Fully resolved assembly of Cryptosporidium parvum.
Cryptosporidium
assembly
assembly comparisons
nanopore
Journal
GigaScience
ISSN: 2047-217X
Titre abrégé: Gigascience
Pays: United States
ID NLM: 101596872
Informations de publication
Date de publication:
15 02 2022
15 02 2022
Historique:
received:
08
10
2021
revised:
07
12
2021
accepted:
20
01
2022
entrez:
15
2
2022
pubmed:
16
2
2022
medline:
5
4
2022
Statut:
ppublish
Résumé
Cryptosporidium parvum is an apicomplexan parasite commonly found across many host species with a global infection prevalence in human populations of 7.6%. Understanding its diversity and genomic makeup can help in fighting established infections and prohibiting further transmission. The basis of every genomic study is a high-quality reference genome that has continuity and completeness, thus enabling comprehensive comparative studies. Here, we provide a highly accurate and complete reference genome of Cryptosporidium parvum. The assembly is based on Oxford Nanopore reads and was improved using Illumina reads for error correction. We also outline how to evaluate and choose from different assembly methods based on 2 main approaches that can be applied to other Cryptosporidium species. The assembly encompasses 8 chromosomes and includes 13 telomeres that were resolved. Overall, the assembly shows a high completion rate with 98.4% single-copy BUSCO genes. This high-quality reference genome of a zoonotic IIaA17G2R1 C. parvum subtype isolate provides the basis for subsequent comparative genomic studies across the Cryptosporidium clade. This will enable improved understanding of diversity, functional, and association studies.
Sections du résumé
BACKGROUND
Cryptosporidium parvum is an apicomplexan parasite commonly found across many host species with a global infection prevalence in human populations of 7.6%. Understanding its diversity and genomic makeup can help in fighting established infections and prohibiting further transmission. The basis of every genomic study is a high-quality reference genome that has continuity and completeness, thus enabling comprehensive comparative studies.
FINDINGS
Here, we provide a highly accurate and complete reference genome of Cryptosporidium parvum. The assembly is based on Oxford Nanopore reads and was improved using Illumina reads for error correction. We also outline how to evaluate and choose from different assembly methods based on 2 main approaches that can be applied to other Cryptosporidium species. The assembly encompasses 8 chromosomes and includes 13 telomeres that were resolved. Overall, the assembly shows a high completion rate with 98.4% single-copy BUSCO genes.
CONCLUSIONS
This high-quality reference genome of a zoonotic IIaA17G2R1 C. parvum subtype isolate provides the basis for subsequent comparative genomic studies across the Cryptosporidium clade. This will enable improved understanding of diversity, functional, and association studies.
Identifiants
pubmed: 35166336
pii: 6528769
doi: 10.1093/gigascience/giac010
pmc: PMC8848321
pii:
doi:
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Langues
eng
Sous-ensembles de citation
IM
Subventions
Organisme : NIAID NIH HHS
ID : U19 AI144297
Pays : United States
Informations de copyright
© The Author(s) 2022. Published by Oxford University Press GigaScience.
