| 基于两种对虾参考基因组的中国明对虾性别分化区域初步探查 |
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| 引用本文： | 王琼,李健,何玉英.基于两种对虾参考基因组的中国明对虾性别分化区域初步探查[J].水产学报,2023,47(3):039610-039610. |
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| 作者姓名： | 王琼 李健 何玉英 |
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| 作者单位： | 中国水产科学研究院黄海水产研究所，农业农村部海洋渔业可持续发展重点实验室，山东 青岛 266071;青岛海洋科学与技术国家实验室，海洋渔业科学与食物产出过程功能实验室，山东 青岛 266071 |
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| 基金项目： | 国家虾蟹产业技术体系专项 (CARS-48)；国家自然科学基金 (31902367) |
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| 摘 要： | 中国明对虾是我国最重要的养殖虾类之一。性成熟后的中国明对虾在生长和体色上表现出性别二态性。为了探查基因组上潜在的性别分化相关区域，对中国明对虾进行了全基因组重测序研究。分别使用中国明对虾基因组和其近缘物种凡纳滨对虾的基因组作为参考基因组，计算了雌雄中国明对虾之间的遗传分化指数Fst，以筛查基因组上的性别分化相关区域。当使用中国明对虾参考基因组时，有约89%的中国明对虾测序读段全部或部分比对到中国明对虾参考基因，覆盖度大约为84%。基因组上Fst出现较多杂乱的峰，其中LG5的Fst值整体呈升高的趋势，另外LG13、LG17及LG35均有Fst指数相对较高的区域。而当使用凡纳滨对虾参考基因组时，有约60%的中国明对虾测序读段全部或部分比对到凡纳滨对虾参考基因，覆盖度约为52%。Scaffold 2550和Scaffold 3683上分别有2个最显著的峰。将雌雄中国明对虾转录组测序数据与凡纳滨对虾的参考基因组比对后，获得了中国明对虾的粗略表达谱，挖掘出了丰富的差异表达基因。分析了前述2个Scaffold上...
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| 关 键 词： | 中国明对虾 性别分化 基因组 重测序 转录组 |
| 收稿时间： | 2021/7/13 0:00:00 |
| 修稿时间： | 2021/8/25 0:00:00 |
Preliminary investigation of sex-linked loci of Chinese shrimp (Fenneropenaeus chinensis) based on the reference genome of two Penaeus shrimps |
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| WANG Qiong,LI Jian,HE Yuying.Preliminary investigation of sex-linked loci of Chinese shrimp (Fenneropenaeus chinensis) based on the reference genome of two Penaeus shrimps[J].Journal of Fisheries of China,2023,47(3):039610-039610. |
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| Authors: | WANG Qiong LI Jian HE Yuying |
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| Institution: | Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China;Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China |
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| Abstract: | Fenneropenaeus chinensis is one of the most commercially important cultured shrimps in China. It belongs to the family Penaeidae of Crustacea. F. chinensis exhibits a significant sexual dimorphism, the color of adult female shrimps tends to be blue, while the males tend to yellow, and the females were noticeably bigger in body size than males. However, no sex-determining region has been reported. A closely related species, Pacific white shrimp, Litopenaeus vannamei, which also belongs to the Penaeus, has been completely sequenced, and an assembled genome of F. chinensis was published recently, which accelerated the progress of genome research on shrimp culture. Sex-differentiation study has been carried out only in recent years, and this study aspires to screening out the potential sex-linked regions on the genome of F. chinensis. A total of 11 male and 10 female F. chinensis shrimps at 4-months-old were picked randomly, and the DNA samples of these 21 shrimps were extracted from muscle and sequenced using the BGISEQ platform individually. 104.5 Gb clean data of female and 115.4 Gb clean data of male were obtained, and the reference genome of F. chinensis (assembly ASM1692082v1) and L. vannamei (assembly ASM378908v1) were both used. The mapped result was used to evaluate the genetic differentiation between two sexes across the genome, and fixation index (Fst) was calculated across the genome. According to the results using reference genome of F. chinensis, there were many disorderly peaks of Fst on the genome, and the Fst value showed an overall increasing trend on LG5. According to the results using reference genome of L. vannamei, there were 2 most significant peaks located on scaffold 2550 (Accession: NW_020870010.1) and scaffold 3683 (Accession: NW_020871268.1), respectively. Many variants were found showing genetic differentiation between the two sexes. The 2 peaks of the Fst value on 2 scaffolds indicate that the corresponding regions on the genome of F. chinensis may be responsible for sex differentiation. RNA-seq data of gonad and muscle of female and male F. chinensis shrimps at 5-months-old were aligned to the reference genome of L. vannamei to obtain the expression information of genes on these two scaffolds. On scaffold 2550, two genes expressed differentially in muscle, while three genes expressed differentially in gonad. On scaffold 3683, no DEG was found in muscle. Four DEGs were filtered out in gonad, all of which had higher expression levels in males. Coincidentally, they all located on the range of Fst peak. Two DEGs encoded peripheral-type benzodiazepine receptor-associated protein 1, which is a key factor in steroid hormone biosynthesis. The peripheral-type benzodiazepine receptor was detected in many peripheral tissues but showed uniquely high densities in the adrenal cortex and in Leydig cells of the testes. Therefore, it is speculated that these male-biased expression genes were involved in the sex-specific physiological mechanism of male shrimps and participated in the sex differentiation of F. chinensis. In this study, we preliminarily located the sex-linked regions in genome of F. chinensis and filtered candidate genes related to the sex differentiation. The study provides a basis for further research of sexual dimorphism in F. chinensis. |
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| Keywords: | Fenneropenaeus chinensis sex differentiation genome resequencing RNA-seq |
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