The Transposable Elements of the Drosophila serrata Reference Panel.
Drosophila serrata
copy number
inbred lines
transposable elements
Journal
Genome biology and evolution
ISSN: 1759-6653
Titre abrégé: Genome Biol Evol
Pays: England
ID NLM: 101509707
Informations de publication
Date de publication:
01 09 2021
01 09 2021
Historique:
accepted:
30
04
2021
pubmed:
6
5
2021
medline:
1
4
2022
entrez:
5
5
2021
Statut:
ppublish
Résumé
Transposable elements (TEs) are an important component of the complex genomic ecosystem. Understanding the tempo and mode of TE proliferation, that is whether it is in maintained in transposition selection balance, or is induced periodically by environmental stress or other factors, is important for understanding the evolution of organismal genomes through time. Although TEs have been characterized in individuals or limited samples, a true understanding of the population genetics of TEs, and therefore the tempo and mode of transposition, is still lacking. Here, we characterize the TE landscape in an important model Drosophila, Drosophila serrata using the D. serrata reference panel, which is comprised of 102 sequenced inbred genotypes. We annotate the families of TEs in the D. serrata genome and investigate variation in TE copy number between genotypes. We find that many TEs have low copy number in the population, but this varies by family and includes a single TE making up to 50% of the genome content of TEs. We find that some TEs proliferate in particular genotypes compared with population levels. In addition, we characterize variation in each TE family allowing copy number to vary in each genotype and find that some TEs have diversified very little between individuals suggesting recent spread. TEs are important sources of spontaneous mutations in Drosophila, making up a large fraction of the total number of mutations in particular genotypes. Understanding the dynamics of TEs within populations will be an important step toward characterizing the origin of variation within and between species.
Identifiants
pubmed: 33950180
pii: 6265467
doi: 10.1093/gbe/evab100
pmc: PMC8434751
pii:
doi:
Substances chimiques
DNA Transposable Elements
0
Types de publication
Journal Article
Research Support, U.S. Gov't, Non-P.H.S.
Langues
eng
Sous-ensembles de citation
IM
Informations de copyright
© The Author(s) 2021. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.
Références
Nat Commun. 2014 Dec 16;5:5495
pubmed: 25510865
Genome Res. 2010 Sep;20(9):1297-303
pubmed: 20644199
Cold Spring Harb Symp Quant Biol. 2009;74:225-34
pubmed: 20453205
Evolution. 2009 Aug;63(8):1954-63
pubmed: 19473402
EMBO J. 1994 Sep 15;13(18):4401-11
pubmed: 7925283
G3 (Bethesda). 2017 May 5;7(5):1487-1497
pubmed: 28315830
Proc Natl Acad Sci U S A. 1988 Dec;85(23):9153-7
