|
|
细点石斑鱼的基因组注释及比较基因组学分析
|
Abstract:
细点石斑鱼(Epinephelus cyanopodus)，隶属于鲈形目、鮨科、石斑鱼属，是一种栖息于暖水礁区的肉食性鱼类。目前国内已实现人工养殖，但在苗种生产过程中面临雄性亲本获取困难的问题，性别调控的关键基因尚不明确。本试验通过转录组测序、近缘物种比对及从头预测等方法，对细点石斑鱼进行了基因组注释，共获得26,743个编码基因。在此基础上，联合近缘物种开展了比较基因组学分析，揭示了细点石斑鱼与赤点石斑鱼(Epinephelus akaara)之间的基因组差异及基因家族变化情况，同时定位到与性别调控相关的褪黑素(Melatonin, MT)合成基因aanat，为今后的性别调控研究奠定了数据基础。
Epinephelus cyanopodus, belonging to the order Perciformes, family Serranidae, and genus Epinephelus, is a carnivorous fish that inhabits warm-water reef areas. At present, artificial breeding has been achieved in China. However, in the process of seed production, there is a problem of difficulty in obtaining male parents, and the key genes for sex control are still unclear. In this study, strategies such as transcriptome sequencing data, genome comparison with closely related species, and de novo prediction were adopted to complete the genome annotation work, and a total of 26,743 coding genes were identified. Based on this, a comparative genomics analysis was further conducted in combination with closely related species, revealing the quantity and distribution characteristics of various variations in the genome of Epinephelus cyanopodus, as well as the changing trends of gene families during evolution. Moreover, the key gene aanat related to sex regulation and melatonin (MT) synthesis was successfully located, establishes the data foundation for future studies on gender regulation.
| [1] | 李广丽, 刘晓春, 林浩然. 芳香化酶抑制剂Letrozole对赤点石斑鱼(Epinephelus akaara)性逆转的作用[J]. 生理学报, 2005, 57(4): 473-479. |
| [2] | Baranasic, D., Hörtenhuber, M., Balwierz, P.J., Zehnder, T., Mukarram, A.K., Nepal, C., et al. (2022) Multiomic Atlas with Functional Stratification and Developmental Dynamics of Zebrafish Cis-Regulatory Elements. Nature Genetics, 54, 1037-1050. https://doi.org/10.1038/s41588-022-01089-w |
| [3] | Zhou, Q., Gao, H., Zhang, Y., Fan, G., Xu, H., Zhai, J., et al. (2019) A Chromosome-Level Genome Assembly of the Giant Grouper (Epinephelus lanceolatus) Provides Insights into Its Innate Immunity and Rapid Growth. Molecular Ecology Resources, 19, 1322-1332. https://doi.org/10.1111/1755-0998.13048 |
| [4] | Zhou, Q., Gao, H., Xu, H., Lin, H. and Chen, S. (2020) A Chromosomal-Scale Reference Genome of the Kelp Grouper Epinephelus Moara. Marine Biotechnology, 23, 12-16. https://doi.org/10.1007/s10126-020-10003-6 |
| [5] | Li, S., Li, W., Jiang, S., Jing, Y., Xiao, L., Yu, Y., et al. (2023) Mechanisms of Sex Differentiation and Sex Reversal in Hermaphrodite Fish as Revealed by the Epinephelus coioides Genome. Molecular Ecology Resources, 23, 920-932. https://doi.org/10.1111/1755-0998.13753 |
| [6] | Ge, H., Lin, K., Shen, M., Wu, S., Wang, Y., Zhang, Z., et al. (2019) De Novo Assembly of a Chromosome-Level Reference Genome of Red-Spotted Grouper (Epinephelus akaara) Using Nanopore Sequencing and Hi-C. Molecular Ecology Resources, 19, 1461-1469. https://doi.org/10.1111/1755-0998.13064 |
| [7] | Zhuang, X., Qu, M., Zhang, X. and Ding, S. (2013) A Comprehensive Description and Evolutionary Analysis of 22 Grouper (Perciformes, Epinephelidae) Mitochondrial Genomes with Emphasis on Two Novel Genome Organizations. PLOS ONE, 8, e73561. https://doi.org/10.1371/journal.pone.0073561 |
| [8] | Chen, S., Zhang, G., Shao, C., Huang, Q., Liu, G., Zhang, P., et al. (2014) Whole-genome Sequence of a Flatfish Provides Insights into ZW Sex Chromosome Evolution and Adaptation to a Benthic Lifestyle. Nature Genetics, 46, 253-260. https://doi.org/10.1038/ng.2890 |