Références
Methods Mol Biol. 2020;2052:373-402
pubmed: 31452173
Acta Parasitol. 2020 Dec;65(4):882-889
pubmed: 32514837
Emerg Infect Dis. 2006 Apr;12(4):684-6
pubmed: 16704822
Plant Dis. 2021 Nov;105(11):3732-3735
pubmed: 34003033
Vet Parasitol. 2004 Dec 9;126(1-2):37-56
pubmed: 15567578
Nat Biotechnol. 2020 Sep;38(9):1044-1053
pubmed: 32686750
Nat Methods. 2012 Mar 04;9(4):357-9
pubmed: 22388286
Nat Rev Genet. 2018 Jun;19(6):329-346
pubmed: 29599501
Bioinformatics. 2011 Mar 15;27(6):764-70
pubmed: 21217122
Bioinformatics. 2016 Oct 1;32(19):3021-3
pubmed: 27318204
PLoS One. 2014 Oct 24;9(10):e111164
pubmed: 25343501
BMC Genomics. 2021 May 6;22(1):330
pubmed: 33957869
Nat Microbiol. 2018 Jul;3(7):814-823
pubmed: 29946163
Genome Res. 2022 Jan;32(1):203-213
pubmed: 34764149
Front Vet Sci. 2020 Aug 21;7:562
pubmed: 32974408
Science. 2004 Apr 16;304(5669):441-5
pubmed: 15044751
Mol Biochem Parasitol. 1998 Aug 1;94(2):291-6
pubmed: 9747979
Infect Genet Evol. 2012 Aug;12(6):1213-21
pubmed: 22522000
Food Waterborne Parasitol. 2017 Sep 29;8-9:14-32
pubmed: 32095639
Gigascience. 2020 Jan 1;9(1):
pubmed: 31919520
Bioinformatics. 2017 Jul 15;33(14):2202-2204
pubmed: 28369201
Parasitol Res. 2015 Dec;114(12):4709-16
pubmed: 26358098
Genome Biol. 2004;5(2):R12
pubmed: 14759262
Perspect Biol Med. 1998 Autumn;42(1):154-5
pubmed: 10766604
Int J Parasitol. 2000 Nov;30(12-13):1305-22
pubmed: 11113257
Bioinformatics. 2015 Oct 1;31(19):3210-2
pubmed: 26059717
Mol Ecol Resour. 2021 Oct;21(7):2388-2406
pubmed: 34003602
Nat Biotechnol. 2019 May;37(5):540-546
pubmed: 30936562
Bioinformatics. 2016 Apr 15;32(8):1220-2
pubmed: 26647377
Lancet. 2013 Jul 20;382(9888):209-22
pubmed: 23680352
Genome Res. 2017 May;27(5):722-736
pubmed: 28298431
Parasite Immunol. 2012 Feb-Mar;34(2-3):61-71
pubmed: 21595702
MMWR Morb Mortal Wkly Rep. 2011 Jul 15;60(27):918-22
pubmed: 21753745
Nat Commun. 2020 Mar 18;11(1):1432
pubmed: 32188846
Genome Biol. 2019 Nov 20;20(1):246
pubmed: 31747936
J Eukaryot Microbiol. 2006;53 Suppl 1:S24-5
pubmed: 17169057
Malays J Med Sci. 2018 May;25(3):1-6
pubmed: 30899182
Methods Mol Biol. 2020;2052:319-334
pubmed: 31452170
Lancet Glob Health. 2015 Sep;3(9):e564-75
pubmed: 26202075
J Virol Methods. 2021 Aug;294:114180
pubmed: 33965458
Nature. 2015 Jul 23;523(7561):477-80
pubmed: 26176919
Infect Immun. 2000 Jul;68(7):4117-34
pubmed: 10858229
Clin Microbiol Rev. 2013 Jan;26(1):115-34
pubmed: 23297262
Lancet Glob Health. 2020 Oct;8(10):e1295-e1304
pubmed: 32971052
PLoS One. 2014 Nov 19;9(11):e112963
pubmed: 25409509
Nat Methods. 2016 Dec;13(12):1050-1054
pubmed: 27749838
Bioinformatics. 2009 Aug 15;25(16):2078-9
pubmed: 19505943
Genome Biol. 2019 Jan 8;20(1):8
pubmed: 30621750
J Anim Sci Technol. 2020 Nov;62(6):948-951
pubmed: 33987574
Parasit Vectors. 2021 Jan 22;14(1):69
pubmed: 33482898
BMC Microbiol. 2010 Aug 09;10:213
pubmed: 20696051
Nucleic Acids Res. 1994 Nov 11;22(22):4673-80
pubmed: 7984417
Nat Rev Genet. 2021 Sep;22(9):572-587
pubmed: 34050336