A First Genome Survey and Microsatellite Motif Identification of Taihangia rupestris

Abstract

Background:Taihangia rupestris is a perennial herb on the China species red list that is growing on the cliffs of Taihang Mountain in China. However research on the genome of T. rupestris has not been carried out, which severely restricts further research on it. The aim of this study was to conduct a first genome survey of T. rupestris and to develop SSR molecular markers of it. Methods: The genome size and characteristics of T. rupestris were estimated by Illumina Hi-SeqXTen and K-mer analysis. We designed SSR primers in batches with Misa and Primer3, and T. rupestris from different populations were used to verify the selected primers. Finally, datas were analysised by Cervus 3.0 and GenAlex 6.5 for genetic diversity. Results: The genome size of T. rupestris was estimated to be 976.97 Mb with a heterozygosity rate of 0.726% and a sequence repetition rate of 56.93%. The clean reads were assembled into 100973 contigs with the max length of 26073 bp and an N50 value of 2607 bp. Based on the genome data of T. rupestris, a total of 805600 SSR markers were identified and 72769 pairs of primers were designed. In the present study, 100 primers were used to verify that 82 primers were successfully amplified. Conclusion: In general, the genome of T. rupestris is difficult to assemble genome with micro-heterozygosity and high repetition. In this study, 15 pairs of primers with good polymorphism can effectively distinguish different populations of T. rupestris. These analyses laid a foundation for the subsequent whole genome sequencing of T. rupestris.