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08 17, 2023;11 (4): e0072123.

Whole-Genome Sequencing, Assembling, Annotation, and Comparative Analysis.

Qin Liu, Xing-Ai Guan, Dong-Fang Li, Ya-Xin Zheng, Sen Wang, Xue-Nan Xuan, Jun-Long Zhao, Lan He
Author Information
  1. Qin Liu: State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China.
  2. Xing-Ai Guan: State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China. ORCID
  3. Dong-Fang Li: State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China.
  4. Ya-Xin Zheng: State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China.
  5. Sen Wang: State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China.
  6. Xue-Nan Xuan: National Research Center for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine, Obihiro Hokkaido, Japan.
  7. Jun-Long Zhao: State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China.
  8. Lan He: State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China.
PMID: 37432130 DOI: 10.1128/spectrum.00721-23

Abstract

The intracellular protozoan parasite Babesia gibsoni infects canine erythrocytes and causes babesiosis. The hazards to animal health have increased due to the rise of B. gibsoni infections and medication resistance. However, the lack of high-quality full-genome sequencing sets has expanded the obstacles to the development of pathogeneses, drugs, and vaccines. In this study, the whole genome of was sequenced, assembled, and annotated. The genomic size of was 7.94 Mbp in total. Four chromosomes with the size of 0.69 Mb, 2.10 Mb, 2.77 Mb, and 2.38 Mb, respectively, 1 apicoplast (28.4 Kb), and 1 mitochondrion (5.9 Kb) were confirmed. KEGG analysis revealed 2,641 putative proteins enriched on 316 pathways, and GO analysis showed 7,571 annotations of the nuclear genome in total. Synteny analysis showed a high correlation between and B. bovis. A new divergent point of occurred around 297.7 million years ago, which was earlier than that of , B. ovata, and B. bigemina. Orthology analysis revealed 22 and 32 unique genes compared to several spp. and apicomplexan species. The metabolic pathways of were characterized, pointing to a minimal size of the genome. A species-specific secretory protein SA1 and 19 homologous genes were identified. Selected specific proteins, including apetala 2 (AP2) factor, invasion-related proteins BgAMA-1 and BgRON2, and rhoptry function proteins BgWH_04g00700 were predicted, visualized, and modeled. Overall, whole-genome sequencing provided molecular-level support for the diagnosis, prevention, clinical treatment, and further research of . The whole genome of was first sequenced, annotated, and disclosed. The key part of genome composition, four chromosomes, was comparatively analyzed for the first time. A full-scale phylogeny evolution analysis based on the whole-genome-wide data of was performed, and a new divergent point on the evolutionary path was revealed. In previous reports, molecular studies were often limited by incomplete genomic data, especially in key areas like life cycle regulation, metabolism, and host-pathogen interaction. With the whole-genome sequencing of , we provide useful genetic data to encourage the exploration of new terrain and make it feasible to resolve the theoretical and practical problems of babesiosis.

Keywords

Babesia gibsoni apicomplexan apicomplexan parasites comparison analysis genome assembly genome sequencing protozoan

