Genomic and transcriptomic variation defines the chromosome-scale assembly of Haemonchus contortus, a model gastrointestinal worm.
Journal
Communications biology
ISSN: 2399-3642
Titre abrégé: Commun Biol
Pays: England
ID NLM: 101719179
Informations de publication
Date de publication:
09 11 2020
09 11 2020
Historique:
received:
05
03
2020
accepted:
14
10
2020
entrez:
10
11
2020
pubmed:
11
11
2020
medline:
29
6
2021
Statut:
epublish
Résumé
Haemonchus contortus is a globally distributed and economically important gastrointestinal pathogen of small ruminants and has become a key nematode model for studying anthelmintic resistance and other parasite-specific traits among a wider group of parasites including major human pathogens. Here, we report using PacBio long-read and OpGen and 10X Genomics long-molecule methods to generate a highly contiguous 283.4 Mbp chromosome-scale genome assembly including a resolved sex chromosome for the MHco3(ISE).N1 isolate. We show a remarkable pattern of conservation of chromosome content with Caenorhabditis elegans, but almost no conservation of gene order. Short and long-read transcriptome sequencing allowed us to define coordinated transcriptional regulation throughout the parasite's life cycle and refine our understanding of cis- and trans-splicing. Finally, we provide a comprehensive picture of chromosome-wide genetic diversity both within a single isolate and globally. These data provide a high-quality comparison for understanding the evolution and genomics of Caenorhabditis and other nematodes and extend the experimental tractability of this model parasitic nematode in understanding helminth biology, drug discovery and vaccine development, as well as important adaptive traits such as drug resistance.
Identifiants
pubmed: 33168940
doi: 10.1038/s42003-020-01377-3
pii: 10.1038/s42003-020-01377-3
pmc: PMC7652881
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
656Subventions
Organisme : Wellcome Trust
ID : WT206194
Pays : United Kingdom
Organisme : Wellcome Trust
ID : 067811
Pays : United Kingdom
Organisme : Wellcome Trust
Pays : United Kingdom
Organisme : Biotechnology and Biological Sciences Research Council
ID : BB/K020048/1
Pays : United Kingdom
Organisme : Biotechnology and Biological Sciences Research Council
ID : BB/M003949/1
Pays : United Kingdom
Organisme : Biotechnology and Biological Sciences Research Council
ID : BB/P024610/1
Pays : United Kingdom
Références
Genome Biol Evol. 2019 Jul 1;11(7):1965-1970
pubmed: 31263885
Exp Parasitol. 1986 Jun;61(3):294-303
pubmed: 3086114
Nat Genet. 2015 Apr;47(4):416-22
pubmed: 25730766
Bioinformatics. 2015 Oct 15;31(20):3350-2
pubmed: 26099265
Nat Commun. 2019 Jan 16;10(1):260
pubmed: 30651564
Bioinformatics. 2018 Mar 1;34(5):725-731
pubmed: 29069293
Nature. 2013 Apr 04;496(7443):57-63
pubmed: 23485966
