Dataset Information

A High-Quality Genome Assembly of Striped Catfish (Pangasianodon hypophthalmus) Based on Highly Accurate Long-Read HiFi Sequencing Data.

ABSTRACT: The HiFi sequencing technology yields highly accurate long-read data with accuracies greater than 99.9% that can be used to improve results for complex applications such as genome assembly. Our study presents a high-quality chromosome-scale genome assembly of striped catfish (Pangasianodon hypophthalmus), a commercially important species cultured mainly in Vietnam, integrating HiFi reads and Hi-C data. A 788.4 Mb genome containing 381 scaffolds with an N50 length of 21.8 Mb has been obtained from HiFi reads. These scaffolds have been further ordered and clustered into 30 chromosome groups, ranging from 1.4 to 57.6 Mb, based on Hi-C data. The present updated assembly has a contig N50 of 14.7 Mb, representing a 245-fold and 4.2-fold improvement over the previous Illumina and Illumina-Nanopore-Hi-C based version, respectively. In addition, the proportion of repeat elements and BUSCO genes identified in our genome is remarkably higher than in the two previously released striped catfish genomes. These results highlight the power of using HiFi reads to assemble the highly repetitive regions and to improve the quality of genome assembly. The updated, high-quality genome assembled in this work will provide a valuable genomic resource for future population genetics, conservation biology and selective breeding studies of striped catfish.

SUBMITTER: Hai DM

PROVIDER: S-EPMC9141817 | biostudies-literature | 2022 May

REPOSITORIES: biostudies-literature

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Publications

A High-Quality Genome Assembly of Striped Catfish (<i>Pangasianodon hypophthalmus</i>) Based on Highly Accurate Long-Read HiFi Sequencing Data.

Hai Dao Minh DM Yen Duong Thuy DT Liem Pham Thanh PT Tam Bui Minh BM Huong Do Thi Thanh DTT Hang Bui Thi Bich BTB Hieu Dang Quang DQ Garigliany Mutien-Marie MM Coppieters Wouter W Kestemont Patrick P Phuong Nguyen Thanh NT Farnir Frédéric F

Genes 20220522 5

The HiFi sequencing technology yields highly accurate long-read data with accuracies greater than 99.9% that can be used to improve results for complex applications such as genome assembly. Our study presents a high-quality chromosome-scale genome assembly of striped catfish (<i>Pangasianodon hypophthalmus</i>), a commercially important species cultured mainly in Vietnam, integrating HiFi reads and Hi-C data. A 788.4 Mb genome containing 381 scaffolds with an N50 length of 21.8 Mb has been obtai ...[more]

PMID: 35627308

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Project description:Bacterial pathogens are well equipped to adhere to and initiate infection in teleost fish. Fish skin mucus serves as the first barrier against environmental pathogens. The mucus harbors commensal microbes that impact host physiological and immunological responses. However, how the skin mucosal microbiota responds to the presence of pathogens remains largely unexplored. Thus, little is known about the status of skin mucus prior to infection with noticeable symptoms. In this study, we investigated the interactions between pathogens and the skin mucosal microbiota as well as the fish skin immune responses in the presence of pathogens. Striped catfish (Pangasianodon hypophthalmus) were challenged with different concentrations of the bacterial pathogen Aeromonas hydrophila (AH), and the skin immune response and the mucosal microbiota were examined by quantitative PCR (qPCR) and 16S rRNA gene sequence analysis. We determined that the pathogen concentration needed to stimulate the skin immune response was associated with significant mucosal microbiota changes, and we reconfirmed these observations using an ex vivo fish skin model. Further analysis indicated that changes in the microbiota were attributed to a significant increase in opportunistic pathogens over AH. We concluded that the presence and increase of AH result in dysbiosis of the mucosal microbiota that can stimulate skin immune responses. We believe that our work sheds light on host-pathogen-commensal microbiota interactions and therefore contributes to aquaculture fish health. IMPORTANCE The fish skin mucosal microbiota is essential in modulating the host response to the presence of pathogens. Our study provides a platform to study both the correlation and causation of the interactions among the pathogen, fish skin, and the skin mucosal microbiota. Based on these findings, we provide the first mechanistic information on how mucosal microbiota changes induced by the pathogen AH result in skin disturbance with immune stimulation in striped catfish in the natural state and a potential direction for early-infection screening. Thus, this study is highly significant in the prevention of fish disease.

Dataset Information

A High-Quality Genome Assembly of Striped Catfish (Pangasianodon hypophthalmus) Based on Highly Accurate Long-Read HiFi Sequencing Data.

Publications

A High-Quality Genome Assembly of Striped Catfish (<i>Pangasianodon hypophthalmus</i>) Based on Highly Accurate Long-Read HiFi Sequencing Data.

Similar Datasets

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