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首页> 美国卫生研究院文献>Horticulture Research >Identification of SSRs and differentially expressed genes in two cultivars of celery (Apium graveolens L.) by deep transcriptome sequencing
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Identification of SSRs and differentially expressed genes in two cultivars of celery (Apium graveolens L.) by deep transcriptome sequencing

机译：通过深转录组测序鉴定两个芹菜（Apium graveolens L.）中的SSR和差异表达基因

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摘要

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.
机译：芹菜（Apium graveolens L.）是芹菜科中最重要和广泛种植的蔬菜之一。由于缺乏综合的基因组资源，芹菜的研究主要利用生理和生化方法，而不是分子生物学来研究这种作物。转录组测序已成为一种有效且经济的技术，可获取有关基因表达的信息，该信息可极大地促进无法进行测序的基因组物种的分子和基因组研究。在本研究中，通过RNA测序分别从两个芹菜品种“ Ventura”和“ Jinnan Shiqin”获得了15 893 516和19 818 161高质量序列。获得的读段被组装成39 584和41 740 unigene，平均长度分别为683 bp和690 bp。在“文图拉”中共鉴定了1939个简单序列重复（SSR）标记，在“济南石琴”中鉴定了2004个SSR。二核苷酸重复序列是最常见的重复序列，在“文图拉”和“津南世琴”中分别占55.49％和54.84％。比较两个文库中的表达基因，鉴定出338个差异表达基因（DEG）。基于使用八个公共数据库进行的序列相似性搜索，对303个DEG进行了注释。另外，响应非生物胁迫表征了八个带注释的DEG的表达谱。本研究中产生的集体数据代表了芹菜进一步遗传和分子研究的宝贵资源。

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