De novo gonad transcriptome analysis of the common littoral shrimp Palaemon serratus: novel insights into sex-related genes
De novo gonad transcriptome analysis of the common littoral shrimp Palaemon serratus: novel insights into sex-related genes
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DOI：
10.1186/s12864-019-6157-4
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发表时间：
2019-10-22
期刊：
影响因子：
4.4
通讯作者：
Martinez-Lage, Andres
中科院分区：
文献类型：
--
作者：
Gonzalez-Castellano, Ines;Manfrin, Chiara;Martinez-Lage, Andres
背景普通的沿岸的虾Palaemon serratus在一些欧洲社区是经济上重要的十足类资源。水产养殖做法防止了过度捕捞造成的野生种群遗传退化，同时提高了产量。性相关基因的生物技术操作已被证明具有提高水产养殖产量的潜力，但有关锯缘鲈基因组数据的稀缺阻碍了这些应用。已经对卵巢和睾丸样品进行了RNA-Seq分析，以产生参考性腺转录组。利用Illumina HiSeq 4000 PE 100测序仪对3个卵巢和3个睾丸样本进行差异表达分析，以揭示具有性别偏倚或性别特异性表达模式的性别相关基因。结果卵巢和睾丸样本分别产生了2.245亿和2.811亿个双端读段。卵巢和睾丸修剪读段的从头组装产生具有39，186个转录物的转录组。29.57%的转录组检索到至少一个注释，在卵巢和睾丸重复之间检测到11，087个差异表达基因（DEG）。卵巢中有6207个基因表达上调，睾丸中有4880个基因表达上调。从转录组中检索参与性发育和性腺发育过程的候选基因。这些性别相关的基因进行了讨论，考虑到它们是否在卵巢中上调，在睾丸中上调或性腺之间的差异表达，并在以前的研究结果在其他甲壳动物物种的框架。结论这是首次利用RNA-Seq技术对锯缘青蟹性腺进行转录组分析。有趣的发现性别相关的基因从进化的角度（如Dmrt 1）和假定未来的水产养殖应用（Iag或卵黄发生基因）在这里报道。我们提供了一个有价值的数据集，将有助于进一步研究这种虾的生殖生物学。
Background The common littoral shrimp Palaemon serratus is an economically important decapod resource in some European communities. Aquaculture practices prevent the genetic deterioration of wild stocks caused by overfishing and at the same time enhance the production. The biotechnological manipulation of sex-related genes has the proved potential to improve the aquaculture production but the scarcity of genomic data about P. serratus hinders these applications. RNA-Seq analysis has been performed on ovary and testis samples to generate a reference gonadal transcriptome. Differential expression analyses were conducted between three ovary and three testis samples sequenced by Illumina HiSeq 4000 PE100 to reveal sex-related genes with sex-biased or sex-specific expression patterns. Results A total of 224.5 and 281.1 million paired-end reads were produced from ovary and testis samples, respectively. De novo assembly of ovary and testis trimmed reads yielded a transcriptome with 39,186 transcripts. The 29.57% of the transcriptome retrieved at least one annotation and 11,087 differentially expressed genes (DEGs) were detected between ovary and testis replicates. Six thousand two hundred seven genes were up-regulated in ovaries meanwhile 4880 genes were up-regulated in testes. Candidate genes to be involved in sexual development and gonadal development processes were retrieved from the transcriptome. These sex-related genes were discussed taking into account whether they were up-regulated in ovary, up-regulated in testis or not differentially expressed between gonads and in the framework of previous findings in other crustacean species. Conclusions This is the first transcriptome analysis of P. serratus gonads using RNA-Seq technology. Interesting findings about sex-related genes from an evolutionary perspective (such as Dmrt1) and for putative future aquaculture applications (Iag or vitellogenesis genes) are reported here. We provide a valuable dataset that will facilitate further research into the reproductive biology of this shrimp.