Chromosome-level genome assembly of Oncomelania hupensis: the intermediate snail host of Schistosoma japonicum

Lo NC, Bezerra FSM, Colley DG, Fleming FM, Homeida M, Kabatereine N, et al. Review of 2022 WHO guidelines on the control and elimination of schistosomiasis. Lancet Infect Dis. 2022;22(11):e327–35. https://doi.org/10.1016/S1473-3099(22)00221-3.

Article  PubMed  Google Scholar 

Luo F, Yang W, Yin M, Mo X, Pang Y, Sun C, et al. A chromosome-level genome of the human blood fluke Schistosoma japonicum identifies the genomic basis of host-switching. Cell Rep. 2022;39(1): 110638. https://doi.org/10.1016/j.celrep.2022.110638.

Article  CAS  PubMed  Google Scholar 

Zhang L, He J, Yang F, Dang H, Li Y, Guo S, et al. Progress of schistosomiasis control in People’s Republic of China in 2022. Zhongguo Xue Xi Chong Bing Fang Zhi Za Zhi. 2023;35:217–24 (In Chinese).

CAS  PubMed  Google Scholar 

Dai B, Wang TP, Xu XJ, He JC, Wang H, Gao FH, et al. Investigation on newly emerging and re-emerging snail habitats in Anhui, 2017–2021. Chin Trop Med. 2022;22: 935–940 (In Chinese).

Google Scholar 

Lv C, Li YL, Deng WP, Bao ZP, Xu J, Lv S, et al. The current distribution of Oncomelania hupensis snails in the People’s Republic of China based on a nationwide survey. Trop Med Infect Dis. 2023;8(2):120. https://doi.org/10.3390/tropicalmed8020120.

Article  PubMed  PubMed Central  Google Scholar 

Sun CS, Luo F, Liu X, Miao F, Hu W. Oncomelania hupensis retains its ability to transmit Schistosoma japonicum 13 years after migration from permissive to non-permissive areas. Parasit Vectors. 2020;13(1):146. https://doi.org/10.1186/s13071-020-4004-8.

Article  PubMed  PubMed Central  Google Scholar 

Liu CH, Zhang Y, Ren YW, Wang HC, Li SQ, Jiang F, et al. The genome of the golden apple snail provides insight into stress tolerance and invasive adaptation. Gigascience. 2018;7(9): giy101. https://doi.org/10.1093/gigascience/giy101.

Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

Adema CM, Luo MZ, Hanelt B, Hertel LA, Marshall JJ, Zhang SM, et al. A bacterial artificial chromosome library for Biomphalaria glabrata, intermediate snail host of Schistosoma mansoni. Mem Inst Oswaldo Cruz. 2006;101(Suppl 1):167–77. https://doi.org/10.1590/s0074-02762006000900027.

Article  CAS  PubMed  Google Scholar 

Bu L, Lu L, Laidemitt MR, Zhang SM, Mutuku M, Mkoji G, et al. A genome sequence for Biomphalaria pfeifferi, the major vector snail for the human-infecting parasite Schistosoma mansoni. PLoS Negl Trop Dis. 2023;17(3): e0011208. https://doi.org/10.1371/journal.pntd.0011208.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Jin W, Cao XJ, Ma XY, Lv GH, Xu GC, Xu P, et al. Chromosome-level genome assembly of the freshwater snail Bellamya purificata (Caenogastropoda). Zool Res. 2022;43(4):683–6. https://doi.org/10.24272/j.issn.2095-8137.

Article  PubMed  PubMed Central  Google Scholar 

Davis GM. Evolution of prosobranch snails transmitting Asian Schistosoma; coevolution with Schistosoma: a review. Prog Clin Parasitol. 1993;3:145–204. https://doi.org/10.1007/978-1-4612-2732-8_6.

Article  CAS  PubMed  Google Scholar 

Cross JH, Zaraspe G, Lu SK, Chiu KM, Hung HK. Susceptibility of Oncomelania hupensis subspecies to infection with geographic strains of Schistosoma japonicum. Southeast Asian J Trop Med Public Health. 1984;15:155–60.

CAS  PubMed  Google Scholar 

Li J, Cai T, Jiang Y, Chen H, He X, Chen C, et al. Genes with de novo mutations are shared by four neuropsychiatric disorders discovered from NPdenovo database. Mol Psychiatry. 2016;21(2):290–7. https://doi.org/10.1038/mp.2015.40.

Article  CAS  PubMed  Google Scholar 

Walker BJ, Abeel T, Shea T, Priest M, Abouelliel A, Sakthikumar S, et al. Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS ONE. 2014;9(11): e112963. https://doi.org/10.1371/journal.pone.0112963.

Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

Durand NC, Robinson JT, Shamim MS, Machol I, Mesirov JP, Lander ES, et al. Juicebox provides a visualization system for Hi-C contact maps with unlimited zoom. Cell Syst. 2016;3(1):99–101. https://doi.org/10.1016/j.cels.2015.07.012.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Dudchenko O, Batra SS, Omer AD, Nyquist SK, Hoeger M, Durand NC, et al. De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds. Science. 2017;356(6333):92–5. https://doi.org/10.1126/science.aal3327.

Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

Simao FA, Waterhouse RM, Ioannidis P, Kriventseva EV, Zdobnov EM. Busco: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics. 2015;31(19):3210–2. https://doi.org/10.1093/bioinformatics/btv351.

Article  CAS  PubMed  Google Scholar 

Houtgast EJ, Sima VM, Bertels K, Al-Ars Z. Hardware acceleration of bwa-mem genomic short read mapping for longer read lengths. Comput Biol Chem. 2018;75:54–64. https://doi.org/10.1016/j.compbiolchem.

Article  CAS  PubMed  Google Scholar 

Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al. The sequence alignment/map format and samtools. Bioinformatics. 2009;25(16):2078–9. https://doi.org/10.1093/bioinformatics/btp352.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Flynn JM, Hubley R, Goubert C, Rosen J, Clark AG, Feschotte C, et al. Repeatmodeler2 for automated genomic discovery of transposable element families. Proc Natl Acad Sci U S A. 2020;117(17):9451–7. https://doi.org/10.1073/pnas.1921046117.

Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

Chen N. Using repeatmasker to identify repetitive elements in genomic sequences. Curr Protoc Bioinform. 2004;4:4.10.1-4.10.14. https://doi.org/10.1002/0471250953.bi0410s25.

Article  Google Scholar 

Bao W, Kojima KK, Kohany O. Repbase update, a database of repetitive elements in eukaryotic genomes. Mob DNA. 2015;6:11. https://doi.org/10.1159/000084979.

Article  PubMed  PubMed Central  Google Scholar 

Holt C, Yandell M. Maker2: an annotation pipeline and genome-database management tool for second-generation genome projects. BMC Bioinform. 2011;12:491. https://doi.org/10.1186/1471-2105-12-491.

Article  Google Scholar 

Guo Y, Zhang Y, Liu Q, Huang Y, Mao G, Yue Z, et al. A chromosomal-level genome assembly for the giant African snail Achatina fulica. Gigascience. 2019;8(10):giz124. https://doi.org/10.1093/gigascience/giz124.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Simakov O, Marletaz F, Cho SJ, Edsinger-Gonzales E, Havlak P, Hellsten U, et al. Insights into bilaterian evolution from three spiralian genomes. Nature. 2013;493(7433):526–31. https://doi.org/10.1038/nature11696.

Article  ADS  CAS  PubMed  Google Scholar 

Moroz LL, Kohn AB. Do different neurons age differently? Direct genome-wide analysis of aging in single identified cholinergic neurons. Front Aging Neurosci. 2010;2:6. https://doi.org/10.3389/neuro.24.006.2010.

Article  PubMed  PubMed Central  Google Scholar 

Wang S, Zhang J, Jiao W, Li J, Xun X, Sun Y, et al. Scallop genome provides insights into evolution of bilaterian karyotype and development. Nat Ecol Evol. 2017;1(5):120. https://doi.org/10.1038/s41559-017-0120.

Article  PubMed  Google Scholar 

Slater GS, Birney E. Automated generation of heuristics for biological sequence comparison. BMC Bioinform. 2005;6:31. https://doi.org/10.1186/1471-2105-6-31.

Article  CAS  Google Scholar 

Gertz EM, Yu YK, Agarwala R, Schaffer AA, Altschul SF. Composition-based statistics and translated nucleotide searches: improving the tblastn module of blast. BMC Biol. 2006;4:41. https://doi.org/10.1186/1741-7007-4-41.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Kim D, Paggi JM, Park C, Bennett C, Salzberg SL. Graph-based genome alignment and genotyping with hisat2 and hisat-genotype. Nat Biotechnol. 2019;37(8):907–15. https://doi.org/10.1038/s41587-019-0201-4.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Pertea M, Pertea GM, Antonescu CM, Chang TC, Mendell JT, Salzberg SL. StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nat Biotechnol. 2015;33(3):290–5. https://doi.org/10.1038/nbt.3122.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Hoff KJ, Stanke M. Predicting genes in single genomes with AUGUSTUS. Curr Protoc Bioinform. 2019;65(1): e57. https://doi.org/10.1002/cpbi.57.

Article  CAS  Google Scholar 

Lee E, Helt GA, Reese JT, Munoz-Torres MC, Childers CP, Buels RM, et al. Web Apollo: a web-based genomic annotation editing platform. Genome Biol. 2013;14(8):R93. https://doi.org/10.1186/gb-2013-14-8-r93.

留言 (0)

沒有登入
gif