Tandem repeats lead to sequence assembly errors and impose multi-level challenges for genome and protein databases.
Journal
Nucleic acids research
ISSN: 1362-4962
Titre abrégé: Nucleic Acids Res
Pays: England
ID NLM: 0411011
Informations de publication
Date de publication:
02 12 2019
02 12 2019
Historique:
accepted:
01
10
2019
revised:
03
09
2019
received:
07
06
2019
pubmed:
5
10
2019
medline:
12
5
2020
entrez:
5
10
2019
Statut:
ppublish
Résumé
The widespread occurrence of repetitive stretches of DNA in genomes of organisms across the tree of life imposes fundamental challenges for sequencing, genome assembly, and automated annotation of genes and proteins. This multi-level problem can lead to errors in genome and protein databases that are often not recognized or acknowledged. As a consequence, end users working with sequences with repetitive regions are faced with 'ready-to-use' deposited data whose trustworthiness is difficult to determine, let alone to quantify. Here, we provide a review of the problems associated with tandem repeat sequences that originate from different stages during the sequencing-assembly-annotation-deposition workflow, and that may proliferate in public database repositories affecting all downstream analyses. As a case study, we provide examples of the Atlantic cod genome, whose sequencing and assembly were hindered by a particularly high prevalence of tandem repeats. We complement this case study with examples from other species, where mis-annotations and sequencing errors have propagated into protein databases. With this review, we aim to raise the awareness level within the community of database users, and alert scientists working in the underlying workflow of database creation that the data they omit or improperly assemble may well contain important biological information valuable to others.
Identifiants
pubmed: 31584084
pii: 5580909
doi: 10.1093/nar/gkz841
pmc: PMC6868369
doi:
Substances chimiques
DNA
9007-49-2
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Review
Langues
eng
Sous-ensembles de citation
IM
Pagination
10994-11006Informations de copyright
© The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research.
Références
Nucleic Acids Res. 2017 Jan 4;45(D1):D308-D312
pubmed: 27899671
Genome Biol. 2007;8(11):R251
pubmed: 18039395
PLoS One. 2016 Jul 14;11(7):e0159232
pubmed: 27414800
New Phytol. 2015 Apr;206(1):397-410
pubmed: 25420631
Annu Rev Anim Biosci. 2018 Feb 15;6:23-46
pubmed: 29166127
Database (Oxford). 2017 Jan 1;2017:
pubmed: 29220431
Nat Protoc. 2016 Sep;11(9):1650-67
pubmed: 27560171
PLoS One. 2012;7(2):e30087
pubmed: 22347999
Nucleic Acids Res. 2001 Jan 1;29(1):320-2
pubmed: 11125125
Nat Nanotechnol. 2010 Nov;5(11):798-806
pubmed: 20871614
FEMS Immunol Med Microbiol. 2011 Apr;61(3):245-57
pubmed: 21208290
Mol Genet Genomics. 2010 Aug;284(2):75-94
pubmed: 20585957
Genome Biol. 2018 Oct 4;19(1):153
pubmed: 30286803
BMC Genomics. 2018 Apr 10;19(1):240
pubmed: 29636006
Proc Natl Acad Sci U S A. 1997 Apr 15;94(8):3817-22
pubmed: 9108061
Int J Legal Med. 2019 Mar;133(2):325-334
pubmed: 29797283
Proc Natl Acad Sci U S A. 1997 Apr 15;94(8):3811-6
pubmed: 9108060
Brief Bioinform. 2007 Nov;8(6):382-92
pubmed: 17932080
