Chromosome Genome Assembly of <i>Cromileptes altivelis</i> Reveals Loss of Genome Fragment in <i>Cromileptes</i> Compared with <i>Epinephelus</i> Species
The humpback grouper (<i>Cromileptes altivelis</i>), an Epinephelidae species, is patchily distributed in the reef habitats of Western Pacific water. This grouper possesses a remarkably different body shape and notably low growth rate compared with closely related grouper species. For pr...
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MDPI AG
2021-11-01
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| author | Yang Yang Lina Wu Zhuoying Weng Xi Wu Xi Wang Junhong Xia Zining Meng Xiaochun Liu |
| author_facet | Yang Yang Lina Wu Zhuoying Weng Xi Wu Xi Wang Junhong Xia Zining Meng Xiaochun Liu |
| author_sort | Yang Yang |
| collection | DOAJ |
| description | The humpback grouper (<i>Cromileptes altivelis</i>), an Epinephelidae species, is patchily distributed in the reef habitats of Western Pacific water. This grouper possesses a remarkably different body shape and notably low growth rate compared with closely related grouper species. For promoting further research of the grouper, in the present study, a high-quality chromosome-level genome of humpback grouper was assembled using PacBio sequencing and high-throughput chromatin conformation capture (Hi-C) technology. The assembled genome was 1.013 Gb in size with 283 contigs, of which, a total of 143 contigs with 1.011 Gb in size were correctly anchored into 24 chromosomes. Moreover, a total of 26,037 protein-coding genes were predicted, of them, 25,243 (96.95%) genes could be functionally annotated. The high-quality chromosome-level genome assembly will provide pivotal genomic information for future research of the speciation, evolution and molecular-assisted breeding in humpback groupers. In addition, phylogenetic analysis based on shared single-copy orthologues of the grouper species showed that the humpback grouper is included in the <i>Epinephelus</i> genus and clustered with the giant grouper in one clade with a divergence time of 9.86 Myr. In addition, based on the results of collinearity analysis, a gap in chromosome 6 of the humpback grouper was detected; the missed genes were mainly associated with immunity, substance metabolism and the MAPK signal pathway. The loss of the parts of genes involved in these biological processes might affect the disease resistance, stress tolerance and growth traits in humpback groupers. The present research will provide new insight into the evolution and origin of the humpback grouper. |
| first_indexed | 2024-03-10T04:02:48Z |
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| last_indexed | 2024-03-10T04:02:48Z |
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| series | Genes |
| spelling | doaj.art-d257e97ac4804b419181a4b32a3be4f52023-11-23T08:29:42ZengMDPI AGGenes2073-44252021-11-011212187310.3390/genes12121873Chromosome Genome Assembly of <i>Cromileptes altivelis</i> Reveals Loss of Genome Fragment in <i>Cromileptes</i> Compared with <i>Epinephelus</i> SpeciesYang Yang0Lina Wu1Zhuoying Weng2Xi Wu3Xi Wang4Junhong Xia5Zining Meng6Xiaochun Liu7State Key Laboratory of Biocontrol, Life Sciences School, Sun Yat-sen University, Guangzhou 510275, ChinaState Key Laboratory of Biocontrol, Life Sciences School, Sun Yat-sen University, Guangzhou 510275, ChinaState Key Laboratory of Biocontrol, Life Sciences School, Sun Yat-sen University, Guangzhou 510275, ChinaState Key Laboratory of Biocontrol, Life Sciences School, Sun Yat-sen University, Guangzhou 510275, ChinaState Key Laboratory of Biocontrol, Life Sciences School, Sun Yat-sen University, Guangzhou 510275, ChinaState Key Laboratory of Biocontrol, Life Sciences School, Sun Yat-sen University, Guangzhou 510275, ChinaState Key Laboratory of Biocontrol, Life Sciences School, Sun Yat-sen University, Guangzhou 510275, ChinaState Key Laboratory of Biocontrol, Life Sciences School, Sun Yat-sen University, Guangzhou 510275, ChinaThe humpback grouper (<i>Cromileptes altivelis</i>), an Epinephelidae species, is patchily distributed in the reef habitats of Western Pacific water. This grouper possesses a remarkably different body shape and notably low growth rate compared with closely related grouper species. For promoting further research of the grouper, in the present study, a high-quality chromosome-level genome of humpback grouper was assembled using PacBio sequencing and high-throughput chromatin conformation capture (Hi-C) technology. The assembled genome was 1.013 Gb in size with 283 contigs, of which, a total of 143 contigs with 1.011 Gb in size were correctly anchored into 24 chromosomes. Moreover, a total of 26,037 protein-coding genes were predicted, of them, 25,243 (96.95%) genes could be functionally annotated. The high-quality chromosome-level genome assembly will provide pivotal genomic information for future research of the speciation, evolution and molecular-assisted breeding in humpback groupers. In addition, phylogenetic analysis based on shared single-copy orthologues of the grouper species showed that the humpback grouper is included in the <i>Epinephelus</i> genus and clustered with the giant grouper in one clade with a divergence time of 9.86 Myr. In addition, based on the results of collinearity analysis, a gap in chromosome 6 of the humpback grouper was detected; the missed genes were mainly associated with immunity, substance metabolism and the MAPK signal pathway. The loss of the parts of genes involved in these biological processes might affect the disease resistance, stress tolerance and growth traits in humpback groupers. The present research will provide new insight into the evolution and origin of the humpback grouper.https://www.mdpi.com/2073-4425/12/12/1873humpback grouper<i>Cromileptes altivelis</i>genomeevolutioncollinearity |
| spellingShingle | Yang Yang Lina Wu Zhuoying Weng Xi Wu Xi Wang Junhong Xia Zining Meng Xiaochun Liu Chromosome Genome Assembly of <i>Cromileptes altivelis</i> Reveals Loss of Genome Fragment in <i>Cromileptes</i> Compared with <i>Epinephelus</i> Species Genes humpback grouper <i>Cromileptes altivelis</i> genome evolution collinearity |
| title | Chromosome Genome Assembly of <i>Cromileptes altivelis</i> Reveals Loss of Genome Fragment in <i>Cromileptes</i> Compared with <i>Epinephelus</i> Species |
| title_full | Chromosome Genome Assembly of <i>Cromileptes altivelis</i> Reveals Loss of Genome Fragment in <i>Cromileptes</i> Compared with <i>Epinephelus</i> Species |
| title_fullStr | Chromosome Genome Assembly of <i>Cromileptes altivelis</i> Reveals Loss of Genome Fragment in <i>Cromileptes</i> Compared with <i>Epinephelus</i> Species |
| title_full_unstemmed | Chromosome Genome Assembly of <i>Cromileptes altivelis</i> Reveals Loss of Genome Fragment in <i>Cromileptes</i> Compared with <i>Epinephelus</i> Species |
| title_short | Chromosome Genome Assembly of <i>Cromileptes altivelis</i> Reveals Loss of Genome Fragment in <i>Cromileptes</i> Compared with <i>Epinephelus</i> Species |
| title_sort | chromosome genome assembly of i cromileptes altivelis i reveals loss of genome fragment in i cromileptes i compared with i epinephelus i species |
| topic | humpback grouper <i>Cromileptes altivelis</i> genome evolution collinearity |
| url | https://www.mdpi.com/2073-4425/12/12/1873 |
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