Transcriptome using Illumina sequencing reveals the traits of spermatogenesis and developing testes in Eriocheir sinensis.
Transcriptome using Illumina sequencing reveals the traits of spermatogenesis and developing testes in Eriocheir sinensis.
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DOI：
10.1371/journal.pone.0172478
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发表时间：
2017
期刊：
影响因子：
3.7
通讯作者：
Qian H
中科院分区：
文献类型：
--
作者：
Li GL;Qian H
中华绒螯蟹(Eriocheir Sinensis)的精子具有典型的叶状、去凝集的染色质、杯状的核和放射状的手臂。然而，在该物种中产生特定精子的精子发生的机制尚不清楚。本研究利用RNA-seq和生物信息学分析的方法，对中华绒毛虫睾丸发育过程中的转录组进行了分析，以寻找可能参与睾丸发育和精子发生的候选基因。Illumina HiSeq2500对三个复制子样品的测序共产生了145.19 M清洁读数，总共有21.34G碱基和45.48%的GC含量。56.30%的清洁阅读定位于中华绒毛虫的草本基因组。转录组的组装产生了5691802个序列的重叠群和406527个序列的非基因组。使用Swissprot和Nr数据库分别对24246和40793个转录本进行了标注。在Nr和Est数据库中，分别有48213个(70.31%)和7858个(46.25%)的转录本与成熟睾丸非基因组序列的同源性大于99。KOG、GO和KEGG的分析结果表明，转录产物在睾丸发育过程中具有广泛的潜在分子功能。对UNIGNES的KEGG分析共得到9422个预测基因。这些预测基因共涉及216条与发育中睾丸生理活动相关的KEGG通路。1975个预测基因参与了雄性生殖细胞的细胞和亚细胞结构的改变。一些途径在与睾丸发育和精子发生有关的形态和结构生物发生过程中发挥着重要作用。还发现了编码遗传和表观遗传因子的583个非基因组，它们可能有助于精子中去凝集的核的去凝集和稳定性。这些预测事件为中华绒毛虫睾丸发育和精子发生的潜在分子机制提供了一个视角。
Chinese mitten crab (Eriocheir sinensis) has the spermatozoa with typical aflagellate, decondensed chromatin, cup-shaped nuclei, and radial arms. However, the mechanism of spermatogenesis during which the specific spermatozoa are generated in this species is yet unclear. Here, the transcriptome of developing testis in E. sinensis was analyzed using the ways of RNA-seq and bioinformatics analysis to identify candidate genes potentially involved in development of testis and spermatogenesis. The Illumina HiSeq2500 sequencing of three replicons of samples produced a total of 145.19 M clean reads representing with a total of 21.34 Gb bases and 45.48% GC content. 56.30% clean reads were mapped to the draft genome of E. sinensis. The assembly of the transcriptome yielded contigs of 5691802 sequences and unigenes of 406527 sequences. Total 24246 and 40793 transcripts were annotated using Swissprot and Nr database, respectively. There were 48213 (70.31%) and 7858 (46.25%) transcripts with identity of more than 99 matching to mature testis unigenes in the databases of Nr and EST, respectively. The analytic results of KOG, GO and KEGG showed wide potential molecular functions of transcripts in the developing testes. KEGG analysis of unigenes yielded total 9422 predicted genes. Those predicted genes were involved in total 216 KEGG pathways related to the physiological activities of developing testis. 1975 predicted genes were involved in cellular and subcellular structural alteration of male germ cells. There were important roles of some pathways in the processes of morphological and structural biogenesis pertaining to testis development and spermatogenesis. Other 583 unigenes encoding the genetic and epigenetic factors also be found, which might contribute to the decondensation and stability of decondensed nuclei in the spermatozoa. These predicted events provide a view of the potential molecular mechanisms of development of testis and spermatogenesis in E. sinensis.