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

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 hypophtha...

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Autores principales: Hai, Dao Minh, Yen, Duong Thuy, Liem, Pham Thanh, Tam, Bui Minh, Huong, Do Thi Thanh, Hang, Bui Thi Bich, Hieu, Dang Quang, Garigliany, Mutien-Marie, Coppieters, Wouter, Kestemont, Patrick, Phuong, Nguyen Thanh, Farnir, Frédéric
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9141817/
https://www.ncbi.nlm.nih.gov/pubmed/35627308
http://dx.doi.org/10.3390/genes13050923
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author Hai, Dao Minh
Yen, Duong Thuy
Liem, Pham Thanh
Tam, Bui Minh
Huong, Do Thi Thanh
Hang, Bui Thi Bich
Hieu, Dang Quang
Garigliany, Mutien-Marie
Coppieters, Wouter
Kestemont, Patrick
Phuong, Nguyen Thanh
Farnir, Frédéric
author_facet Hai, Dao Minh
Yen, Duong Thuy
Liem, Pham Thanh
Tam, Bui Minh
Huong, Do Thi Thanh
Hang, Bui Thi Bich
Hieu, Dang Quang
Garigliany, Mutien-Marie
Coppieters, Wouter
Kestemont, Patrick
Phuong, Nguyen Thanh
Farnir, Frédéric
author_sort Hai, Dao Minh
collection PubMed
description 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.
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spelling pubmed-91418172022-05-28 A High-Quality Genome Assembly of Striped Catfish (Pangasianodon hypophthalmus) Based on Highly Accurate Long-Read HiFi Sequencing Data Hai, Dao Minh Yen, Duong Thuy Liem, Pham Thanh Tam, Bui Minh Huong, Do Thi Thanh Hang, Bui Thi Bich Hieu, Dang Quang Garigliany, Mutien-Marie Coppieters, Wouter Kestemont, Patrick Phuong, Nguyen Thanh Farnir, Frédéric Genes (Basel) Article 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. MDPI 2022-05-22 /pmc/articles/PMC9141817/ /pubmed/35627308 http://dx.doi.org/10.3390/genes13050923 Text en © 2022 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Hai, Dao Minh
Yen, Duong Thuy
Liem, Pham Thanh
Tam, Bui Minh
Huong, Do Thi Thanh
Hang, Bui Thi Bich
Hieu, Dang Quang
Garigliany, Mutien-Marie
Coppieters, Wouter
Kestemont, Patrick
Phuong, Nguyen Thanh
Farnir, Frédéric
A High-Quality Genome Assembly of Striped Catfish (Pangasianodon hypophthalmus) Based on Highly Accurate Long-Read HiFi Sequencing Data
title A High-Quality Genome Assembly of Striped Catfish (Pangasianodon hypophthalmus) Based on Highly Accurate Long-Read HiFi Sequencing Data
title_full A High-Quality Genome Assembly of Striped Catfish (Pangasianodon hypophthalmus) Based on Highly Accurate Long-Read HiFi Sequencing Data
title_fullStr A High-Quality Genome Assembly of Striped Catfish (Pangasianodon hypophthalmus) Based on Highly Accurate Long-Read HiFi Sequencing Data
title_full_unstemmed A High-Quality Genome Assembly of Striped Catfish (Pangasianodon hypophthalmus) Based on Highly Accurate Long-Read HiFi Sequencing Data
title_short A High-Quality Genome Assembly of Striped Catfish (Pangasianodon hypophthalmus) Based on Highly Accurate Long-Read HiFi Sequencing Data
title_sort high-quality genome assembly of striped catfish (pangasianodon hypophthalmus) based on highly accurate long-read hifi sequencing data
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9141817/
https://www.ncbi.nlm.nih.gov/pubmed/35627308
http://dx.doi.org/10.3390/genes13050923
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