Zhejiang Provincial Top Key Discipline of Modern Microbiology and Application, College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo 315100, China.
J Zhejiang Univ Sci B. 2013 Jan;14(1):58-67. doi: 10.1631/jzus.B1200219.
The soft-shelled turtle Pelodiscus sinensis is a high-profile turtle species because of its nutritional and medicinal value in Asian countries. However, little is known about the genes that are involved in formation of their nutritional quality traits, especially the molecular mechanisms responsible for unsaturated fatty acid and collagen biosynthesis. In the present study, the transcriptomes from six tissues from Pelodiscus sinensis were sequenced using an Illumina paired-end sequencing platform. We obtained more than 47 million sequencing reads and 73954 unigenes with an average size of 754 bp by de-novo assembly. In total, 55.19% of the unigenes (40814) had significant similarity with proteins in the National Center of Biotechnology Information (NCBI) non-redundant protein database and Swiss-Prot database (E-value <10(-5)). Of these annotated unigenes, 9156 and 11947 unigenes were assigned to 52 gene ontology categories (GO) and 25 clusters of orthologous groups (COG), respectively. In total, 26496 (35.83%) unigenes were assigned to 242 pathways using the Kyoto Encyclopedia of Genes and Genomes pathway database (KEGG). In addition, we found a number of highly expressed genes involved in the regulation of P. sinensis unsaturated fatty acid biosynthesis and collagen formation, including desaturases, growth factors, transcription factors, and extracellular matrix components. Our data represent the most comprehensive sequence resource available for the Chinese soft-shelled turtle and could provide a basis for new research on this turtle as well as the molecular genetics and functional genomics of other terrapins. To our knowledge, we report for the first time, the large-scale RNA sequencing (RNA-Seq) of terrapin animals and would enrich the knowledge of turtles for future research.
中华鳖（Pelodiscus sinensis）是一种具有重要经济价值的龟鳖类动物，其肉和卵具有很高的营养价值，在亚洲国家被广泛食用。然而，关于影响其营养品质性状形成的基因，特别是负责不饱和脂肪酸和胶原蛋白生物合成的分子机制，人们知之甚少。本研究采用 Illumina 高通量测序平台对中华鳖 6 个组织的转录组进行测序。通过 de novo 组装，我们获得了超过 4700 万个测序reads 和 73954 条 unigenes，平均长度为 754bp。总的来说，55.19%的 unigenes（40814 条）与 NCBI 非冗余蛋白数据库和 Swiss-Prot 数据库中的蛋白具有显著相似性（E-value <10(-5)）。在这些注释的 unigenes中，9156 和 11947 条 unigenes分别被分配到 52 个 GO 类别和 25 个 COG 簇中。总共，26496 条（35.83%）unigenes被分配到 242 个京都基因与基因组百科全书（KEGG）通路数据库中的通路。此外，我们发现了一些参与中华鳖不饱和脂肪酸生物合成和胶原蛋白形成调节的高度表达基因，包括去饱和酶、生长因子、转录因子和细胞外基质成分。我们的数据代表了中华鳖最全面的序列资源，可为今后对该龟的研究以及其他龟鳖类的分子遗传学和功能基因组学提供基础。据我们所知，我们首次报道了龟鳖动物的大规模 RNA 测序（RNA-Seq），并为未来的研究丰富了龟鳖类的知识。
