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

Hai, D.M.; Yen, D.T.; Liem, P.T.; Tam, B.M.; Huong, D.T.T.; Hang, B.T.B.; Hieu, D.Q.; Garigliany, Mutien-Marie; Coppieters, Wouter; Kestemont, P.; Phuong, N.T.; Farnir, Frédéric

doi:10.3390/genes13050923

Article (Scientific journals)

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

Hai, D.M.; Yen, D.T.; Liem, P.T. et al.

2022 • In Genes, 13 (5)

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https://hdl.handle.net/2268/302610

DOI
10.3390/genes13050923

PubMed
35627308

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Keywords :

chromosome-scale genome assembly; HiFi reads; selective breeding; striped catfish; animal; catfish; chromosome; genetics; genome; genomics; molecular genetics; procedures; Animals; Catfishes; Chromosomes; Genome; Genomics; Molecular Sequence Annotation

Abstract :

[en] 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. © 2022 by the authors. Licensee MDPI, Basel, Switzerland.

Disciplines :

Animal production & animal husbandry

Author, co-author :

Hai, D.M.; FARAH/Sustainable Animal Production, Faculty of Veterinary Medicine, University of Liege (B43), Liege, 4000, Belgium, College of Aquaculture and Fisheries, Can Tho University, Can Tho, 900000, Viet Nam

Yen, D.T.; College of Aquaculture and Fisheries, Can Tho University, Can Tho, 900000, Viet Nam

Liem, P.T.; College of Aquaculture and Fisheries, Can Tho University, Can Tho, 900000, Viet Nam

Tam, B.M.; College of Aquaculture and Fisheries, Can Tho University, Can Tho, 900000, Viet Nam

Huong, D.T.T.; College of Aquaculture and Fisheries, Can Tho University, Can Tho, 900000, Viet Nam

Hang, B.T.B.; College of Aquaculture and Fisheries, Can Tho University, Can Tho, 900000, Viet Nam

Hieu, D.Q.; College of Aquaculture and Fisheries, Can Tho University, Can Tho, 900000, Viet Nam

Garigliany, Mutien-Marie ; Université de Liège - ULiège > Département de morphologie et pathologie (DMP) > Pathologie générale et autopsies

Coppieters, Wouter ; Université de Liège - ULiège > GIGA > GIGA Platform Genomics

Kestemont, P.; Research Unit in Environmental and Evolutionary Biology, Institute of Life, Earth & Environnment, University of Namur, rue de Bruxelles 61, Namur, 5000, Belgium

Phuong, N.T.; College of Aquaculture and Fisheries, Can Tho University, Can Tho, 900000, Viet Nam

Farnir, Frédéric ; Université de Liège - ULiège > Département de gestion vétérinaire des Ressources Animales (DRA)

Language :

English

Title :

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

Publication date :

May 2022

Journal title :

Genes

ISSN :

2073-4425

Publisher :

MDPI

Volume :

Issue :

Peer reviewed :

Peer Reviewed verified by ORBi

Funding text :

Funding: This work was part of PANGAGEN project, supported by ARES‐CCD (Académie de Re‐ cherche et d’Enseignement Supérieur—Commission de la Coopération au Développement) and funded by the Belgian Development Cooperation (DRP/TPS 2017).

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