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

Oncomelania hupensis Schistosoma japonicum Chromosome-level genome Schistosomiasis

Journal

Infectious diseases of poverty
ISSN: 2049-9957
Titre abrégé: Infect Dis Poverty
Pays: England
ID NLM: 101606645

Informations de publication

Date de publication:
27 Feb 2024
Historique:
received: 27 09 2023
accepted: 01 02 2024
medline: 28 2 2024
pubmed: 28 2 2024
entrez: 28 2 2024
Statut: epublish

Résumé

Schistosoma japonicum is a parasitic flatworm that causes human schistosomiasis, which is a significant cause of morbidity in China, the Philippines and Indonesia. Oncomelania hupensis (Gastropoda: Pomatiopsidae) is the unique intermediate host of S. japonicum. A complete genome sequence of O. hupensis will enable the fundamental understanding of snail biology as well as its co-evolution with the S. japonicum parasite. Assembling a high-quality reference genome of O. hupehensis will provide data for further research on the snail biology and controlling the spread of S. japonicum. The draft genome was de novo assembly using the long-read sequencing technology (PacBio Sequel II) and corrected with Illumina sequencing data. Then, using Hi-C sequencing data, the genome was assembled at the chromosomal level. CAFE was used to do analysis of contraction and expansion of the gene family and CodeML module in PAML was used for positive selection analysis in protein coding sequences. A total length of 1.46 Gb high-quality O. hupensis genome with 17 unique full-length chromosomes (2n = 34) of the individual including a contig N50 of 1.35 Mb and a scaffold N50 of 75.08 Mb. Additionally, 95.03% of these contig sequences were anchored in 17 chromosomes. After scanning the assembled genome, a total of 30,604 protein-coding genes were predicted. Among them, 86.67% were functionally annotated. Further phylogenetic analysis revealed that O. hupensis was separated from a common ancestor of Pomacea canaliculata and Bellamya purificata approximately 170 million years ago. Comparing the genome of O. hupensis with its most recent common ancestor, it showed 266 significantly expanded and 58 significantly contracted gene families (P < 0.05). Functional enrichment of the expanded gene families indicated that they were mainly involved with intracellular, DNA-mediated transposition, DNA integration and transposase activity. Integrated use of multiple sequencing technologies, we have successfully constructed the genome at the chromosomal-level of O. hupensis. These data will not only provide the compressive genomic information, but also benefit future work on population genetics of this snail as well as evolutional studies between S. japonicum and the snail host.

Sections du résumé

BACKGROUND BACKGROUND
Schistosoma japonicum is a parasitic flatworm that causes human schistosomiasis, which is a significant cause of morbidity in China, the Philippines and Indonesia. Oncomelania hupensis (Gastropoda: Pomatiopsidae) is the unique intermediate host of S. japonicum. A complete genome sequence of O. hupensis will enable the fundamental understanding of snail biology as well as its co-evolution with the S. japonicum parasite. Assembling a high-quality reference genome of O. hupehensis will provide data for further research on the snail biology and controlling the spread of S. japonicum.
METHODS METHODS
The draft genome was de novo assembly using the long-read sequencing technology (PacBio Sequel II) and corrected with Illumina sequencing data. Then, using Hi-C sequencing data, the genome was assembled at the chromosomal level. CAFE was used to do analysis of contraction and expansion of the gene family and CodeML module in PAML was used for positive selection analysis in protein coding sequences.
RESULTS RESULTS
A total length of 1.46 Gb high-quality O. hupensis genome with 17 unique full-length chromosomes (2n = 34) of the individual including a contig N50 of 1.35 Mb and a scaffold N50 of 75.08 Mb. Additionally, 95.03% of these contig sequences were anchored in 17 chromosomes. After scanning the assembled genome, a total of 30,604 protein-coding genes were predicted. Among them, 86.67% were functionally annotated. Further phylogenetic analysis revealed that O. hupensis was separated from a common ancestor of Pomacea canaliculata and Bellamya purificata approximately 170 million years ago. Comparing the genome of O. hupensis with its most recent common ancestor, it showed 266 significantly expanded and 58 significantly contracted gene families (P < 0.05). Functional enrichment of the expanded gene families indicated that they were mainly involved with intracellular, DNA-mediated transposition, DNA integration and transposase activity.
CONCLUSIONS CONCLUSIONS
Integrated use of multiple sequencing technologies, we have successfully constructed the genome at the chromosomal-level of O. hupensis. These data will not only provide the compressive genomic information, but also benefit future work on population genetics of this snail as well as evolutional studies between S. japonicum and the snail host.

