Zhenzhen Xie, Ling Xiao, Dengdong Wang, Chao Fang, Qiongyu Liu, Zihao Li, Xiaochun Liu, Yong Zhang, Shuisheng Li, Haoran Lin
State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals, and the Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China.
State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals, and the Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China; College of Ocean, Hainan University, Haikou, Hainan, China.
PLoS One. 2014 Oct 10;9(10):e109419. doi: 10.1371/journal.pone.0109419. eCollection 2014.
The Trachinotus ovatus (Teleostei, Carangidae) is an economically important marine fish species in the world. However, the lack of genomic information regarding this species limits our understanding of the genetics and biological mechanisms in Trachinotus ovatus. In this study, high throughput transcriptome sequencing was used to obtain comprehensive genomic information in Trachinotus ovatus.
Transcriptome sequencing was performed by using Illumina paired-end sequencing technology. The 98,534,862 high quality reads were yielded, and were de novo assembled into 156,094 unigenes with an average sequence length of 1179 bp. Transcriptome annotation revealed that 75,586 and 67,923 unigenes were functionally annotated in the NCBI non-redundant database and Swiss-Prot protein database, respectively. Functional analysis demonstrated that 67,923 unigenes were grouped into 25 Cluster of Orthologous Groups (COG) functional categories, 37,976 unigenes were clustered into 61 Gene Ontology (GO) terms, and 38,172 unigenes were assigned to 275 different Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Based on the transcriptome dataset, a large number of unigenes associated with reproduction, growth and immunity were identified. Furthermore, a total number of 38,794 simple sequence repeats (SSRs) were discovered and 16 polymorphic loci were characterized in Trachinotus ovatus.
CONCLUSION/SIGNIFICANCE: The present study is the first transcriptome analysis of a fish species belonging to the genus Trachinotus and provides a valuable genomic resource for novel gene discovery, gene expression and regulation studies, and the identification of genetic markers in Trachinotus ovatus and the other fish of the genus Trachinotus.
卵形鲳鲹（硬骨鱼纲，鲹科）是世界上具有重要经济价值的海洋鱼类。然而，该物种基因组信息的缺乏限制了我们对卵形鲳鲹遗传和生物学机制的理解。在本研究中，采用高通量转录组测序来获取卵形鲳鲹全面的基因组信息。
使用Illumina双末端测序技术进行转录组测序。共产生了98,534,862条高质量读段，并将其从头组装成156,094个单基因，平均序列长度为1179 bp。转录组注释显示，分别有75,586个和67,923个单基因在NCBI非冗余数据库和Swiss-Prot蛋白质数据库中得到功能注释。功能分析表明，67,923个单基因被归入25个直系同源基因簇（COG）功能类别，37,976个单基因被聚集成61个基因本体（GO）术语，38,172个单基因被分配到275条不同的京都基因与基因组百科全书（KEGG）通路。基于转录组数据集，鉴定出了大量与繁殖、生长和免疫相关的单基因。此外，在卵形鲳鲹中总共发现了38,794个简单序列重复（SSR），并对16个多态性位点进行了特征分析。
结论/意义：本研究是对鲳鲹属鱼类的首次转录组分析，为卵形鲳鲹及其他鲳鲹属鱼类的新基因发现、基因表达与调控研究以及遗传标记鉴定提供了宝贵的基因组资源。
