Low genetic diversity, limited gene flow and long-term genetic bottleneck effects in a threatened Gentianaceae species, Swertia przewalskii Pissjauk

We collected 106 Swertia przewalskii samples from the Qilian Mountains in the eastern portion of the Qinghai-Tibet Plateau between 2019 and 2021. Fresh leaves were dried in silica gel. DNA was extracted from the leaf tissues of all samples using the CTAB method.The DNA extraction and Double Digest Restriction-site Associated DNA Sequencing (ddRAD Sequencing) technology were employed to obtain genetic data from these samples. The DNA was diluted to a concentration of 10 ng/μL and digested with EcoRI and MseI enzyme pair. A series of procedures, including end repair and phosphorylation, a-tail addition, sequencing connector addition, purification, and PCR amplification, were carried out to finish the ddRAD library construction. The sequencing platform Illumina HiSeq X-ten at BENAGEN Co. Ltd (Wuhan, China) was employed to generate 150 bp paired-end reads for each sample (~ 0.5 Gb data for each). The raw reads were processed using the fastp software to obtain clean reads for Swertia przewalskii population genetic analyses.A total of 852,819,096 raw reads were generated from 106 individuals. After the quality filter (using the fastp software), we retained a total of 852,766,822 clean reads, with an average of 8,044,970 reads per sample. Clean reads were stored in the format of fq.gz.