The first draft genome assembly and data analysis of the Malaysian mahseer (Tor tambroides)

The Malaysian mahseer (Tor tambroides), one of the most valuable freshwater fish in the world, is mainly targeted for human consumption. The mitogenomic data of this species is available to date, but the genomic information is still lacking. For the first time, we sequenced the whole genome of an ad...

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Main Authors: Chung, Hung Hui, Melinda Mei Lin, Lau, Leonard Whye Kit, Lim, Han Ming, Gan
Format: Article
Language:English
Published: Elsevier B.V. 2022
Subjects:
Online Access:http://ir.unimas.my/id/eprint/39794/2/The%20first%20draft%20-%20Copy.pdf
http://ir.unimas.my/id/eprint/39794/
https://www.sciencedirect.com/science/article/pii/S2468550X22000818
https://doi.org/10.1016/j.aaf.2022.05.002
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spelling my.unimas.ir.397942022-09-19T01:36:00Z http://ir.unimas.my/id/eprint/39794/ The first draft genome assembly and data analysis of the Malaysian mahseer (Tor tambroides) Chung, Hung Hui Melinda Mei Lin, Lau Leonard Whye Kit, Lim Han Ming, Gan QL Zoology SF Animal culture SH Aquaculture. Fisheries. Angling The Malaysian mahseer (Tor tambroides), one of the most valuable freshwater fish in the world, is mainly targeted for human consumption. The mitogenomic data of this species is available to date, but the genomic information is still lacking. For the first time, we sequenced the whole genome of an adult fish on both Illumina and Nanopore platforms. The hybrid genome assembly had resulted in a sum of 1.23 Gb genomic sequence from the 44,726 contigs found with 44 kb N50 length and BUSCO genome completeness of 87.6%. Four types of SSRs had been detected and identified within the genome with a greater AT abundance than that of GC. Predicted protein sequences had been functionally annotated to public databases, namely GO, KEGG and COG. A maximum likelihood phylogenomic tree containing 52 Actinopterygii species and one Sarcopterygii species as outgroup was constructed, providing first insights into the genome-based evolutionary relationship of T. tambroides with other ray-finned fish. These data are crucial in facilitating the study of population genomics, species identification, morphological variations, and evolutionary biology, which are helpful in the conservation of this species. Elsevier B.V. 2022-05-27 Article PeerReviewed text en http://ir.unimas.my/id/eprint/39794/2/The%20first%20draft%20-%20Copy.pdf Chung, Hung Hui and Melinda Mei Lin, Lau and Leonard Whye Kit, Lim and Han Ming, Gan (2022) The first draft genome assembly and data analysis of the Malaysian mahseer (Tor tambroides). Aquaculture and Fisheries. pp. 1-11. ISSN 2468-550X (In Press) https://www.sciencedirect.com/science/article/pii/S2468550X22000818 https://doi.org/10.1016/j.aaf.2022.05.002
institution Universiti Malaysia Sarawak
building Centre for Academic Information Services (CAIS)
collection Institutional Repository
continent Asia
country Malaysia
content_provider Universiti Malaysia Sarawak
content_source UNIMAS Institutional Repository
url_provider http://ir.unimas.my/
language English
topic QL Zoology
SF Animal culture
SH Aquaculture. Fisheries. Angling
spellingShingle QL Zoology
SF Animal culture
SH Aquaculture. Fisheries. Angling
Chung, Hung Hui
Melinda Mei Lin, Lau
Leonard Whye Kit, Lim
Han Ming, Gan
The first draft genome assembly and data analysis of the Malaysian mahseer (Tor tambroides)
description The Malaysian mahseer (Tor tambroides), one of the most valuable freshwater fish in the world, is mainly targeted for human consumption. The mitogenomic data of this species is available to date, but the genomic information is still lacking. For the first time, we sequenced the whole genome of an adult fish on both Illumina and Nanopore platforms. The hybrid genome assembly had resulted in a sum of 1.23 Gb genomic sequence from the 44,726 contigs found with 44 kb N50 length and BUSCO genome completeness of 87.6%. Four types of SSRs had been detected and identified within the genome with a greater AT abundance than that of GC. Predicted protein sequences had been functionally annotated to public databases, namely GO, KEGG and COG. A maximum likelihood phylogenomic tree containing 52 Actinopterygii species and one Sarcopterygii species as outgroup was constructed, providing first insights into the genome-based evolutionary relationship of T. tambroides with other ray-finned fish. These data are crucial in facilitating the study of population genomics, species identification, morphological variations, and evolutionary biology, which are helpful in the conservation of this species.
format Article
author Chung, Hung Hui
Melinda Mei Lin, Lau
Leonard Whye Kit, Lim
Han Ming, Gan
author_facet Chung, Hung Hui
Melinda Mei Lin, Lau
Leonard Whye Kit, Lim
Han Ming, Gan
author_sort Chung, Hung Hui
title The first draft genome assembly and data analysis of the Malaysian mahseer (Tor tambroides)
title_short The first draft genome assembly and data analysis of the Malaysian mahseer (Tor tambroides)
title_full The first draft genome assembly and data analysis of the Malaysian mahseer (Tor tambroides)
title_fullStr The first draft genome assembly and data analysis of the Malaysian mahseer (Tor tambroides)
title_full_unstemmed The first draft genome assembly and data analysis of the Malaysian mahseer (Tor tambroides)
title_sort first draft genome assembly and data analysis of the malaysian mahseer (tor tambroides)
publisher Elsevier B.V.
publishDate 2022
url http://ir.unimas.my/id/eprint/39794/2/The%20first%20draft%20-%20Copy.pdf
http://ir.unimas.my/id/eprint/39794/
https://www.sciencedirect.com/science/article/pii/S2468550X22000818
https://doi.org/10.1016/j.aaf.2022.05.002
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score 13.159267