Plant Physiol. 2014 Feb;164(2):513-24
pubmed: 24306534
Stand Genomic Sci. 2015 Nov 19;10:108
pubmed: 26594309
Nucleic Acids Res. 2014 Jan;42(Database issue):D273-8
pubmed: 24150944
G3 (Bethesda). 2014 Jan 10;4(1):67-78
pubmed: 24192840
Nat Genet. 2005 Sep;37(9):986-90
pubmed: 16086015
Bioinformatics. 2015 Sep 15;31(18):3051-3
pubmed: 25987568
Nucleic Acids Res. 2013 Sep;41(17):e162
pubmed: 23877246
FEMS Microbiol Rev. 2014 Jan;38(1):119-41
pubmed: 23927439
Bioinformatics. 2008 Mar 1;24(5):637-44
pubmed: 18218656
J Mol Biol. 1999 Oct 15;293(1):151-60
pubmed: 10512723
Annu Rev Immunol. 2012;30:203-20
pubmed: 22224775
Genome Res. 2000 Jul;10(7):899-907
pubmed: 10899139
Sci Rep. 2017 Mar 23;7(1):371
pubmed: 28336969
Nat Biotechnol. 2011 May 15;29(7):644-52
pubmed: 21572440
Genome Res. 2018 Aug;28(8):1169-1178
pubmed: 29970452
Bioinformatics. 2010 Sep 15;26(18):i420-5
pubmed: 20823302
Bioinformatics. 2014 May 1;30(9):1236-40
pubmed: 24451626
BMC Bioinformatics. 2011 Dec 22;12:491
pubmed: 22192575
J Mol Biol. 2000 May 5;298(3):521-37
pubmed: 10772867
Microbiology (Reading). 2003 Mar;149(Pt 3):643-654
pubmed: 12634333
PLoS One. 2008 Feb 27;3(2):e1694
pubmed: 18301771
Am J Hum Genet. 1989 Mar;44(3):397-401
pubmed: 2563634
Proc Natl Acad Sci U S A. 1995 Apr 25;92(9):3636-41
pubmed: 7731957
PLoS Comput Biol. 2013 Apr;9(4):e1003031
pubmed: 23592973
Nucleic Acids Res. 2012 Nov 1;40(20):10005-17
pubmed: 22923522
Mol Biol Evol. 2013 Jan;30(1):140-53
pubmed: 22949522
Curr Opin Insect Sci. 2015 Feb;7:8-14
pubmed: 32846689
Nature. 1999 Nov 4;402(6757):86-90
pubmed: 10573422
Anthropol Anz. 2017 Dec 1;74(4):263-268
pubmed: 28817155
BMC Evol Biol. 2017 Jan 11;17(1):10
pubmed: 28077068
Curr Opin Struct Biol. 1998 Jun;8(3):338-45
pubmed: 9666330
Forensic Sci Int Genet. 2017 Sep;30:134-140
pubmed: 28728056
PLoS Biol. 2004 Jul;2(7):E206
pubmed: 15252449
Nucleic Acids Res. 2005 Nov 28;33(20):6494-506
pubmed: 16314312
Nature. 2011 Aug 10;477(7363):207-10
pubmed: 21832995
Nucleic Acids Res. 1999 Jan 15;27(2):573-80
pubmed: 9862982
Int J Legal Med. 2018 May;132(3):713-725
pubmed: 29464313
PLoS One. 2012;7(11):e48805
pubmed: 23144980
Genetics. 2010 Sep;186(1):207-18
pubmed: 20457880
Mol Biol Evol. 2014 May;31(5):1132-48
pubmed: 24497029
Mar Biotechnol (NY). 2014 Oct;16(5):604-19
pubmed: 24939717
FEBS J. 2010 Jun;277(12):2673-82
pubmed: 20553501
Bioessays. 2003 Sep;25(9):847-55
pubmed: 12938174
Adv Protein Chem Struct Biol. 2010;79:59-88
pubmed: 20621281
J Struct Biol. 2018 Feb;201(2):171-183
pubmed: 28888816
Chromosome Res. 2005;13(5):505-15
pubmed: 16132815
Nat Genet. 2018 Feb;50(2):270-277
pubmed: 29358652
BMC Evol Biol. 2012 Aug 24;12:155
pubmed: 22920595
BMC Genomics. 2012 Jul 02;13:293
pubmed: 22747999
Genome Res. 2008 May;18(5):821-9
pubmed: 18349386
Genome Biol Evol. 2010 Jul 12;2:441-53
pubmed: 20624746
Nat Biotechnol. 2019 Oct;37(10):1155-1162
pubmed: 31406327
Cold Spring Harb Perspect Med. 2012 Dec 01;2(12):a011627
pubmed: 23209182
Bioinformatics. 2017 Apr 15;33(8):1221-1223
pubmed: 28031183
Genome Biol Evol. 2018 Mar 1;10(3):816-825
pubmed: 29608721
Genome Biol Evol. 2017 Jan 1;9(1):161-177
pubmed: 28158585
Open Biol. 2016 Apr;6(4):160009
pubmed: 27248802