| [9] | Zhou, Q., Guo, X., Huang, Y., Gao, H., Xu, H., Liu, S., et al. (2020) De Novo Sequencing and Chromosomal-Scale Genome Assembly of Leopard Coral Grouper, Plectropomus Leopardus. Molecular Ecology Resources, 20, 1403-1413. https://doi.org/10.1111/1755-0998.13207 |
| [10] | Cao, X., Zhang, J., Deng, S. and Ding, S. (2022) Chromosome-Level Genome Assembly of the Speckled Blue Grouper (Epinephelus cyanopodus) Provides Insight into Its Adaptive Evolution. Biology, 11, Article 1810. https://doi.org/10.3390/biology11121810 |
| [11] | 王卫东, 邱昌恩. 松果体与褪黑素[J]. 生物学通报, 2000, 35(5): 26. |
| [12] | Acuña-Castroviejo, D., Escames, G., Venegas, C., Díaz-Casado, M.E., Lima-Cabello, E., López, L.C., et al. (2014) Extrapineal Melatonin: Sources, Regulation, and Potential Functions. Cellular and Molecular Life Sciences, 71, 2997-3025. https://doi.org/10.1007/s00018-014-1579-2 |
| [13] | Chen, S., Zhou, Y., Chen, Y. and Gu, J. (2018) FASTP: An Ultra-Fast All-in-One FASTQ Preprocessor. Bioinformatics, 34, i884-i890. https://doi.org/10.1093/bioinformatics/bty560 |
| [14] | Stanke, M., Steinkamp, R., Waack, S. and Morgenstern, B. (2004) AUGUSTUS: A Web Server for Gene Finding in Eukaryotes. Nucleic Acids Research, 32, W309-W312. https://doi.org/10.1093/nar/gkh379 |
| [15] | Majoros, W.H., Pertea, M. and Salzberg, S.L. (2004) TigrScan and GlimmerHMM: Two Open Source Ab Initio Eukaryotic Gene-Finders. Bioinformatics, 20, 2878-2879. https://doi.org/10.1093/bioinformatics/bth315 |
| [16] | Haas, B.J. (2003) Improving the Arabidopsis Genome Annotation Using Maximal Transcript Alignment Assemblies. Nucleic Acids Research, 31, 5654-5666. https://doi.org/10.1093/nar/gkg770 |
| [17] | Haas, B.J., Salzberg, S.L., Zhu, W., Pertea, M., Allen, J.E., Orvis, J., et al. (2008) Automated Eukaryotic Gene Structure Annotation Using Evidencemodeler and the Program to Assemble Spliced Alignments. Genome Biology, 9, R7. |
| [18] | Kurtz, S., Phillippy, A., Delcher, A.L., Smoot, M., Shumway, M., Antonescu, C., et al. (2004) Versatile and Open Software for Comparing Large Genomes. Genome Biology, 5, R12. https://doi.org/10.1186/gb-2004-5-2-r12 |
| [19] | Goel, M., Sun, H., Jiao, W. and Schneeberger, K. (2019) Syri: Finding Genomic Rearrangements and Local Sequence Differences from Whole-Genome Assemblies. Genome Biology, 20, Article No. 277. https://doi.org/10.1186/s13059-019-1911-0 |
| [20] | Li, L., Stoeckert, C.J. and Roos, D.S. (2003) Orthomcl: Identification of Ortholog Groups for Eukaryotic Genomes. Genome Research, 13, 2178-2189. https://doi.org/10.1101/gr.1224503 |
| [21] | Yang, Z. (1997) PAML: A Program Package for Phylogenetic Analysis by Maximum Likelihood. Bioinformatics, 13, 555-556. https://doi.org/10.1093/bioinformatics/13.5.555 |
| [22] | De Bie, T., Cristianini, N., Demuth, J.P. and Hahn, M.W. (2006) CAFE: A Computational Tool for the Study of Gene Family Evolution. Bioinformatics, 22, 1269-1271. https://doi.org/10.1093/bioinformatics/btl097 |
| [23] | Li, J., You, X., Bian, C., Yu, H., Coon, S. and Shi, Q. (2015) Molecular Evolution of Aralkylamine N-Acetyltransferase in Fish: A Genomic Survey. International Journal of Molecular Sciences, 17, Article 51. https://doi.org/10.3390/ijms17010051 |
| [24] | Wu, X., Yang, Y., Zhong, C., Guo, Y., Wei, T., Li, S., et al. (2020) Integration of ATAC-Seq and RNA-Seq Unravels Chromatin Accessibility during Sex Reversal in Orange-Spotted Grouper (Epinephelus coioides). International Journal of Molecular Sciences, 21, Article 2800. https://doi.org/10.3390/ijms21082800 |
