Genome survey sequencing and characterization of simple sequence repeat (SSR) markers in Platostoma palustre (Blume) A.J.Paton (Chinese mesona)

Platostoma palustre (Blume) A.J.Paton is an annual herbaceous persistent plant of the Labiatae family. However, there is a lack of genomic data for this plant, which severely restricts its genetic improvement. In this study, we performed genome survey sequencing of P. palustre and developed simple sequence repeat (SSR) markers based on the resulting sequence. K-mer analysis revealed that the assembled genome size was approximately 1.21 Gb. A total of 15,498 SSR motifs were identified and characterized in this study; among them, dinucleotide, and hexanucleotide repeats had the highest and lowest, respectively. Among the dinucleotide repeat motifs, AT/TA repeat motifs were the most abundant, and GC/CG repeat motifs were rather rare, accounting for 44.28% and 0.63%, respectively. Genetic similarity coefficient analysis by the UPMGA methods clustered 12 clones, of P. palustre and related species into two subgroups. These results provide helpful information for further research on P. palustre resources and variety improvements.

Genome Survey Sequencing of Acer truncatum Bunge to Identify Genomic Information, Simple Sequence Repeat (SSR) Markers and Complete Chloroplast Genome

The Acer truncatum Bunge is a particular forest tree species found in the north of China. Due to the recent discovery that its seeds contain a considerable amount of nervonic acid, this species has received more and more attention. However, there have been no reports of the genome in this species. In this study, we report on the Acer truncatum genome sequence produced by genome survey sequencing. In total, we obtained 61.90 Gbp of high-quality data, representing approximately 116x coverage of the Acer truncatum genome. The genomic characteristics of Acer truncatum include a genome size of 529.88 Mbp, a heterozygosis rate of 1.06% and a repeat rate of 48.8%. A total of 392,961 high-quality genomic SSR markers were developed and a graphical map of the annotated circular chloroplast genome was generated. Thus far, this is the first report of de novo whole genome sequencing and assembly of Acer truncatum. We believe that this genome sequence dataset may provide a new resource for future genomic analysis and molecular breeding studies of Acer truncatum.