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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...
Autores principales: | , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2022
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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. |
format | Online Article Text |
id | pubmed-9141817 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
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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