AUTHOR=Hu Ke , Chen Min , Li Pan , Sun Xiaoqin , Lu Ruisen 

TITLE=Intraspecific phylogeny and genomic resources development for an important medical plant Dioscorea nipponica, based on low-coverage whole genome sequencing data

JOURNAL=Frontiers in Plant Science

VOLUME=14

YEAR=2023

URL=https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2023.1320473

DOI=10.3389/fpls.2023.1320473

ISSN=1664-462X

ABSTRACT=<p><italic>Dioscorea nipponica</italic> Makino, a perennial twining herb with medicinal importance, has a disjunctive distribution in the Sino-Japanese Floristic Region. It has a long history in traditional Chinese medicine, with demonstrated efficacy against various health conditions. However, the limited genomic data and knowledge of genetic variation have hindered its comprehensive exploration, utilization and conservation. In this study, we undertook low-coverage whole genome sequencing of diverse <italic>D. nipponica</italic> accessions to develop both plastome (including whole plastome sequences, plastome-derived SSRs and plastome-divergent hotspots) and nuclear genomic resources (including polymorphic nuclear SSRs and single-copy nuclear genes), as well as elucidate the intraspecific phylogeny of this species. Our research revealed 639 plastome-derived SSRs and highlighted six key mutational hotspots (namely CDS <italic>ycf1</italic>, IGS <italic>trnL</italic>-<italic>rpl32</italic>, IGS <italic>trnE</italic>-<italic>trnT</italic>, IGS <italic>rps16</italic>-<italic>trnQ</italic>, Intron 1 of <italic>clpP</italic>, and Intron <italic>trnG</italic>) within these accessions. Besides, three IGS regions (i.e., <italic>ndhD</italic>-<italic>cssA</italic>, <italic>trnL</italic>-<italic>rpl32</italic>, <italic>trnD</italic>-<italic>trnY</italic>), and the intron <italic>rps16</italic> were identified as potential markers for distinguishing <italic>D. nipponica</italic> from its closely related species. In parallel, we successfully developed 988 high-quality candidate polymorphic nuclear SSRs and identified 17 single-copy nuclear genes for <italic>D. nipponica</italic>, all of which empower us to conduct in-depth investigations into phylogenetics and population genetics of this species. Although our phylogenetic analyses, based on plastome sequences and single-copy nuclear genes revealed cytonuclear discordance within <italic>D. nipponica</italic>, both findings challenged the current subspecies classification. In summary, this study developed a wealth of genomic resources for <italic>D. nipponica</italic> and enhanced our understanding of the intraspecific phylogeny of this species, offering valuable insights that can be instrumental in the conservation and strategic utilization of this economically significant plant.</p>