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

Preliminary investigation of sex-linked loci of Chinese shrimp(Fenneropenaeus chinensis)based on the reference genome of two Penaeus shrimps

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F_(st),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F_(st)出现较多杂乱的峰,其中LG5的F_(st)值整体呈升高的趋势,另外LG13、LG17及LG35均有F_(st)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上的基因表达情况。在Scaffold 2550上,有2个肌肉中的差异表达基因,有3个性腺中的差异表达基因;在Scaffold 3683上,有4个性腺中的差异表达基因,全部都是雄性高表达,且都位于F_(st)峰值区域,其中2个基因编码外周型苯二氮卓受体相关蛋白1(peripheral-type benzodiazepine receptor-associated protein 1),参与类固醇激素生物合成,推测这两个雄性高表达基因参与了雄虾的性别特异性生理机制,与雄性生殖功能相关,在性别分化过程中发挥一定作用。本研究初步筛选到了与中国明对虾性别分化相关的区域和基因,为中国明对虾性别二态性的进一步研究提供了依据。

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(F_(st))was calculated across the genome.According to the results using reference genome of F.chinensis,there were many disorderly peaks of F_(st)on the genome,and the F_(st)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 F_(st)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 F_(st)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.