References

Trans R Soc Trop Med Hyg. 1989;83 Suppl:95-6 [PMID: 2623757]
Front Microbiol. 2021 Sep 03;12:697669 [PMID: 34539601]
BMC Genomics. 2017 Oct 27;18(1):832 [PMID: 29078748]
PLoS Negl Trop Dis. 2016 Nov 10;10(11):e0004983 [PMID: 27832060]
Parasit Vectors. 2015 Oct 09;8:518 [PMID: 26452623]
Trends Parasitol. 2016 Jan;32(1):56-70 [PMID: 26472327]
Vet Clin North Am Small Anim Pract. 2003 Jul;33(4):885-904, viii [PMID: 12910748]
Nucleic Acids Res. 2019 Jan 8;47(D1):D427-D432 [PMID: 30357350]
Nat Chem Biol. 2012 Sep;8(9):774-83 [PMID: 22820419]
Nature. 2004 Oct 28;431(7012):1107-12 [PMID: 15510150]
Science. 2004 Apr 16;304(5669):441-5 [PMID: 15044751]
Int J Parasitol. 2019 Feb;49(2):153-163 [PMID: 30391230]
Nucleic Acids Res. 2012 Apr;40(7):e49 [PMID: 22217600]
Bioinformatics. 2003 Jan 22;19(2):301-2 [PMID: 12538260]
PLoS Pathog. 2007 Oct 19;3(10):1401-13 [PMID: 17953480]
PLoS One. 2014 Oct 03;9(10):e107939 [PMID: 25280009]
Vaccine. 2022 Feb 16;40(8):1108-1115 [PMID: 35078663]
Trends Parasitol. 2019 May;35(5):356-368 [PMID: 30733093]
Parasitology. 2015 Apr;142(4):534-42 [PMID: 25363531]
Parasitol Res. 2019 Jan;118(1):235-243 [PMID: 30474737]
Mol Biochem Parasitol. 1992 Oct;55(1-2):85-94 [PMID: 1279421]
PLoS Pathog. 2014 Jul 17;10(7):e1004263 [PMID: 25032958]
Nucleic Acids Res. 2012 Oct;40(18):9102-14 [PMID: 22833609]
Int J Parasitol. 2019 Feb;49(2):127-137 [PMID: 30367864]
J Biol Chem. 2012 Jun 29;287(27):22938-47 [PMID: 22563079]
Bioinformatics. 2014 May 1;30(9):1312-3 [PMID: 24451623]
Genome Biol. 2009;10(5):R53 [PMID: 19457243]
Nucleic Acids Res. 1997 Mar 1;25(5):955-64 [PMID: 9023104]
Crit Rev Biochem Mol Biol. 2017 Jun;52(3):254-273 [PMID: 28276701]
Parasitology. 2009 Sep;136(10):1147-60 [PMID: 19631010]
BMC Bioinformatics. 2005 Feb 15;6:31 [PMID: 15713233]
Science. 2005 Jul 1;309(5731):134-7 [PMID: 15994558]
Vet Parasitol. 2012 Apr 30;185(2-4):145-50 [PMID: 21996003]
Exp Parasitol. 2019 Nov;206:107771 [PMID: 31585116]
Trends Parasitol. 2005 Apr;21(4):179-84 [PMID: 15780840]
Protein Eng. 1997 Jun;10(6):673-6 [PMID: 9278280]
Prog Lipid Res. 2013 Oct;52(4):488-512 [PMID: 23827884]
Int J Parasitol. 2019 Feb;49(2):175-181 [PMID: 30684517]
Curr Opin Microbiol. 2006 Aug;9(4):374-80 [PMID: 16814594]
Parasit Vectors. 2009 Mar 26;2 Suppl 1:S4 [PMID: 19426443]
Mol Biol Evol. 2004 Mar;21(3):489-97 [PMID: 14694073]
Nucleic Acids Res. 1999 Jan 15;27(2):573-80 [PMID: 9862982]
PLoS One. 2013 Sep 04;8(9):e72657 [PMID: 24023759]
Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W451-4 [PMID: 15980510]
Exp Parasitol. 1972 Feb;31(1):153-9 [PMID: 4622045]
Nat Commun. 2014 Jun 17;5:4098 [PMID: 24934579]
Nucleic Acids Res. 2014 Jun;42(11):7113-31 [PMID: 24799432]
Nat Biotechnol. 2015 Mar;33(3):290-5 [PMID: 25690850]
Nucleic Acids Res. 2019 Jul 2;47(W1):W256-W259 [PMID: 30931475]
Nature. 2002 Oct 3;419(6906):498-511 [PMID: 12368864]
Science. 2005 Jul 1;309(5731):72-3 [PMID: 15994520]
