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. 2019 Jun 25;39(6):BSR20190146.
doi: 10.1042/BSR20190146. Print 2019 Jun 28.

Genome Survey and SSR Analysis of Apocynum venetum

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Free PMC article

Genome Survey and SSR Analysis of Apocynum venetum

Guo-Qi Li et al. Biosci Rep. .
Free PMC article

Abstract

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.

Keywords: Apocynum venetum; GC content; K-mer analysis; SSR molecular marker; genome sequencing; heterozygosity ratio.

Conflict of interest statement

The authors declare that there are no competing interests associated with the manuscript.

Figures

Figure 1
Figure 1. Distribution figure of GC content
The left half of the dotted line in this figure is the read-1 GC content distribution, and the right half is the read-2 GC content distribution, different colors represent different base types, which is used to detect whether AT, GC separation is present.
Figure 2
Figure 2. Distribution curve of K-mer
It is an analysis of the genome size prediction of Apocynum, which determines the expected depth of K-mer from the position of the main peak.
Figure 3
Figure 3. Distribution figure of contig coverage depth and length
In the figure, the peak with the most distribution is the main peak, the heterozygosity of the genome was judged according to the peak of 1/2 position before the main peak.
Figure 4
Figure 4. Distribution figure of contig coverage depth and number
In the figure, the peak with the most distribution is the main peak, the heterozygosity of the genome was judged according to the peak of 1/2 position before the main peak.
Figure 5
Figure 5. Distribution figure of GC_depth

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