Int J Parasitol. 2018 Feb;48(2):159-165
pubmed: 29111440
PLoS One. 2011;6(8):e23216
pubmed: 21858033
Nature. 1954 Oct 9;174(4432):704-5
pubmed: 13213990
Bioinformatics. 2011 Feb 15;27(4):578-9
pubmed: 21149342
DNA Res. 2018 Oct 1;25(5):499-510
pubmed: 29947776
Int J Parasitol. 2015 Apr;45(5):333-43
pubmed: 25746136
Bioinformatics. 2011 Apr 1;27(7):1017-8
pubmed: 21330290
Genes Dev. 1988 Oct;2(10):1277-83
pubmed: 3203906
Nat Methods. 2017 Jul;14(7):687-690
pubmed: 28581496
Genome Res. 2017 May;27(5):757-767
pubmed: 28381613
Nat Commun. 2020 Apr 23;11(1):1964
pubmed: 32327641
Genome Res. 2011 Feb;21(2):255-64
pubmed: 21177958
J Helminthol. 2015 Sep;89(5):517-25
pubmed: 25891536
Nat Biotechnol. 2019 Aug;37(8):953-961
pubmed: 31375809
Gigascience. 2019 May 1;8(5):
pubmed: 31089679
Bioinformatics. 2018 Jul 15;34(14):2490-2492
pubmed: 29506019
Genome Biol. 2004;5(2):R12
pubmed: 14759262
Nat Biotechnol. 2016 May;34(5):525-7
pubmed: 27043002
Int J Parasitol Drugs Drug Resist. 2011 Oct 14;1(1):2-13
pubmed: 24533259
BMC Bioinformatics. 2005 Feb 15;6:31
pubmed: 15713233
Genes (Basel). 2019 Jan 18;10(1):
pubmed: 30669388
PLoS Pathog. 2009 Apr;5(4):e1000380
pubmed: 19360096
Nat Methods. 2013 Nov;10(11):1096-8
pubmed: 24056875
PeerJ. 2014 Mar 04;2:e281
pubmed: 24688859
Pharmacogenet Genomics. 2010 Jul;20(7):414-25
pubmed: 20531256
Int J Parasitol. 2019 Oct;49(11):847-858
pubmed: 31525371
Nature. 2008 Mar 13;452(7184):176-80
pubmed: 18337814
Genome Biol Evol. 2018 Feb 1;10(2):396-409
pubmed: 29267942
Development. 2004 Jan;131(2):311-23
pubmed: 14668411
Genetics. 1995 Nov;141(3):1007-14
pubmed: 8582607
Nucleic Acids Res. 2019 Jul 2;47(W1):W191-W198
pubmed: 31066453
Int J Parasitol. 2006 Oct;36(12):1305-16
pubmed: 16950266
BMC Genomics. 2019 Mar 15;20(1):218
pubmed: 30876405
Bioinformatics. 2011 Jun 15;27(12):1653-9
pubmed: 21543442
PLoS Comput Biol. 2019 Feb 6;15(2):e1006790
pubmed: 30726205
Dev Biol. 2005 Jan 1;277(1):142-54
pubmed: 15572146
Genome Biol Evol. 2018 Apr 1;10(4):1064-1078
pubmed: 29635328
Genome Biol. 2013 Aug 28;14(8):R89
pubmed: 23985341
Genome Biol. 2013 Aug 28;14(8):R88
pubmed: 23985316
Bioinformatics. 2015 Oct 1;31(19):3210-2
pubmed: 26059717
Bioinformatics. 2014 Oct;30(19):2811-2
pubmed: 24930139
Adv Parasitol. 2016;93:31-68
pubmed: 27238002
Nucleic Acids Res. 2003 Oct 1;31(19):5654-66
pubmed: 14500829
Nat Genet. 2018 Jan;50(1):151-158
pubmed: 29229983
PLoS Negl Trop Dis. 2011 Dec;5(12):e1409
pubmed: 22180794
Bioinformatics. 2007 May 1;23(9):1061-7
pubmed: 17332020
Genome Res. 2017 May;27(5):722-736
pubmed: 28298431
Lancet Infect Dis. 2008 May;8(5):310-22
pubmed: 18471776
Genome Biol. 2010;11(4):R41
pubmed: 20388197
BMC Bioinformatics. 2008 Jan 14;9:18
pubmed: 18194517
Nat Biotechnol. 2018 Oct 22;:
pubmed: 30346939
Nat Genet. 2016 Mar;48(3):299-307
pubmed: 26829753
Int J Parasitol. 2015 Feb;45(2-3):149-59
pubmed: 25449043
