Lipidomic insights into the immune response and pearl formation in transplanted pearl oyster Pinctada fucata martensii

Wu, Hailing; Yang, Chuangye; Hao, Ruijuan; Liao, Yongshan; Wang, Qingheng; Deng, Yuewen

doi:10.3389/fimmu.2022.1018423

Cited by 9 publications

(2 citation statements)

References 71 publications

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“…We also found that ABC transporters, arachidonic acid metabolism, linoleic acid metabolism, antifolate resistance and ovarian steroidogenesis gene families contracted significantly in the snails, which may be related to feeding habits, reproductive, environmental adaptation and immune defense behavior [ 49 – 51 ]. In China, the ribbed-shell snail populations and the smooth-shell snail populations are distributed in different ecological environments, and their compatibility with S. japonicum is also different.…”

Section: Discussionmentioning

confidence: 99%

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

Liu,

Duan,

Guo

et al. 2024

Infect Dis Poverty

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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 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 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 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. Graphical Abstract

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Section: Discussionmentioning

confidence: 99%

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

Liu,

Duan,

Guo

et al. 2024

Infect Dis Poverty

View full text Add to dashboard Cite

show abstract

Section: Discussionmentioning

confidence: 99%

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

Liu,

Duan,

Guo

et al. 2023

Preprint

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Background Schistosomiasis is a zoonotic parasitic disease that is estimated to affect almost 300 million people worldwide. As one of the three major human parasites, Schistosoma japonicum is endemic in Southeast Asia, including China, Philippines and Indonesia. Transmission relies only on one snail host Oncomelania hupensis (Gastropoda: Pomatiopsidae). However, no genomic information for this important intermediate host is available. Methods Contig-level of O. hupensis assembly of an individual male O. hupensis snail was performed with full PacBio long reads using Next Denovo. The completeness and continuity of the assembly were assessed with Benchmarking Universal Single-Copy Orthologs (BUSCO). CAFÉ 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 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 using single copy protein-coding genes revealed that O. hupensis was separated from a common ancestors 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 gene families (p < 0.05) 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, transposase activity and hyalurononglucosaminidase activity. Additionally, a total of 281 protein-coding genes related to protein kinase activity, protein phosphorylation, catalytic activity and metabolic process under positive selection were identified in O. hupensis (FDR < 0.05). Conclusion A complete genome sequence of O. hupensis would enable the fundamental understanding of snail biology as well as its co-evolution with the S. japonicum parasite causing schistosomiasis in humans. Using a single molecular DNA sequencing technology, we have successfully constructed the genome at the chromosomal-level. These data will not only provide the compressive genomic information for the sole intermediated host of S. japonicum, but also benefit future work on population genetics of this snail as well as evolutional studies between S. japonicum and the snail host.

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Identification of Shell Color-Associated Genes Using Mantle Branch-Specific RNA Sequencing of Yellow-Colored Line of Pearl Oyster Pinctada fucata martensii

Peng,

Liao,

Yang

et al. 2024

J. Ocean Univ. China

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Lipidomic insights into the immune response and pearl formation in transplanted pearl oyster Pinctada fucata martensii

Cited by 9 publications

References 71 publications

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

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

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

Identification of Shell Color-Associated Genes Using Mantle Branch-Specific RNA Sequencing of Yellow-Colored Line of Pearl Oyster Pinctada fucata martensii

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