Identifiants

DOI: 10.1186/s40249-024-01187-3 PMID: 38414088
pubmed: 38414088
doi: 10.1186/s40249-024-01187-3
pii: 10.1186/s40249-024-01187-3
doi:

Types de publication

Journal Article

Langues

eng

Sous-ensembles de citation

IM

Pagination

19

Subventions

Organisme : National Key Research and Development Program of China
ID : 2021YFC2300800
Organisme : National Key Research and Development Program of China
ID : 2021YFC2300803

Informations de copyright

© 2024. The Author(s).

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Auteurs

Qin Liu (Q)

National Institute of Parasitic Diseases at Chinese Center for Disease Control and Prevention (Chinese Center for Tropical Diseases Research); NHC Key Laboratory of Parasite and Vector Biology; WHO Collaborating Centre for Tropical Diseases; National Center for International Research on Tropical Diseases; National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Shanghai, 200025, People's Republic of China.

Lei Duan (L)

National Institute of Parasitic Diseases at Chinese Center for Disease Control and Prevention (Chinese Center for Tropical Diseases Research); NHC Key Laboratory of Parasite and Vector Biology; WHO Collaborating Centre for Tropical Diseases; National Center for International Research on Tropical Diseases; National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Shanghai, 200025, People's Republic of China.
School of Life Science, Fudan University, Shanghai, 200438, People's Republic of China.

Yun-Hai Guo (YH)

National Institute of Parasitic Diseases at Chinese Center for Disease Control and Prevention (Chinese Center for Tropical Diseases Research); NHC Key Laboratory of Parasite and Vector Biology; WHO Collaborating Centre for Tropical Diseases; National Center for International Research on Tropical Diseases; National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Shanghai, 200025, People's Republic of China.

Li-Min Yang (LM)

National Institute of Parasitic Diseases at Chinese Center for Disease Control and Prevention (Chinese Center for Tropical Diseases Research); NHC Key Laboratory of Parasite and Vector Biology; WHO Collaborating Centre for Tropical Diseases; National Center for International Research on Tropical Diseases; National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Shanghai, 200025, People's Republic of China.

Yi Zhang (Y)

National Institute of Parasitic Diseases at Chinese Center for Disease Control and Prevention (Chinese Center for Tropical Diseases Research); NHC Key Laboratory of Parasite and Vector Biology; WHO Collaborating Centre for Tropical Diseases; National Center for International Research on Tropical Diseases; National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Shanghai, 200025, People's Republic of China.
School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, People's Republic of China.

Shi-Zhu Li (SZ)

National Institute of Parasitic Diseases at Chinese Center for Disease Control and Prevention (Chinese Center for Tropical Diseases Research); NHC Key Laboratory of Parasite and Vector Biology; WHO Collaborating Centre for Tropical Diseases; National Center for International Research on Tropical Diseases; National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Shanghai, 200025, People's Republic of China.
School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, People's Republic of China.

Shan Lv (S)

National Institute of Parasitic Diseases at Chinese Center for Disease Control and Prevention (Chinese Center for Tropical Diseases Research); NHC Key Laboratory of Parasite and Vector Biology; WHO Collaborating Centre for Tropical Diseases; National Center for International Research on Tropical Diseases; National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Shanghai, 200025, People's Republic of China.
School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, People's Republic of China.

Wei Hu (W)

School of Life Science, Fudan University, Shanghai, 200438, People's Republic of China.

Nan-Sheng Chen (NS)

CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, Shandong, 266071, People's Republic of China.

Xiao-Nong Zhou (XN)

National Institute of Parasitic Diseases at Chinese Center for Disease Control and Prevention (Chinese Center for Tropical Diseases Research); NHC Key Laboratory of Parasite and Vector Biology; WHO Collaborating Centre for Tropical Diseases; National Center for International Research on Tropical Diseases; National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Shanghai, 200025, People's Republic of China. zhouxn1@chinacdc.cn.
School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, People's Republic of China. zhouxn1@chinacdc.cn.
ORCID: 0000-0003-1417-8427

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