J S Afr Vet Assoc. 2007 Mar;78(1):2-5 [PMID: 17665757]
Parasite. 2011 Nov;18(4):311-8 [PMID: 22091461]
Trends Genet. 2000 Sep;16(9):418-20 [PMID: 10973072]
Nat Rev Microbiol. 2017 Aug;15(8):479-491 [PMID: 28603279]
J Vet Intern Med. 2017 Jul;31(4):1108-1112 [PMID: 28625019]
Parasit Vectors. 2020 Jul 22;13(1):369 [PMID: 32698835]
Korean J Parasitol. 2014 Aug;52(4):345-53 [PMID: 25246713]
Proc Natl Acad Sci U S A. 2013 Apr 2;110(14):5392-7 [PMID: 23471987]
J Clin Microbiol. 2003 Sep;41(9):4172-7 [PMID: 12958243]
Int J Parasitol. 2001 Oct;31(12):1285-92 [PMID: 11566296]
Nucleic Acids Res. 2014 Jul;42(13):8271-84 [PMID: 24957599]
Microorganisms. 2022 Aug 15;10(8): [PMID: 36014069]
J Vet Med Sci. 2020 Dec 5;82(11):1700-1703 [PMID: 32908117]
Nucleic Acids Res. 2018 Jul 2;46(W1):W296-W303 [PMID: 29788355]
Curr Drug Targets. 2007 Jan;8(1):31-47 [PMID: 17266529]
Mol Biochem Parasitol. 2009 Mar;164(1):1-8 [PMID: 19110007]
Vet Clin North Am Small Anim Pract. 2010 Nov;40(6):1141-56 [PMID: 20933141]
PLoS Pathog. 2012;8(6):e1002755 [PMID: 22737069]
Nucleic Acids Res. 1997 Sep 1;25(17):3389-402 [PMID: 9254694]
BMC Biol. 2022 Jul 5;20(1):153 [PMID: 35790982]
Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W465-7 [PMID: 15980513]
Nat Methods. 2015 Apr;12(4):357-60 [PMID: 25751142]
Vet Parasitol. 2004 Sep 20;124(1-2):9-18 [PMID: 15350657]
Genome Res. 1999 Sep;9(9):868-77 [PMID: 10508846]
PLoS Pathog. 2012;8(3):e1002567 [PMID: 22457617]
Ann N Y Acad Sci. 2008 Dec;1149:145-8 [PMID: 19120194]
Parasitology. 2014 Jul 28;:1-30 [PMID: 25068315]
Genome Biol. 2008 Jan 11;9(1):R7 [PMID: 18190707]
Nat Protoc. 2013 Aug;8(8):1494-512 [PMID: 23845962]
J Lipid Res. 2007 May;48(5):993-1011 [PMID: 17361015]
Nat Methods. 2013 Jun;10(6):563-9 [PMID: 23644548]
Int J Mol Sci. 2018 Nov 22;19(12): [PMID: 30469512]
Vet Parasitol. 2018 Apr 30;254:58-63 [PMID: 29657012]
Mol Biol Evol. 2016 Jul;33(7):1870-4 [PMID: 27004904]
Science. 1979 Jun 29;204(4400):1431-2 [PMID: 451574]
Sci Rep. 2017 Jun 13;7(1):3357 [PMID: 28611446]
Bioinformatics. 2014 Mar 15;30(6):884-6 [PMID: 24162465]
Nat Commun. 2020 Mar 16;11(1):1411 [PMID: 32179747]
Exp Parasitol. 2006 Dec;114(4):329-33 [PMID: 16777097]
Trends Parasitol. 2011 Mar;27(3):131-40 [PMID: 21145790]
Genome Biol. 2015 Aug 06;16:157 [PMID: 26243257]
Science. 2005 Jul 1;309(5731):131-3 [PMID: 15994557]
J Mol Biol. 1990 Oct 5;215(3):403-10 [PMID: 2231712]
Vet Res. 2009 Mar-Apr;40(2):37 [PMID: 19379662]
Nucleic Acids Res. 2004 Mar 19;32(5):1792-7 [PMID: 15034147]
Nucleic Acids Res. 2007;35(9):3100-8 [PMID: 17452365]
Mol Biol Evol. 2017 Aug 1;34(8):2115-2122 [PMID: 28460117]
Nucleic Acids Res. 2019 Jan 8;47(D1):D309-D314 [PMID: 30418610]

MeSH Term

Animals
Dogs
Babesia
Babesiosis
Whole Genome Sequencing
Genomics
Genome
Dog Diseases
Journal Article Research Support, Non-U.S. Gov't

Links to CNCB-NGDC Resources

GWH: GWHBJTY00000000 (Babesia gibsoni)

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