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Tian CX, Lin XH, Zhou DY, Chen Y, Shen YJ, Ye MH, Duan CY, Zhang YL, Yang BL, Deng SP, Zhu CH, Li GL. A chromosome-level genome assembly of Hong Kong catfish (Clarias fuscus) uncovers a sex-determining region. BMC Genomics 2023; 24:291. [PMID: 37254055 DOI: 10.1186/s12864-023-09394-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 05/19/2023] [Indexed: 06/01/2023] Open
Abstract
BACKGROUND Hong Kong catfish (Clarias fuscus) is an ecologically and economically important species that is widely distributed in freshwater regions of southern China. Hong Kong catfish has significant sexual growth dimorphism. The genome assembly of the Hong Kong catfish would facilitate study of the sex determination and evolution mechanism of the species. RESULTS The first high-quality chromosome-level genome of the Hong Kong catfish was constructed. The total genome was 933.4 Mb, with 416 contigs and a contig N50 length of 8.52 Mb. Using high-throughput chromosome conformation capture (Hi-C) data, the genome assembly was divided into 28 chromosomes with a scaffold N50 length of 36.68 Mb. A total of 23,345 protein-coding genes were predicted in the genome, and 94.28% of the genes were functionally annotated in public databases. Phylogenetic analysis indicated that C. fuscus and Clarias magur diverged approximately 63.7 million years ago. The comparative genome results showed that a total of 60 unique, 353 expanded and 851 contracted gene families were identified in Hong Kong catfish. A sex-linked quantitative trait locus identified in a previous study was located in a sex-determining region of 30.26 Mb (0.02 to 30.28 Mb) on chromosome 13 (Chr13), the predicted Y chromosome. This QTL region contained 785 genes, of which 18 were identified as sex-related genes. CONCLUSIONS This study is the first to report the chromosome-level genome assembly of Hong Kong catfish. The study provides an excellent genetic resource that will facilitate future studies of sex determination mechanisms and evolution in fish.
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Affiliation(s)
- Chang-Xu Tian
- Fisheries College, Guangdong Ocean University, Zhanjiang, 524088, China.
- Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Guangdong Provincial Engineering Laboratory for Mariculture Organism Breeding, Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy culture, Zhanjiang, 524088, China.
- Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), Zhanjiang, 524088, China.
| | - Xing-Hua Lin
- Fisheries College, Guangdong Ocean University, Zhanjiang, 524088, China
- Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Guangdong Provincial Engineering Laboratory for Mariculture Organism Breeding, Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy culture, Zhanjiang, 524088, China
| | - Da-Yan Zhou
- Guangxi Introduction and Breeding Center of Aquaculture, Nanning, 530001, China
| | - Yu Chen
- Fisheries College, Guangdong Ocean University, Zhanjiang, 524088, China
- Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Guangdong Provincial Engineering Laboratory for Mariculture Organism Breeding, Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy culture, Zhanjiang, 524088, China
| | - Yi-Jun Shen
- Fisheries College, Guangdong Ocean University, Zhanjiang, 524088, China
- Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Guangdong Provincial Engineering Laboratory for Mariculture Organism Breeding, Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy culture, Zhanjiang, 524088, China
| | - Ming-Hui Ye
- Fisheries College, Guangdong Ocean University, Zhanjiang, 524088, China
- Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Guangdong Provincial Engineering Laboratory for Mariculture Organism Breeding, Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy culture, Zhanjiang, 524088, China
| | - Cun-Yu Duan
- Fisheries College, Guangdong Ocean University, Zhanjiang, 524088, China
- Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Guangdong Provincial Engineering Laboratory for Mariculture Organism Breeding, Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy culture, Zhanjiang, 524088, China
| | - Yu-Lei Zhang
- Fisheries College, Guangdong Ocean University, Zhanjiang, 524088, China
- Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Guangdong Provincial Engineering Laboratory for Mariculture Organism Breeding, Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy culture, Zhanjiang, 524088, China
| | - Bin-Lan Yang
- Guangxi Introduction and Breeding Center of Aquaculture, Nanning, 530001, China
| | - Si-Ping Deng
- Fisheries College, Guangdong Ocean University, Zhanjiang, 524088, China
- Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Guangdong Provincial Engineering Laboratory for Mariculture Organism Breeding, Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy culture, Zhanjiang, 524088, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), Zhanjiang, 524088, China
| | - Chun-Hua Zhu
- Fisheries College, Guangdong Ocean University, Zhanjiang, 524088, China
- Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Guangdong Provincial Engineering Laboratory for Mariculture Organism Breeding, Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy culture, Zhanjiang, 524088, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), Zhanjiang, 524088, China
| | - Guang-Li Li
- Fisheries College, Guangdong Ocean University, Zhanjiang, 524088, China.
- Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Guangdong Provincial Engineering Laboratory for Mariculture Organism Breeding, Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy culture, Zhanjiang, 524088, China.
- Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), Zhanjiang, 524088, China.
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Rao G, Zhang J, Liu X, Lin C, Xin H, Xue L, Wang C. De novo assembly of a new Olea europaea genome accession using nanopore sequencing. HORTICULTURE RESEARCH 2021; 8:64. [PMID: 33790235 PMCID: PMC8012569 DOI: 10.1038/s41438-021-00498-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 01/04/2021] [Accepted: 01/11/2021] [Indexed: 05/17/2023]
Abstract
Olive (Olea europaea L.) is internationally renowned for its high-end product, extra virgin olive oil. An incomplete genome of O. europaea was previously obtained using shotgun sequencing in 2016. To further explore the genetic and breeding utilization of olive, an updated draft genome of olive was obtained using Oxford Nanopore third-generation sequencing and Hi-C technology. Seven different assembly strategies were used to assemble the final genome of 1.30 Gb, with contig and scaffold N50 sizes of 4.67 Mb and 42.60 Mb, respectively. This greatly increased the quality of the olive genome. We assembled 1.1 Gb of sequences of the total olive genome to 23 pseudochromosomes by Hi-C, and 53,518 protein-coding genes were predicted in the current assembly. Comparative genomics analyses, including gene family expansion and contraction, whole-genome replication, phylogenetic analysis, and positive selection, were performed. Based on the obtained high-quality olive genome, a total of nine gene families with 202 genes were identified in the oleuropein biosynthesis pathway, which is twice the number of genes identified from the previous data. This new accession of the olive genome is of sufficient quality for genome-wide studies on gene function in olive and has provided a foundation for the molecular breeding of olive species.
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Affiliation(s)
- Guodong Rao
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China.
- Collaborative Innovation Center of Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China.
- Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China.
| | - Jianguo Zhang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China.
- Collaborative Innovation Center of Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China.
- Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China.
| | - Xiaoxia Liu
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Chunfu Lin
- MIANNING Yuansheng Agricultural Science and Technology Co., Ltd., Liangshan Yi Autonomous Prefecture Mianning County, Sichuan, 615600, China
| | - Huaigen Xin
- Biomarker Technologies Corporation, Beijing, 101300, China
| | - Li Xue
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Chenhe Wang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
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Lin X, Xu H, Liu L, Li H, Gao Z. Draft genome sequence of Neonectria sp. DH2 isolated from Meconopsis grandis Prain in Tibet. 3 Biotech 2020; 10:346. [PMID: 32728513 DOI: 10.1007/s13205-020-02345-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Accepted: 07/17/2020] [Indexed: 11/26/2022] Open
Abstract
In the current study, we report the high-quality draft genome sequence of Neonectria sp. DH2, an endophytic fungus isolated from Meconopsis grandis Prain in Tibet. The whole genome is about 45.8 Mbp, with a GC content of 53%. A total of 14,163 genes are predicted to encode proteins, and 557 of them are considered as unique, as no matches are found in five gene databases. A neighbor-joining phylogenetic tree based on internal transcribed spacer (ITS) region sequences shows that Neonectria sp. DH2 was most closely related to Neonectria ramulariae. 47 biosynthetic gene clusters (BGC) were identified in Neonectria sp. DH2 genome, and only 5 BGCs shows significant similarities to previously reported BGCs. The presence of 42 unique BGCs in Neonectria sp. DH2 suggests that it has great potential to produce novel secondary metabolites.
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Affiliation(s)
- Xiaojing Lin
- School of Marine Sciences, Sun Yat-sen University, Guangzhou, 510006 China
- Research Center of Chinese Herbal Resource Science and Engineering, Guangzhou University of Chinese Medicine, Guangzhou, 510006 China
| | - Hui Xu
- Research Center of Chinese Herbal Resource Science and Engineering, Guangzhou University of Chinese Medicine, Guangzhou, 510006 China
| | - Lan Liu
- School of Marine Sciences, Sun Yat-sen University, Guangzhou, 510006 China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519000 China
| | - Huixian Li
- School of Marine Sciences, Sun Yat-sen University, Guangzhou, 510006 China
| | - Zhizeng Gao
- School of Marine Sciences, Sun Yat-sen University, Guangzhou, 510006 China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519000 China
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