Chromosome-level genome assembly of the largefin longbarbel catfish (Hemibagrus macropterus)
The largefin longbarbel catfish, Hemibagrus macropterus, is an economically important fish species in southwestern China, with males growing faster than females. This study presents a high-quality chromosome-level genome assembly of the largefin longbarbel catfish, generated by integrating Illumina...
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Frontiers Media S.A.
2023-11-01
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| Series: | Frontiers in Genetics |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fgene.2023.1297119/full |
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| author | Huan Ye Jiahui Fan Yanling Hou Huamei Yue Rui Ruan Shuang Li Chongjiang Hu Yong Xie Chuangju Li |
| author_facet | Huan Ye Jiahui Fan Yanling Hou Huamei Yue Rui Ruan Shuang Li Chongjiang Hu Yong Xie Chuangju Li |
| author_sort | Huan Ye |
| collection | DOAJ |
| description | The largefin longbarbel catfish, Hemibagrus macropterus, is an economically important fish species in southwestern China, with males growing faster than females. This study presents a high-quality chromosome-level genome assembly of the largefin longbarbel catfish, generated by integrating Illumina short reads, PacBio HiFi long reads, and Hi-C data. The assembled genome size was 858.5 Mb, with a contig and scaffold N50 of 5.8 Mb and 28.4 Mb, respectively. A total of 656 contigs were successfully anchored to 30 pseudochromosomes with a BUSCO score of 97.7%, consistent with the number of chromosomes analyzed by karyotype. The genome contained 29.5% repeat sequences, and a predicted total of 26,613 protein-coding genes, of which 25,769 (96.8%) were functionally annotated in different databases. Evolutionary analysis showed that H. macropterus was most closely related to H. wyckioides, with a divergence time of approximately 16.3 million years. Chromosomal syntenic relationships among H. macropterus, H. wyckioides, and Pelteobagrus fulvidraco revealed a one-to-one relationship for most chromosomes, except for break, fission, and inversion of some chromosomes. The first high-quality reference genome will not only provide a valuable genetic resource for the study of sex determination mechanisms and genetic breeding of largefin longbarbel catfish, but also contribute to comparative analyses of genome and chromosome evolution within Siluriformes. |
| first_indexed | 2024-03-11T14:12:58Z |
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| institution | Directory Open Access Journal |
| issn | 1664-8021 |
| language | English |
| last_indexed | 2024-03-11T14:12:58Z |
| publishDate | 2023-11-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Genetics |
| spelling | doaj.art-2825d1f126474a60a4e63a4c998043a72023-11-01T16:48:07ZengFrontiers Media S.A.Frontiers in Genetics1664-80212023-11-011410.3389/fgene.2023.12971191297119Chromosome-level genome assembly of the largefin longbarbel catfish (Hemibagrus macropterus)Huan Ye0Jiahui Fan1Yanling Hou2Huamei Yue3Rui Ruan4Shuang Li5Chongjiang Hu6Yong Xie7Chuangju Li8Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture and Rural Affairs, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, ChinaKey Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture and Rural Affairs, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, ChinaKey Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture and Rural Affairs, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, ChinaKey Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture and Rural Affairs, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, ChinaKey Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture and Rural Affairs, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, ChinaChongqing Fishery Sciences Research Institute, Chongqing, ChinaChongqing Fishery Sciences Research Institute, Chongqing, ChinaChongqing Fishery Sciences Research Institute, Chongqing, ChinaKey Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture and Rural Affairs, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, ChinaThe largefin longbarbel catfish, Hemibagrus macropterus, is an economically important fish species in southwestern China, with males growing faster than females. This study presents a high-quality chromosome-level genome assembly of the largefin longbarbel catfish, generated by integrating Illumina short reads, PacBio HiFi long reads, and Hi-C data. The assembled genome size was 858.5 Mb, with a contig and scaffold N50 of 5.8 Mb and 28.4 Mb, respectively. A total of 656 contigs were successfully anchored to 30 pseudochromosomes with a BUSCO score of 97.7%, consistent with the number of chromosomes analyzed by karyotype. The genome contained 29.5% repeat sequences, and a predicted total of 26,613 protein-coding genes, of which 25,769 (96.8%) were functionally annotated in different databases. Evolutionary analysis showed that H. macropterus was most closely related to H. wyckioides, with a divergence time of approximately 16.3 million years. Chromosomal syntenic relationships among H. macropterus, H. wyckioides, and Pelteobagrus fulvidraco revealed a one-to-one relationship for most chromosomes, except for break, fission, and inversion of some chromosomes. The first high-quality reference genome will not only provide a valuable genetic resource for the study of sex determination mechanisms and genetic breeding of largefin longbarbel catfish, but also contribute to comparative analyses of genome and chromosome evolution within Siluriformes.https://www.frontiersin.org/articles/10.3389/fgene.2023.1297119/fullHemibagrus macropterusgenome assemblygenome annotationcomparative genomicsHi-CPacBio |
| spellingShingle | Huan Ye Jiahui Fan Yanling Hou Huamei Yue Rui Ruan Shuang Li Chongjiang Hu Yong Xie Chuangju Li Chromosome-level genome assembly of the largefin longbarbel catfish (Hemibagrus macropterus) Frontiers in Genetics Hemibagrus macropterus genome assembly genome annotation comparative genomics Hi-C PacBio |
| title | Chromosome-level genome assembly of the largefin longbarbel catfish (Hemibagrus macropterus) |
| title_full | Chromosome-level genome assembly of the largefin longbarbel catfish (Hemibagrus macropterus) |
| title_fullStr | Chromosome-level genome assembly of the largefin longbarbel catfish (Hemibagrus macropterus) |
| title_full_unstemmed | Chromosome-level genome assembly of the largefin longbarbel catfish (Hemibagrus macropterus) |
| title_short | Chromosome-level genome assembly of the largefin longbarbel catfish (Hemibagrus macropterus) |
| title_sort | chromosome level genome assembly of the largefin longbarbel catfish hemibagrus macropterus |
| topic | Hemibagrus macropterus genome assembly genome annotation comparative genomics Hi-C PacBio |
| url | https://www.frontiersin.org/articles/10.3389/fgene.2023.1297119/full |
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