Bioinformatics. 2016 Oct 1;32(19):3047-8
pubmed: 27312411
Parasit Vectors. 2019 Aug 14;12(1):403
pubmed: 31412938
Genome Res. 2019 Jun;29(6):1009-1022
pubmed: 31123080
Nat Genet. 2019 Jan;51(1):163-174
pubmed: 30397333
Bioinformatics. 2011 Aug 1;27(15):2156-8
pubmed: 21653522
Genome Res. 2004 Jun;14(6):1188-90
pubmed: 15173120
Curr Genomics. 2012 Aug;13(5):343-9
pubmed: 23372420
Genome Res. 2007 Oct;17(10):1478-85
pubmed: 17712020
WormBook. 2007 Mar 05;:1-13
pubmed: 18050498
Genome Biol. 2019 Nov 14;20(1):238
pubmed: 31727128
Adv Parasitol. 2016;93:569-98
pubmed: 27238013
Nat Genet. 2013 Nov;45(11):1337-44
pubmed: 24036951
Nat Genet. 2014 Mar;46(3):261-269
pubmed: 24441737
Genetics. 2014 Jul;197(3):865-83
pubmed: 24793291
Proc Natl Acad Sci U S A. 2013 Oct 1;110(40):16033-8
pubmed: 24046365
Bioinformatics. 2013 Jan 1;29(1):15-21
pubmed: 23104886
Mol Biol Evol. 2015 Jan;32(1):268-74
pubmed: 25371430
PLoS Pathog. 2019 Sep 25;15(9):e1008041
pubmed: 31553770
Genome Res. 2009 Mar;19(3):470-80
pubmed: 19204328
WormBook. 2015 Apr 28;:1-20
pubmed: 25936768
Int J Parasitol. 2003 Sep 30;33(11):1129-37
pubmed: 13678629
Mol Biochem Parasitol. 2001 Sep 28;117(1):107-10
pubmed: 11551637
Genome Biol. 2013 May 27;14(5):R47
pubmed: 23710727
Nucleic Acids Res. 2014 Sep;42(15):e119
pubmed: 24990371
IEEE/ACM Trans Comput Biol Bioinform. 2013 May-Jun;10(3):645-56
pubmed: 24091398
Nat Biotechnol. 2018 Apr;36(4):338-345
pubmed: 29431738
PLoS Genet. 2009 Mar;5(3):e1000419
pubmed: 19283065
Genome Biol. 2018 Oct 25;19(1):172
pubmed: 30359297
Nat Methods. 2015 Apr;12(4):357-60
pubmed: 25751142
Gigascience. 2015 Aug 04;4:35
pubmed: 26244089
Gigascience. 2018 Apr 1;7(4):1-5
pubmed: 29635297
PLoS One. 2014 Nov 19;9(11):e112963
pubmed: 25409509
Nat Methods. 2016 Dec;13(12):1050-1054
pubmed: 27749838
Nat Commun. 2019 Oct 22;10(1):4811
pubmed: 31641125
Science. 2010 Dec 24;330(6012):1775-87
pubmed: 21177976
Trends Parasitol. 2019 Apr;35(4):289-301
pubmed: 30733094
Parasitology. 2013 Oct;140(12):1506-22
pubmed: 23998513
Genome Biol. 2008 Jan 11;9(1):R7
pubmed: 18190707
Bioinformatics. 2009 Aug 15;25(16):2078-9
pubmed: 19505943
Nat Methods. 2017 Jun;14(6):587-589
pubmed: 28481363
Bioinformatics. 2016 Mar 1;32(5):767-9
pubmed: 26559507
Bioinformatics. 2018 Sep 15;34(18):3094-3100
pubmed: 29750242
Bioinformatics. 2010 Mar 15;26(6):841-2
pubmed: 20110278
Genetics. 2008 Dec;180(4):1877-87
pubmed: 18854587
Bioinformatics. 2010 Jul 15;26(14):1699-703
pubmed: 20513662
Mol Biochem Parasitol. 2017 Jul;215:2-10
pubmed: 27899279
Nat Plants. 2018 Nov;4(11):879-887
pubmed: 30390080
Microb Genom. 2016 Nov 30;2(11):e000093
pubmed: 28348833
Bioinformatics. 2020 Aug 07;:
pubmed: 32766814
Mol Biochem Parasitol. 2010 Apr;170(2):105-7
pubmed: 19932716
BMC Genomics. 2010 May 14;11:307
pubmed: 20470405
Nat Microbiol. 2016 Nov 21;2:16216
pubmed: 27869790