De novo assembly, gene annotation and marker development using Illumina paired-end transcriptome sequences in celery (Apium graveolens L.).
De novo assembly, gene annotation and marker development using Illumina paired-end transcriptome sequences in celery (Apium graveolens L.).
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DOI：
10.1371/journal.pone.0057686
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发表时间：
2013
期刊：
影响因子：
3.7
通讯作者：
Shen HL
中科院分区：
文献类型：
--
作者：
Fu N;Wang Q;Shen HL
芹菜是一种日益受欢迎的蔬菜品种，但其转录组和基因组数据的有限性阻碍了芹菜的研究，同时芹菜分子标记的缺乏也限制了芹菜分子遗传育种的进程。高通量转录组测序是一种高效的方法，可以产生大量的转录组序列数据集，用于基因发现、分子标记开发和标记辅助选择育种。采用Illumina双末端测序技术对来自四种组织的芹菜转录组进行测序。进行从头组装以产生代表该物种的第一转录组的42，280个单基因（平均长度为502.6bp）的集合。与美国国家生物技术信息中心（NCBI）非冗余蛋白质数据库（Nr）和Swiss-Prot数据库中的蛋白质相似性分别为78.43%和48.93%，其中10，473个（24.77%）被归属到同源群（COG）中。21，126个（49.97%）含有Interpro结构域的unigenes被注释，其中15，409个（36.45%）被分配到Gene Ontology（GO）类别。此外，使用京都基因百科全书和基因组途径数据库（KEGG）将7，478个单基因定位到228个途径上。对31份芹菜材料进行了大量的SSR扩增，并对扩增成功率和多态性进行了分析。本研究证明了通过Illumina双末端测序和高效组装产生大规模序列信息的可行性。本研究结果为芹菜的研究提供了宝贵的资源。分子标记的建立是进一步进行遗传连锁分析和基因定位的基础，对加快育种进程具有重要意义。
Celery is an increasing popular vegetable species, but limited transcriptome and genomic data hinder the research to it. In addition, a lack of celery molecular markers limits the process of molecular genetic breeding. High-throughput transcriptome sequencing is an efficient method to generate a large transcriptome sequence dataset for gene discovery, molecular marker development and marker-assisted selection breeding. Celery transcriptomes from four tissues were sequenced using Illumina paired-end sequencing technology. De novo assembling was performed to generate a collection of 42,280 unigenes (average length of 502.6 bp) that represent the first transcriptome of the species. 78.43% and 48.93% of the unigenes had significant similarity with proteins in the National Center for Biotechnology Information (NCBI) non-redundant protein database (Nr) and Swiss-Prot database respectively, and 10,473 (24.77%) unigenes were assigned to Clusters of Orthologous Groups (COG). 21,126 (49.97%) unigenes harboring Interpro domains were annotated, in which 15,409 (36.45%) were assigned to Gene Ontology(GO) categories. Additionally, 7,478 unigenes were mapped onto 228 pathways using the Kyoto Encyclopedia of Genes and Genomes Pathway database (KEGG). Large numbers of simple sequence repeats (SSRs) were indentified, and then the rate of successful amplication and polymorphism were investigated among 31 celery accessions. This study demonstrates the feasibility of generating a large scale of sequence information by Illumina paired-end sequencing and efficient assembling. Our results provide a valuable resource for celery research. The developed molecular markers are the foundation of further genetic linkage analysis and gene localization, and they will be essential to accelerate the process of breeding.