De Novo Plastome Assembly and Comparative Genomics of Elatostema lineolatum var. major: Insights into Urticaceae Orthologs, Phylogeny, and Comparative Analysis of 242 Plastomes

This study presented the first complete plastome of Elatostema lineolatum var. major, a wild edible plant from Kanglung, Bhutan. The 150 292 bp genome exhibited the typical quadripartite angiosperm structure, comprising a large single-copy (LSC) region (83 953 bp), a small single-copy (SSC) region (17 207 bp), and two inverted repeats (24 566 bp each). It encoded 131 genes, including 86 protein-coding, 37 tRNAs, and 8 rRNAs. Comparative analysis revealed high synteny and gene order conservation among Elatostema species, reinforcing its monophyly. Analysis of 242 Urticaceae plastomes showed conserved structures, with genome sizes ranging from 142 627 to 170 958 bp (mean: 154 906.10 ± 5432.30 bp). GC content varied slightly (35.32–37.22%, mean: 36.31 ± 0.47%), aligning with values for Procris crenata (36.5%) and Urtica fissa (36.60%). The quadripartite structure remained stable, with LSC (83 919.20 ± 4288.10 bp), SSC (18 611.88 ± 2407.50 bp), and IR (26 186.78 ± 3841.20 bp) regions consistent across Urticaceae. Eleven hypervariable regions were identified through nucleotide diversity analysis, with ycf1 emerging as a promising DNA barcode. Additionally, SSRs serve as valuable molecular markers for population genetics. Phylogenetic analysis placed E. lineolatum near E. dissectum, supporting recent divergence. Ortholog analysis suggested evolutionary stability, aiding taxonomic resolution. Ka/Ks analysis detected positive selection in ycf2, indicating adaptation to diverse habitats in Bhutan. This study provides insights into the genomic structure and evolutionary dynamics of E. lineolatum, a wild edible plant, contributing to our understanding of Urticaceae evolution and offering valuable resources for future research on biodiversity, conservation, and its ecological significance in Bhutan.