Philos Trans R Soc Lond B Biol Sci. 2015 Sep 26;370(1678):20140331
pubmed: 26323762
Front Bioeng Biotechnol. 2015 Sep 24;3:143
pubmed: 26442257
Genome Biol. 2009;10(6):R59
pubmed: 19486509
Trends Genet. 2000 Sep;16(9):418-20
pubmed: 10973072
Proc Natl Acad Sci U S A. 1980 Oct;77(10):5802-6
pubmed: 6934511
Protein Pept Lett. 2019;26(2):108-131
pubmed: 30526451
Genome Res. 2002 Jun;12(6):996-1006
pubmed: 12045153
Nature. 2008 Nov 6;456(7218):53-9
pubmed: 18987734
Nucleic Acids Res. 2007 Jan;35(Database issue):D80-7
pubmed: 17175540
Genome. 2016 May;59(5):295-310
pubmed: 27064176
Nat Genet. 2018 Jan;50(1):20-25
pubmed: 29255259
J Biol Chem. 1983 Mar 10;258(5):3028-31
pubmed: 6298218
J Comput Biol. 2012 May;19(5):455-77
pubmed: 22506599
Nature. 2015 Oct 1;526(7571):68-74
pubmed: 26432245
Proc Natl Acad Sci U S A. 2011 Jan 25;108(4):1513-8
pubmed: 21187386
Genome Res. 2017 May;27(5):697-708
pubmed: 28360231
Mol Biol Evol. 2018 Mar 1;35(3):593-606
pubmed: 29216381
Proc Natl Acad Sci U S A. 2013 Apr 9;110(15):6043-8
pubmed: 23487799
Nucleic Acids Res. 2018 Sep 28;46(17):8953-8965
pubmed: 30137508
Int J Legal Med. 2018 Sep;132(5):1301-1304
pubmed: 29500610
F1000Res. 2017 Feb 3;6:100
pubmed: 28868132
BMC Genomics. 2018 Jun 27;19(1):500
pubmed: 29945549
Nucleic Acids Res. 2015 Jan;43(Database issue):D204-12
pubmed: 25348405
Genome Res. 2010 Jun;20(6):745-54
pubmed: 20335526
Trends Genet. 2006 May;22(5):253-9
pubmed: 16567018
Mol Ecol Resour. 2011 Sep;11(5):759-69
pubmed: 21592312
Nature. 1999 Nov 4;402(6757):83-6
pubmed: 10573421
Mol Genet Genomics. 2017 Aug;292(4):883-894
pubmed: 28409264
PLoS Pathog. 2009 Aug;5(8):e1000560
pubmed: 19696920
Mol Microbiol. 1999 Jul;33(1):208-19
pubmed: 10411737
Biosci Rep. 2013 Jan 24;33(1):175-84
pubmed: 23167261
Sci Rep. 2017 Aug 11;7(1):7956
pubmed: 28801564
Nat Rev Genet. 2011 Nov 29;13(1):36-46
pubmed: 22124482
Genes (Basel). 2011 Jul 13;2(3):449-501
pubmed: 24710207
Genome Biol. 2016 Jan 26;17:13
pubmed: 26813401
Genome Biol. 2008 Jan 11;9(1):R7
pubmed: 18190707
Front Bioeng Biotechnol. 2015 Mar 17;3:31
pubmed: 25853125
Proc Natl Acad Sci U S A. 2018 Apr 24;115(17):4325-4333
pubmed: 29686065
Genomics Proteomics Bioinformatics. 2015 Oct;13(5):278-89
pubmed: 26542840
Sci Adv. 2017 Aug 09;3(8):e1701440
pubmed: 28808685
Nat Biotechnol. 2019 Feb;37(2):124-126
pubmed: 30670796
Nature. 1985 Mar 7-13;314(6006):67-73
pubmed: 3856104
J Mol Biol. 1978 Mar 25;120(1):33-53
pubmed: 642006
J Mol Evol. 1992 Oct;35(4):286-91
pubmed: 1404414
Genomics. 2010 Jun;95(6):315-27
pubmed: 20211242
J Struct Biol. 2012 Sep;179(3):279-88
pubmed: 21884799
BMC Genomics. 2017 Jan 18;18(1):95
pubmed: 28100185
Genome Biol Evol. 2015 Jan 09;7(2):567-80
pubmed: 25577199
Curr Opin Genet Dev. 2017 Jun;44:9-16
pubmed: 28213161
Nat Biotechnol. 2019 Feb;37(2):127-128
pubmed: 30670797
Sci Rep. 2014 May 23;4:5052
pubmed: 24852006
Nat Plants. 2018 Nov;4(11):879-887
pubmed: 30390080
BMC Genomics. 2010 Apr 30;11:277
pubmed: 20433735
Nat Rev Genet. 2012 Apr 18;13(5):329-42
pubmed: 22510764
Science. 2000 Mar 24;287(5461):2196-204
pubmed: 10731133
Science. 2009 Jan 2;323(5910):133-8
pubmed: 19023044
Genetica. 2002 May;115(1):49-63
pubmed: 12188048
Nucleic Acids Res. 2018 Jan 4;46(D1):D41-D47
pubmed: 29140468