pubmed: 2848256
J Hered. 2004 Jul-Aug;95(4):284-90
pubmed: 15247307
Genetica. 1997;100(1-3):167-75
pubmed: 9440270
Plant Physiol. 2018 Feb;176(2):1410-1422
pubmed: 29233850
Genet Res. 1990 Aug;56(1):3-14
pubmed: 2172082
Nucleic Acids Res. 2016 Jan 4;44(D1):D81-9
pubmed: 26612867
Heredity (Edinb). 2007 Nov;99(5):525-30
pubmed: 17622267
PLoS Genet. 2011 Oct;7(10):e1002337
pubmed: 22028673
Cell. 1983 Aug;34(1):75-84
pubmed: 6309414
BMC Genomics. 2007 Nov 16;8:422
pubmed: 18021408
Genetics. 1991 Oct;129(2):501-12
pubmed: 1660427
PLoS One. 2016 Jan 26;11(1):e0147903
pubmed: 26812285
Proc Natl Acad Sci U S A. 2013 Dec 3;110(49):19842-7
pubmed: 24248389
Cell. 1984 Sep;38(2):471-81
pubmed: 6088083
Proc Natl Acad Sci U S A. 2007 Jul 3;104(27):11340-5
pubmed: 17592135
Mob DNA. 2019 Dec 30;10:53
pubmed: 31892957
Philos Trans R Soc Lond B Biol Sci. 2010 Apr 27;365(1544):1219-28
pubmed: 20308097
Science. 2009 Nov 20;326(5956):1112-5
pubmed: 19965430
Genome Biol Evol. 2016 Jan 21;8(2):403-10
pubmed: 26802115
Nat Biotechnol. 2011 May 15;29(7):644-52
pubmed: 21572440
Gene. 1997 Dec 31;205(1-2):229-43
pubmed: 9461397
Proc Natl Acad Sci U S A. 2015 May 26;112(21):6659-63
pubmed: 25964349
Mol Biol Evol. 2004 Jan;21(1):36-44
pubmed: 12949132
Mol Cell Biol. 1986 Apr;6(4):1129-34
pubmed: 3023871
Science. 2002 Sep 27;297(5590):2253-6
pubmed: 12351787
Proc Natl Acad Sci U S A. 2001 Jul 17;98(15):8714-9
pubmed: 11447285
Proc Natl Acad Sci U S A. 2003 May 27;100(11):6569-74
pubmed: 12743378
Genome Res. 2006 Oct;16(10):1262-9
pubmed: 16963705
PLoS Genet. 2014 Aug 14;10(8):e1004560
pubmed: 25122208
Evolution. 1993 Aug;47(4):1271-1285
pubmed: 28564291
Genome Res. 2019 Jan;29(1):85-95
pubmed: 30541785
Nature. 2012 Feb 08;482(7384):173-8
pubmed: 22318601
Nature. 1987 Oct 22-28;329(6141):742-4
pubmed: 2823144
Proc Natl Acad Sci U S A. 2014 Jul 15;111(28):10263-8
pubmed: 24982153
Genetics. 1994 Feb;136(2):573-83
pubmed: 8150284
Genetics. 2006 May;173(1):189-96
pubmed: 16387876
Mob DNA. 2014 Aug 01;5:22
pubmed: 25126116
Mol Biol Evol. 2019 Jul 1;36(7):1457-1472
pubmed: 30968135
Genes Dev. 1994 Sep 1;8(17):2046-57
pubmed: 7958877
Cell. 2007 Mar 23;128(6):1089-103
pubmed: 17346786
G3 (Bethesda). 2017 Mar 10;7(3):781-788
pubmed: 28143951
Proc Natl Acad Sci U S A. 2017 May 2;114(18):4721-4726
pubmed: 28416702
Genetics. 1985 Feb;109(2):459-80
pubmed: 2982700
G3 (Bethesda). 2018 Mar 28;8(4):1335-1346
pubmed: 29487184
Methods Mol Biol. 2019;1910:177-207
pubmed: 31278665
BMC Bioinformatics. 2008 Jan 14;9:18
pubmed: 18194517
PLoS Genet. 2014 Feb 06;10(2):e1004138
pubmed: 24516406
Appl Plant Sci. 2014 Jan 07;2(1):
pubmed: 25202595
Mol Biol Evol. 1999 Nov;16(11):1503-10
pubmed: 10555281
Nat Rev Genet. 2019 Feb;20(2):89-108
pubmed: 30446728
Heredity (Edinb). 2011 Dec;107(6):487-95
pubmed: 21673742
Syst Biol. 2012 May;61(3):539-42
