Chromosome-level genome of Schistosoma haematobium underpins genome-wide explorations of molecular variation.
Journal
PLoS pathogens
ISSN: 1553-7374
Titre abrégé: PLoS Pathog
Pays: United States
ID NLM: 101238921
Informations de publication
Date de publication:
02 2022
02 2022
Historique:
received:
28
10
2021
accepted:
19
01
2022
entrez:
15
2
2022
pubmed:
16
2
2022
medline:
1
3
2022
Statut:
epublish
Résumé
Urogenital schistosomiasis is caused by the blood fluke Schistosoma haematobium and is one of the most neglected tropical diseases worldwide, afflicting > 100 million people. It is characterised by granulomata, fibrosis and calcification in urogenital tissues, and can lead to increased susceptibility to HIV/AIDS and squamous cell carcinoma of the bladder. To complement available treatment programs and break the transmission of disease, sound knowledge and understanding of the biology and ecology of S. haematobium is required. Hybridisation/introgression events and molecular variation among members of the S. haematobium-group might effect important biological and/or disease traits as well as the morbidity of disease and the effectiveness of control programs including mass drug administration. Here we report the first chromosome-contiguous genome for a well-defined laboratory line of this blood fluke. An exploration of this genome using transcriptomic data for all key developmental stages allowed us to refine gene models (including non-coding elements) and annotations, discover 'new' genes and transcription profiles for these stages, likely linked to development and/or pathogenesis. Molecular variation within S. haematobium among some geographical locations in Africa revealed unique genomic 'signatures' that matched species other than S. haematobium, indicating the occurrence of introgression events. The present reference genome (designated Shae.V3) and the findings from this study solidly underpin future functional genomic and molecular investigations of S. haematobium and accelerate systematic, large-scale population genomics investigations, with a focus on improved and sustained control of urogenital schistosomiasis.
Identifiants
pubmed: 35167626
doi: 10.1371/journal.ppat.1010288
pii: PPATHOGENS-D-21-02181
pmc: PMC8846543
doi:
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, U.S. Gov't, Non-P.H.S.
Langues
eng
Sous-ensembles de citation
IM
Pagination
e1010288Subventions
Organisme : NHGRI NIH HHS
ID : UM1 HG009375
Pays : United States
Organisme : NHGRI NIH HHS
ID : RM1 HG011016
Pays : United States
Déclaration de conflit d'intérêts
The authors have declared that no competing interests exist.
Références
Nat Protoc. 2016 Sep;11(9):1650-67
pubmed: 27560171
Parasitology. 2017 Jan;144(1):65-80
pubmed: 27572906
Int J Mol Sci. 2021 Feb 11;22(4):
pubmed: 33670420
Trends Cancer. 2015 Nov 1;1(3):174-182
pubmed: 26618199
Nucleic Acids Res. 2016 Jan 4;44(D1):D457-62
pubmed: 26476454
Trends Parasitol. 2015 Jul;31(7):324-32
pubmed: 25933926
Microorganisms. 2021 Aug 20;9(8):
pubmed: 34442855
Sci Rep. 2020 Oct 28;10(1):18528
pubmed: 33116178
Methods Mol Biol. 2016;1374:23-54
pubmed: 26519399
Front Med (Lausanne). 2018 Aug 10;5:223
pubmed: 30159314
Parasitology. 2001;123 Suppl:S245-60
pubmed: 11769287
PLoS Negl Trop Dis. 2012;6(4):e1589
pubmed: 22509414
Cell. 2014 Dec 18;159(7):1665-80
pubmed: 25497547
Nat Commun. 2021 Aug 6;12(1):4776
pubmed: 34362894
Science. 2017 Apr 7;356(6333):92-95
pubmed: 28336562
Cell Syst. 2016 Jul;3(1):95-8
pubmed: 27467249
PLoS Negl Trop Dis. 2012 Jan;6(1):e1455
pubmed: 22253936
Parasit Vectors. 2012 Sep 03;5:185
pubmed: 22943137
Genome Res. 2010 Sep;20(9):1297-303
pubmed: 20644199
Parasitology. 2012 Sep;139(10):1231-45
pubmed: 22717097
J Infect Dis. 2015 Mar 15;211(6):861-9
pubmed: 25240172
PLoS Negl Trop Dis. 2008 Jul 30;2(7):e267
pubmed: 18665228
Bioinformatics. 2014 Aug 1;30(15):2114-20
pubmed: 24695404
PLoS Negl Trop Dis. 2016 Sep 27;10(9):e0004930
pubmed: 27677173
Parasit Vectors. 2016 Jun 10;9(1):328
pubmed: 27283196
