Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, China ; Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China.
PLoS One. 2013 Sep 20;8(9):e75211. doi: 10.1371/journal.pone.0075211. eCollection 2013.
Transcriptome profiles provide a practical and inexpensive alternative to explore genomic data in non-model organisms, particularly in amphibians where the genomes are very large and complex. The odorous frog Odorranamargaretae (Anura: Ranidae) is a dominant species in the mountain stream ecosystem of western China. Limited knowledge of its genetic background has hindered research on this species, despite its importance in the ecosystem and as biological resources. Here we report the transcriptome of O. margaretae in order to establish the foundation for genetic research. Using an Illumina sequencing platform, 62,321,166 raw reads were acquired. After a de novo assembly, 37,906 transcripts were obtained, and 18,933 transcripts were annotated to 14,628 genes. We functionally classified these transcripts by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). A total of 11,457 unique transcripts were assigned to 52 GO terms, and 1,438 transcripts were assigned to 128 KEGG pathways. Furthermore, we identified 27 potential antimicrobial peptides (AMPs), 50,351 single nucleotide polymorphism (SNP) sites, and 2,574 microsatellite DNA loci. The transcriptome profile of this species will shed more light on its genetic background and provide useful tools for future studies of this species, as well as other species in the genus Odorrana. It will also contribute to the accumulation of amphibian genomic data.
转录组图谱为研究非模式生物的基因组数据提供了一种实用且经济的替代方法，特别是在基因组非常大且复杂的两栖动物中。臭蛙（Odorranamargaretae）（无尾目：Ranidae）是中国西部山区溪流生态系统中的优势物种。尽管臭蛙在生态系统和生物资源方面具有重要意义，但对其遗传背景的了解有限，阻碍了对该物种的研究。本研究报告了 O. margaretae 的转录组，以期为遗传研究奠定基础。使用 Illumina 测序平台，共获得了 62,321,166 条原始reads。经过从头组装，获得了 37,906 条转录本，其中 18,933 条转录本被注释到 14,628 个基因。我们通过基因本体论（GO）和京都基因与基因组百科全书（KEGG）对这些转录本进行了功能分类。共有 11,457 个独特的转录本被分配到 52 个 GO 术语，1,438 个转录本被分配到 128 个 KEGG 途径。此外，我们鉴定了 27 个潜在的抗菌肽（AMPs）、50,351 个单核苷酸多态性（SNP）位点和 2,574 个微卫星 DNA 位点。该物种的转录组图谱将进一步揭示其遗传背景，并为该物种以及其他臭蛙属物种的未来研究提供有用的工具。它还将有助于积累两栖动物的基因组数据。