pubmed: 22357727
Mutat Res. 1964 May;106:2-9
pubmed: 14195748
Genet Res. 2002 Apr;79(2):141-8
pubmed: 12073552
Evolution. 1999 Dec;53(6):1823-1834
pubmed: 28565454
Mol Biol Evol. 2016 Oct;33(10):2759-64
pubmed: 27486221
Gene. 2014 Mar 1;537(1):149-53
pubmed: 24361206
J Econ Entomol. 1993 Jun;86(3):645-51
pubmed: 8391554
Heredity (Edinb). 1994 Oct;73 ( Pt 4):377-85
pubmed: 7989218
Genetics. 2012 Dec;192(4):1411-32
pubmed: 22997235
Genes Dev. 1989 Jan;3(1):73-84
pubmed: 2540060
EMBO Rep. 2014 Apr;15(4):411-8
pubmed: 24562610
Evolution. 2002 May;56(5):1068-73
pubmed: 12093021
Genome Biol. 2004;5(6):225
pubmed: 15186483
Mob DNA. 2019 Dec 12;10:48
pubmed: 31857828
Trends Genet. 2007 Oct;23(10):521-9
pubmed: 17850916
Mol Biol Evol. 1990 Nov;7(6):589-606
pubmed: 2178210
Nat Rev Genet. 2008 May;9(5):411-2; author reply 414
pubmed: 18421312
Genetics. 1991 Jun;128(2):319-29
pubmed: 1649069
PLoS Genet. 2016 May 11;12(5):e1006058
pubmed: 27166958
Genome Biol. 2006;7(11):R112
pubmed: 17134480
Plant Physiol. 2019 Aug;180(4):1803-1815
pubmed: 31152127
Genome Biol. 2019 Dec 16;20(1):275
pubmed: 31843001
PLoS Genet. 2007 Sep;3(9):1633-43
pubmed: 17941712
Proc Natl Acad Sci U S A. 1983 Mar;80(6):1655-9
pubmed: 6300863
Wiley Interdiscip Rev RNA. 2011 Nov-Dec;2(6):772-86
pubmed: 21976282
Genome Biol Evol. 2015 Mar 11;7(4):1192-205
pubmed: 25767248
Nucleic Acids Res. 2015 Dec 15;43(22):10655-72
pubmed: 26578579
Nucleic Acids Res. 2007 Jul;35(Web Server issue):W265-8
pubmed: 17485477
Proc Natl Acad Sci U S A. 1950 Jun;36(6):344-55
pubmed: 15430309
Proc Natl Acad Sci U S A. 1994 Feb 15;91(4):1285-9
pubmed: 8108403
Bioinformatics. 2009 Aug 15;25(16):2078-9
pubmed: 19505943
Science. 2005 Jul 29;309(5735):764-7
pubmed: 16051794
Science. 1984 Nov 16;226(4676):792-801
pubmed: 15739260
Mol Biol Evol. 1997 Nov;14(11):1132-44
pubmed: 9364771
Genome. 2013 Sep;56(9):475-86
pubmed: 24168668
Cell. 2009 May 1;137(3):522-35
pubmed: 19395010
Bioinformatics. 2004 Jan 22;20(2):289-90
pubmed: 14734327
Genetica. 1999;107(1-3):129-37
pubmed: 10952206
Bioinformatics. 2010 Mar 15;26(6):841-2
pubmed: 20110278
Nat Rev Genet. 2007 Dec;8(12):973-82
pubmed: 17984973
Genome Res. 2020 Apr;30(4):566-575
pubmed: 32238416
Genetica. 1999;105(1):43-62
pubmed: 10483093
Science. 2021 Feb 19;371(6531):
pubmed: 33602827
Genetics. 1991 Jun;128(2):471-86
pubmed: 1649073
BMC Bioinformatics. 2009 Dec 15;10:421
pubmed: 20003500
Genes (Basel). 2019 May 30;10(6):
pubmed: 31151307
Nature. 1980 Apr 17;284(5757):601-3
pubmed: 6245369
Heredity (Edinb). 2012 May;108(5):461-8
pubmed: 21971178
Proc Natl Acad Sci U S A. 2019 Apr 2;116(14):6908-6913
pubmed: 30877258
Genetics. 1990 Feb;124(2):339-55
pubmed: 2155157
Mol Biol Evol. 1999 Sep;16(9):1251-5
pubmed: 10486980
Ecol Evol. 2020 Mar 13;10(7):3402-3412
pubmed: 32273997