Trends Genet. 2000 Jun;16(6):276-7
pubmed: 10827456
Mol Biochem Parasitol. 2009 Jul;166(1):4-14
pubmed: 19428667
PLoS Negl Trop Dis. 2019 Sep 30;13(9):e0007013
pubmed: 31568484
Nat Biotechnol. 2019 Aug;37(8):907-915
pubmed: 31375807
Int J Infect Dis. 2021 Jan;102:544-553
pubmed: 33157296
Bioinformatics. 2018 Sep 1;34(17):i884-i890
pubmed: 30423086
Genome Res. 2016 Dec;26(12):1721-1729
pubmed: 27852649
Int J Parasitol Drugs Drug Resist. 2020 Dec;14:183-187
pubmed: 33125936
Nucleic Acids Res. 2019 Jan 8;47(D1):D351-D360
pubmed: 30398656
Trop Med Infect Dis. 2021 Jun 22;6(3):
pubmed: 34206495
Gigascience. 2021 Feb 16;10(2):
pubmed: 33590861
PLoS Pathog. 2019 Jan 23;15(1):e1007513
pubmed: 30673782
Nat Genet. 2012 Jan 15;44(2):221-5
pubmed: 22246508
Lancet. 2014 Jun 28;383(9936):2253-64
pubmed: 24698483
BMC Bioinformatics. 2018 Nov 29;19(1):460
pubmed: 30497373
PLoS Negl Trop Dis. 2012;6(11):e1912
pubmed: 23209855
Nature. 2021 Aug;596(7873):583-589
pubmed: 34265844
Lancet Planet Health. 2020 Aug;4(8):e330-e342
pubmed: 32800151
PLoS Negl Trop Dis. 2013 Apr 04;7(4):e2110
pubmed: 23593513
Am J Trop Med Hyg. 2020 Jul;103(1_Suppl):80-91
pubmed: 32400355
Genome Res. 2009 Sep;19(9):1639-45
pubmed: 19541911
Infect Immun. 2017 Nov 17;85(12):
pubmed: 28923894
Genome Res. 2017 May;27(5):722-736
pubmed: 28298431
PLoS Negl Trop Dis. 2012;6(10):e1882
pubmed: 23145200
Nat Methods. 2012 Mar 04;9(4):357-9
pubmed: 22388286
Curr Protoc Bioinformatics. 2019 Mar;65(1):e57
pubmed: 30466165
Fly (Austin). 2012 Apr-Jun;6(2):80-92
pubmed: 22728672
PLoS Negl Trop Dis. 2015 Dec 31;9(12):e0004334
pubmed: 26719891
Int J Parasitol. 2006 Jul;36(8):947-55
pubmed: 16730013
Genome Biol. 2019 Nov 14;20(1):238
pubmed: 31727128
Genome Biol. 2019 Dec 16;20(1):278
pubmed: 31842956
PLoS Negl Trop Dis. 2019 Aug 7;13(8):e0007612
pubmed: 31390359
Nat Rev Dis Primers. 2018 Aug 9;4(1):13
pubmed: 30093684
Elife. 2018 Jul 25;7:
pubmed: 30044216
Nucleic Acids Res. 2019 Jan 8;47(D1):D853-D858
pubmed: 30407534
Nat Commun. 2020 Mar 18;11(1):1438
pubmed: 32188845
Emerg Infect Dis. 2019 Jun;25(6):1245-1247
pubmed: 31107237
PLoS Negl Trop Dis. 2019 May 6;13(5):e0007268
pubmed: 31059495
Sci Rep. 2016 Aug 08;6:31150
pubmed: 27499125
Mol Biochem Parasitol. 2020 Nov;240:111322
pubmed: 32961206
Sci Rep. 2017 Apr 10;7:45910
pubmed: 28393916
Clin Infect Dis. 2016 Nov 1;63(9):1151-1159
pubmed: 27470241
Elife. 2019 Jan 15;8:
pubmed: 30644357
PLoS Negl Trop Dis. 2011 Aug;5(8):e1274
pubmed: 21912711
PLoS Negl Trop Dis. 2020 Jul 2;14(7):e0008201
pubmed: 32614820
Mol Biol Evol. 2019 Oct 1;36(10):2127-2142
pubmed: 31251352
PLoS One. 2014 Nov 19;9(11):e112963
pubmed: 25409509
Bioinformatics. 2017 Sep 15;33(18):2938-2940
pubmed: 28645171
Genome Biol. 2008 Jan 11;9(1):R7
pubmed: 18190707
Mol Biochem Parasitol. 2005 Nov;144(1):123-7
pubmed: 16143411
Nat Protoc. 2013 Aug;8(8):1494-512
pubmed: 23845962
Nucleic Acids Res. 2005 Apr 22;33(7):2302-9
pubmed: 15849316
Infect Genet Evol. 2021 Apr;89:104727
pubmed: 33486128
PLoS Negl Trop Dis. 2009 Aug 18;3(8):e504
pubmed: 19688043
Bioinformatics. 2018 Sep 15;34(18):3094-3100
pubmed: 29750242
Nat Commun. 2019 Apr 12;10(1):1702
pubmed: 30979905
Mol Biol Evol. 2018 Mar 1;35(3):543-548
pubmed: 29220515
Parasitology. 1991 Oct;103 Pt 2:225-36
pubmed: 1745548
Gigascience. 2019 Sep 1;8(9):
pubmed: 31494670
PLoS Negl Trop Dis. 2019 May 15;13(5):e0007362
pubmed: 31091291
J Parasitol. 2012 Dec;98(6):1257-61
pubmed: 22519732
PLoS Pathog. 2012;8(3):e1002605
pubmed: 22479181
Parasit Vectors. 2020 May 24;13(1):268
pubmed: 32448268
Mol Biochem Parasitol. 2017 Jul;215:2-10
pubmed: 27899279
PLoS Negl Trop Dis. 2013;7(3):e1961
pubmed: 23556007
Biotechnol Adv. 2016 Sep-Oct;34(5):663-686
pubmed: 26956711
Genome Res. 2016 Mar;26(3):342-50
pubmed: 26848124
Mol Biol Evol. 2017 Aug 1;34(8):2115-2122
pubmed: 28460117
Nucleic Acids Res. 2019 Jan 8;47(D1):D309-D314
pubmed: 30418610
Parasite Immunol. 2009 Apr;31(4):163-76
pubmed: 19292768
PLoS Pathog. 2021 Feb 5;17(2):e1009313
pubmed: 33544762