An Jianyu, Yin Mengqi, Zhang Qin, Gong Dongting, Jia Xiaowen, Guan Yajing, Hu Jin
Seed Science Center, Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, China.
Int J Mol Sci. 2017 Sep 11;18(9):1942. doi: 10.3390/ijms18091942.
(L.) Roem. is an economically important vegetable crop in China. However, the genomic information on this species is currently unknown. In this study, for the first time, a genome survey of was carried out using next-generation sequencing (NGS) technology. In total, 43.40 Gb sequence data of , about 54.94× coverage of the estimated genome size of 789.97 Mb, were obtained from HiSeq 2500 sequencing, in which the guanine plus cytosine (GC) content was calculated to be 37.90%. The heterozygosity of genome sequences was only 0.24%. In total, 1,913,731 contigs (>200 bp) with 525 bp N length and 1,410,117 scaffolds (>200 bp) with 885.01 Mb total length were obtained. From the initial assembled genome, 431,234 microsatellites (SSRs) (≥5 repeats) were identified. The motif types of SSR repeats included 62.88% di-nucleotide, 31.03% tri-nucleotide, 4.59% tetra-nucleotide, 0.96% penta-nucleotide and 0.54% hexa-nucleotide. Eighty genomic SSR markers were developed, and 51/80 primers could be used in both "Zheda 23" and "Zheda 83". Nineteen SSRs were used to investigate the genetic diversity among 32 accessions through SSR-HRM analysis. The unweighted pair group method analysis (UPGMA) dendrogram tree was built by calculating the SSR-HRM raw data. SSR-HRM could be effectively used for genotype relationship analysis of species.
（L.）Roem. 是中国一种具有重要经济价值的蔬菜作物。然而，该物种目前尚无基因组信息。在本研究中，首次利用新一代测序（NGS）技术对 进行了基因组调查。通过HiSeq 2500测序，共获得了43.40 Gb的 序列数据，约为估计基因组大小789.97 Mb的54.94倍覆盖度，其中鸟嘌呤加胞嘧啶（GC）含量经计算为37.90%。基因组序列的杂合度仅为0.24%。共获得1,913,731个重叠群（>200 bp），N长度为525 bp，以及1,410,117个支架（>200 bp），总长度为885.01 Mb。从初步组装的 基因组中，鉴定出431,234个微卫星（SSRs）（≥5个重复）。SSRs重复的基序类型包括62.88%的二核苷酸、31.03%的三核苷酸、4.5 nine%的四核苷酸、0.96%的五核苷酸和0.54%的六核苷酸。开发了80个基因组SSR标记，其中51/80引物可同时用于“浙达23”和“浙达83”。通过SSR-HRM分析，利用19个SSRs对32份材料的遗传多样性进行了研究。通过计算SSR-HRM原始数据构建了非加权配对组方法分析（UPGMA）聚类树状图。SSR-HRM可有效用于 物种的基因型关系分析。
