Genome survey and SSR analysis of Apocynum venetum
Genome survey and SSR analysis of Apocynum venetum
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DOI：
10.1042/bsr20190146
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发表时间：
2019-06-25
影响因子：
4
通讯作者：
Wang, Ya-fang
中科院分区：
文献类型：
--
作者：
Li, Guo-qi;Song, Li-xiao;Wang, Ya-fang
罗布麻是一种抗逆性强的生态经济植物。本论文对A.委内瑞拉，以提供其全基因组测序的基础。高通量测序技术（Illumina NovaSep）首先用于测量A.应用生物信息学方法对该菌株的基因组大小、杂合性、重复序列和GC含量进行了分析，为后续的全基因组测序奠定了基础。测序分析结果表明，初步估计的A. venetum的基因组长度为254.40 Mbp，其杂合率和重复序列百分率分别为0.63和40.87%，表明venetum的基因组结构复杂。采用k-mer = 41进行初步拼接，获得了3841 bp的重叠群N50，其全长为223949699 bp。进一步拼接得到骨架N50，全长6196 bp，总长度为227322054 bp。我们在A. venetum基因组数据，共鉴定出101918个SSR。不同类型的核苷酸重复序列之间的差异很大，单核苷酸重复序列最多，六核苷酸重复序列最少。我们建议在未来的A.委内瑞拉产的
Apocynum venetum is an eco-economic plant that exhibits high stress resistance. In the present paper, we carried out a whole-genome survey of A. venetum in order to provide a foundation for its whole-genome sequencing. High-throughput sequencing technology (Illumina NovaSep) was first used to measure the genome size of A. venetum, and bioinformatics methods were employed for the evaluation of the genome size, heterozygosity ratio, repeated sequences, and GC content in order to provide a foundation for subsequent whole-genome sequencing. The sequencing analysis results indicated that the preliminary estimated genome size of A. venetum was 254.40 Mbp, and its heterozygosity ratio and percentage of repeated sequences were 0.63 and 40.87%, respectively, indicating that it has a complex genome. We used k-mer = 41 to carry out a preliminary assembly and obtained contig N50, which was 3841 bp with a total length of 223949699 bp. We carried out further assembly to obtain scaffold N50, which was 6196 bp with a total length of 227322054 bp. We performed simple sequence repeat (SSR) molecular marker prediction based on the A. venetum genome data and identified a total of 101918 SSRs. The differences between the different types of nucleotide repeats were large, with mononucleotide repeats being most numerous and hexanucleotide repeats being least numerous. We recommend the use of the '2+3' (Illumina+PacBio) sequencing combination to supplement the Hi-C technique and resequencing technique in future whole-genome research in A. venetum.