Identification of SSRs and differentially expressed genes in two cultivars of celery (Apium graveolens L.) by deep transcriptome sequencing.
Identification of SSRs and differentially expressed genes in two cultivars of celery (Apium graveolens L.) by deep transcriptome sequencing.
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通过深度转录组测序鉴定两个芹菜品种（ApiumgravolensL.）的SSR和差异表达基因。
DOI：
10.1038/hortres.2014.10
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发表时间：
2014
影响因子：
8.7
通讯作者：
Xiong AS
中科院分区：
文献类型：
--
作者：
Li MY;Wang F;Jiang Q;Ma J;Xiong AS
芹菜（Apium graveolens L.）是伞形科中最重要和广泛种植的蔬菜之一。由于缺乏全面的基因组资源，芹菜的研究主要是利用生理生化方法，而不是分子生物学。转录组测序已成为一种有效和经济的技术，用于获得基因表达的信息，可以大大促进分子和基因组研究的物种，其中测序的基因组是不可用的。本研究利用RNA-seq技术从两个芹菜品种'Ventura'和'晋南食芹'中分别获得了15 893 516和19 818 161条高质量序列。将获得的读段分别组装成39 584和41 740个单基因，平均长度分别为683 bp和690 bp。在‘文图拉’和‘晋南十亲’中分别鉴定出1939个和2004个SSR标记。二核苷酸重复是最常见的重复基序，在‘文图拉’和‘晋南十亲’中分别占55.49%和54.84%。比较两个文库的表达基因，鉴定出338个差异表达基因（DEG）。303的DEG进行了注释的基础上，利用8个公共数据库的序列相似性搜索。此外，8个注释的DEG的表达谱的特征在于在响应非生物胁迫。本研究中产生的集体数据为芹菜的进一步遗传和分子研究提供了宝贵的资源。
Celery (Apium graveolens L.) is one of the most important and widely grown vegetables in the Apiaceae family. Due to the lack of comprehensive genomic resources, research on celery has mainly utilized physiological and biochemical approaches, rather than molecular biology, to study this crop. Transcriptome sequencing has become an efficient and economic technology for obtaining information on gene expression that can greatly facilitate molecular and genomic studies of species for which a sequenced genome is not available. In the present study, 15 893 516 and 19 818 161 high-quality sequences were obtained by RNA-seq from two celery varieties ‘Ventura’ and ‘Jinnan Shiqin’, respectively. The obtained reads were assembled into 39 584 and 41 740 unigenes with mean lengths of 683 bp and 690 bp, respectively. A total of 1939 simple sequence repeat (SSR) markers were identified in ‘Ventura’ and 2004 SSRs in ‘Jinnan Shiqin’. Di-nucleotide repeats were the most common repeat motif, accounting for 55.49% and 54.84% in ‘Ventura’ and ‘Jinnan Shiqin’, respectively. A comparison of expressed genes between the two libraries, identified 338 differentially expressed genes (DEGs). Three hundred and three of the DEGs were annotated based on a sequence similarity search utilizing eight public databases. Additionally, the expression profile of eight annotated DEGs was characterized in response to abiotic stresses. The collective data generated in the present research represent a valuable resource for further genetic and molecular studies in celery.