Transcriptome sequencing of mung bean (Vigna radiate L.) genes and the identification of EST-SSR markers.
Transcriptome sequencing of mung bean (Vigna radiate L.) genes and the identification of EST-SSR markers.
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绿豆（Vigna radiate L.）基因转录组测序及EST-SSR标记鉴定。
DOI：
10.1371/journal.pone.0120273
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发表时间：
2015
期刊：
影响因子：
3.7
通讯作者：
Cheng X
中科院分区：
文献类型：
--
作者：
Chen H;Wang L;Wang S;Liu C;Blair MW;Cheng X
绿豆（Vigna radially（L.）Wilczek）是一种重要的传统食用豆类作物，具有很高的经济价值和营养价值。它广泛生长在中国和其他亚洲国家。尽管它的重要性，基因组信息是目前无法获得这种作物植物物种或它的一些近亲在豇豆属。在这项研究中，超过1.03亿高质量的cDNA序列读取从绿豆使用Illumina双端测序技术。将处理的读段组装成48，693个单基因，平均长度为874 bp。在这些单基因中，分别有25，820（53.0%）和23，235（47.7%）与NCBI非冗余蛋白质和核苷酸序列数据库中的蛋白质显示出显著的相似性。此外，19，242个（39.5%）可归入基因本体类别，18，316个（37.6%）可归入Swiss-Prot类别，10，918个（22.4%）可归入KOG数据库类别（E值< 1.0E-5）。使用京都基因和基因组百科全书（KEGG）通路数据库，共将6，585个（8.3%）映射到244条通路上。在单基因中，10,053个序列含有一个唯一的简单重复序列（SSR），2,303个序列在同一表达序列标签（EST）中含有一个以上的SSR。共有13，134个EST-SSR被鉴定为潜在的分子标记，其中单核苷酸A/T重复序列是最丰富的基序类，G/C重复序列很少。在SSR分析中发现了5个主要的重复基序：AG/CT（30.8%）、GAA/TTC（12.6%）、AAAT/ATTT（6.8%）、AAAAT/ATTTT（6.2%）和AAAAAT/ATTTTT（1.9%）。随机选取200个SSR位点作为EST-SSR标记进行PCR扩增验证。其中，66个标记引物对产生可重复的扩增子，从不同的地理位置选择的31个绿豆种质之间的多态性。本研究中发现的大量含SSR标记的序列将为构建高分辨率的豇豆遗传连锁图谱、关联或比较作图以及不同豇豆品种的遗传分析提供有价值的信息。
Mung bean (Vigna radiate (L.) Wilczek) is an important traditional food legume crop, with high economic and nutritional value. It is widely grown in China and other Asian countries. Despite its importance, genomic information is currently unavailable for this crop plant species or some of its close relatives in the Vigna genus. In this study, more than 103 million high quality cDNA sequence reads were obtained from mung bean using Illumina paired-end sequencing technology. The processed reads were assembled into 48,693 unigenes with an average length of 874 bp. Of these unigenes, 25,820 (53.0%) and 23,235 (47.7%) showed significant similarity to proteins in the NCBI non-redundant protein and nucleotide sequence databases, respectively. Furthermore, 19,242 (39.5%) could be classified into gene ontology categories, 18,316 (37.6%) into Swiss-Prot categories and 10,918 (22.4%) into KOG database categories (E-value < 1.0E-5). A total of 6,585 (8.3%) were mapped onto 244 pathways using the Kyoto Encyclopedia of Genes and Genome (KEGG) pathway database. Among the unigenes, 10,053 sequences contained a unique simple sequence repeat (SSR), and 2,303 sequences contained more than one SSR together in the same expressed sequence tag (EST). A total of 13,134 EST-SSRs were identified as potential molecular markers, with mono-nucleotide A/T repeats being the most abundant motif class and G/C repeats being rare. In this SSR analysis, we found five main repeat motifs: AG/CT (30.8%), GAA/TTC (12.6%), AAAT/ATTT (6.8%), AAAAT/ATTTT (6.2%) and AAAAAT/ATTTTT (1.9%). A total of 200 SSR loci were randomly selected for validation by PCR amplification as EST-SSR markers. Of these, 66 marker primer pairs produced reproducible amplicons that were polymorphic among 31 mung bean accessions selected from diverse geographical locations. The large number of SSR-containing sequences found in this study will be valuable for the construction of a high-resolution genetic linkage maps, association or comparative mapping and genetic analyses of various Vigna species.
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影响因子：
14.9
作者：
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通讯作者：
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作者：
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作者：
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DOI：
10.1159/000090694
发表时间：
2006-01-01
期刊：
COMMUNITY GENETICS
影响因子：
--
作者：
Krawczak, M;Nikolaus, S;Schreiber, S
通讯作者：
Schreiber, S