Genome survey and SSR analysis of Apocynum venetum.

Genome survey and SSR analysis of Apocynum venetum. Biosci Rep. 2019 Jun 12;: Authors: Li GQ, Song LX, Jin CQ, Li M, Gong SP, Wang YF Abstract Apocynum venetum is an eco-economic plant that exhibits high stress resistance. In this 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 3,841 bp with a total length of 223,949,699 bp. We carried out further assembly to obtain scaffold N50, which was 6196 bp with a total length of 227,322,054 bp. We performed simple sequence repeat (SSR) molecular marker prediction based on the A. venetum genome data and identified a total of 101,918 SSRs. The differences between the different types of nucleotide repeats were large, with mononucleotide repeats being most numerou...
Source: Bioscience Reports - Category: Biomedical Science Authors: Tags: Biosci Rep Source Type: research