Chen Honglin, Wang Lixia, Wang Suhua, Liu Chunji, Blair Matthew Wohlgemuth, Cheng Xuzhen
The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China.
CSIRO Plant Industry, Queensland Bioscience Precinct, Queensland, Australia.
PLoS One. 2015 Apr 1;10(4):e0120273. doi: 10.1371/journal.pone.0120273. eCollection 2015.
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.
绿豆（Vigna radiate (L.) Wilczek）是一种重要的传统食用豆类作物，具有很高的经济和营养价值。它在中国和其他亚洲国家广泛种植。尽管其很重要，但目前该作物物种或其豇豆属的一些近缘物种尚无基因组信息。在本研究中，使用Illumina双末端测序技术从绿豆中获得了超过1.03亿条高质量的cDNA序列读数。经过处理的读数被组装成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个（53.0%）和23,235个（47.7%）与NCBI非冗余蛋白质和核苷酸序列数据库中的蛋白质具有显著相似性。此外，19,242个（39.5%）可归类到基因本体类别，18,316个（37.6%）归类到Swiss-Prot类别，10,918个（22.4%）归类到KOG数据库类别（E值<1.0E - 5）。使用京都基因与基因组百科全书（KEGG）途径数据库，共有6,585个（8.3%）被映射到244条途径上。在这些单基因中，10,053个序列包含一个独特的简单序列重复（SSR），2,303个序列在同一表达序列标签（EST）中共同包含多个SSR。总共鉴定出13,134个EST - SSR作为潜在的分子标记，其中单核苷酸A/T重复是最丰富的基序类别，G/C重复很少见。在该SSR分析中，我们发现了五个主要的重复基序：AG/CT（30.8%）、GAA/TTC（12.6%）、AAAT/ATTT（6.8%）、AAAAT/ATTTT（6.2%）和AAAAAT/ATTTTT（1.9%）。总共随机选择了200个SSR位点通过PCR扩增进行验证作为EST - SSR标记。其中，66对标记引物产生了可重复的扩增子，这些扩增子在从不同地理位置选取的31份绿豆种质中具有多态性。本研究中发现的大量含SSR序列对于构建高分辨率遗传连锁图谱、关联或比较图谱以及各种豇豆属物种的遗传分析将具有重要价值。
