019 Sep 1;59(3):638-655
pubmed: 31127281
Mol Ecol. 2021 Dec;30(23):6144-6161
pubmed: 33971056
Genome Res. 2000 May;10(5):672-8
pubmed: 10810090
Gigascience. 2021 Feb 16;10(2):
pubmed: 33590861
PLoS One. 2013;8(2):e56497
pubmed: 23418579
Genome Biol Evol. 2017 Jun 1;9(6):1351-1373
pubmed: 28605529
Physiol Genomics. 2016 May;48(5):325-35
pubmed: 26931356
Genes (Basel). 2020 Feb 05;11(2):
pubmed: 32033434
Science. 2017 Feb 10;355(6325):627-630
pubmed: 28183978
PLoS Genet. 2013;9(1):e1003242
pubmed: 23359205
Mol Biol Evol. 2021 Jun 25;38(7):2958-2966
pubmed: 33681998
Genome Biol. 2021 May 10;22(1):146
pubmed: 33971925
Bioessays. 2014 May;36(5):475-81
pubmed: 24615986
Nat Commun. 2019 Apr 2;10(1):1489
pubmed: 30940804
Nucleic Acids Res. 2011 Jan;39(Database issue):D19-21
pubmed: 21062823
Methods Mol Biol. 2008;422:31-49
pubmed: 18629659
Proc Natl Acad Sci U S A. 2021 Feb 9;118(6):
pubmed: 33526666
Sci Rep. 2019 Nov 13;9(1):16672
pubmed: 31723199
Annu Rev Genet. 1985;19:253-72
pubmed: 3909943
Nat Genet. 2000 Apr;24(4):363-7
pubmed: 10742098
F1000Res. 2016 Jun 23;5:1479
pubmed: 27429743
Nature. 2013 Jul 4;499(7456):74-8
pubmed: 23803765
Annu Rev Genet. 2001;35:501-38
pubmed: 11700292
Mol Cell. 2018 May 3;70(3):408-421.e8
pubmed: 29628311
Chromosome Res. 2000;8(8):659-70
pubmed: 11196129
Genome Res. 2013 Dec;23(12):2042-52
pubmed: 24026178
Curr Biol. 2015 Oct 19;25(20):R973-8
pubmed: 26485367
F1000Res. 2020 Apr 28;9:304
pubmed: 32489650
Mob DNA. 2016 Nov 11;7:21
pubmed: 27843499
PLoS One. 2012;7(7):e39929
pubmed: 22808074
Anim Sci J. 2016 Feb;87(2):159-67
pubmed: 26260584
Commun Biol. 2018 Nov 16;1:197
pubmed: 30456315
Evol Appl. 2022 Apr 25;15(5):891-901
pubmed: 35603034
Mol Biol Evol. 2008 Jun;25(6):1148-57
pubmed: 18343891
Bioinformatics. 2006 Jun 15;22(12):1540-2
pubmed: 16595560
Nucleic Acids Res. 2014 Jul;42(Web Server issue):W494-500
pubmed: 24810850
Mol Cell Biol. 2001 Feb;21(4):1429-39
pubmed: 11158327
Chromosome Res. 1997 Nov;5(7):433-43
pubmed: 9421259
Front Oncol. 2021 May 07;11:656172
pubmed: 34026630
Cells. 2021 Apr 15;10(4):
pubmed: 33921034
Proc Natl Acad Sci U S A. 1997 Mar 4;94(5):1872-7
pubmed: 9050872
Bioinformatics. 2018 Sep 15;34(18):3094-3100
pubmed: 29750242
Genome Biol. 2013 Mar 13;14(3):R22
pubmed: 23497673
Proc Natl Acad Sci U S A. 2014 Dec 30;111(52):18655-60
pubmed: 25453089
FEBS Lett. 2003 Jan 30;535(1-3):61-5
pubmed: 12560079
Brief Bioinform. 2013 Mar;14(2):178-92
pubmed: 22517427
Trends Genet. 2022 Jan;38(1):59-72
pubmed: 34294428
Nucleic Acids Res. 2004 Mar 19;32(5):1792-7
pubmed: 15034147
Proc Natl Acad Sci U S A. 2021 Mar 16;118(11):
pubmed: 33836575
Am J Cancer Res. 2020 Dec 01;10(12):4624-4639
pubmed: 33415023
Annu Rev Anim Biosci. 2021 Feb 16;9:81-101
pubmed: 33197207