Taihangia rupestris: First Genome Survey and Microsatellite Motif Identification

Abstract

Taihangia rupestris(T. rupestris) is a perennial herb on the China species red list that grows on the cliffs of Taihang Mountain. However, there has been limited research on the genome of T. rupestris, severely restricting further research. Here, a first genome survey of T. rupestris was conducted. The genome size and characteristics of T. rupestris were estimated using Illumina HiSeq X Ten and K-mer analysis, respectively. Additionally, simple sequence repeat predictions were obtained tested. The genome size of T. rupestris was estimated to be 976.97 Mb, with a heterozygosity rate of 0.726% and sequence repetition rate of 56.93%. The clean reads were assembled into 100,973 contigs, with the max length of 26,073 bp and an N50 value of 2,607 bp. Based on the T. rupestris genome data, 805,600 simple sequence repeat markers were identified and 72,769 pairs of primers were designed. In the present study, 100 primers were tested and 82 resulted in successful amplicon generation. In total, 15 primer pairs amplifying good polymorphisms effectively distinguished different T. rupestris populations. In general, the T. rupestris genome was difficult to assemble owing to micro-heterozygosity and high repetition levels. These analyses lay a foundation for the subsequent whole-genome sequencing of T. rupestris.