Insights into the plastome evolution and phylogenetic relationships of Lepidium (Brassicaceae)

Lepidium represents one of the most species-rich genera in the Brassicaceae, encompassing numerous taxa with excellent medicinal value. Although the plastome architecture of Brassicaceae has been extensively characterized, its evolutionary dynamics within Lepidium remain poorly understood. Besides, the intrageneric taxonomy has long been problematic, primarily due to subtle morphological differences or overlapping morphological characteristics. Here, 15 Lepidium plastomes (11 newly sequenced and 4 published) were subject to comparative genomic and phylogenetic analyses to investigate plastome evolution and phylogenetic relationships.

The total length of the 11 newly sequenced Lepidium plastomes varied from 153,803 bp to 154,997 bp, with 111-112 unique genes. The Lepidium plastomes exhibited strong conservatism in genome size, gene order, plastome structure, IR/SC borders, codon usage, mVISTA analysis, Pi value, and genetic distance. However, minor variations were observed in IR border shifts. Analysis of repeat sequences revealed interspecific differences in both long repeat sequences (24-40) and simple sequence repeats (78-98) among 15 Lepidium plastomes. Six divergence hotspots (ycf1, ccsA, matK, rps15-ycf1, trnH-GUG-psbA, and rpl32-trnL-UAG) were identified as potential DNA barcodes for both species identification and phylogenetic analyses of Lepidium. The ycf1 gene was under relaxed selection. Furthermore, our phylogenetic studies clarified that all 15 Lepidium species formed a strongly supported monophyletic group within the tribe Lepidieae, while the cytonuclear discordance between ITS and plastome trees was found within Lepidium.

Our findings suggested that cytonuclear discordance within Lepidium likely results from hybridization/introgression and incomplete lineage sorting. Meanwhile, we proposed the reclassification of L. perfoliatum within Section Lepia. This study clearly documented global patterns of plastome structural evolution, and constructed a well-supported phylogeny of Lepidium. The reliable phylogenetic tree not only provides a new viewpoint into the intrageneric relationships and sectional classification of Lepidium, but also advances our understanding of the evolutionary history of this genus.