Chloroplast genome characteristics and phylogenetic analysis of Ramie (Boehmeria nivea (L.) Gaudich).

BACKGROUND: Ramie (Boehmeria nivea (L.) Gaudich) is an economically and ecologically important phloem fiber crop belonging to the Urticaceae family. Research on its chloroplast genome is crucial for elucidating evolutionary relationships within Urticaceae and for establishing a foundation for genetic breeding and germplasm resource utilization in ramie. METHODS AND RESULTS: In this study, the complete chloroplast genome of B. nivea was assembled using high-throughput Illumina NovaSeq X Plus sequencing data. The genome has a total length of 155,806 bp and exhibits a typical quadripartite structure, consisting of a Large Single Copy (LSC) region (85,717 bp), a Small Single Copy (SSC) region (18,693 bp), and two identical Inverted Repeat (IR) regions (25,698 bp each). The overall GC content is 36.36%, with the IR regions (42.63%) having a significantly higher GC content than the LSC (34.03%) and SSC (29.78%) regions. A total of 130 genes were annotated, including 84 protein-coding genes (mRNAs), 37 transfer RNA (tRNA) genes, and 8 ribosomal RNA (rRNA) genes. Further analysis identified 263 chloroplast SSR (cpSSR) markers (70.0% being mononucleotide repeats dominated by A/T) and 40 dispersed repeats (25 palindromic repeats, 12 forward repeats, 3 reverse repeats). Codon usage bias analysis revealed that leucine (Leu) had the highest codon usage frequency (10.6%), and 26 out of 28 preferred codons (RSCU > 1) ended with A/U. Comparative evolutionary analysis showed that B. nivea shared over 95% collinearity with closely related species (e.g., Boehmeria clidemioides var. diffusa, Boehmeria tomentosa). Ka/Ks analysis indicated that core chloroplast genes (e.g., rps2, rpoC2) were under purifying selection (Ka/Ks = 0.2–0.8). Nucleotide diversity (pi) analysis identified the SSC region as the most variable (average pi = 0.018), with the ycf1 gene (pi = 0.034) emerges as a potential high-resolution molecular marker. Phylogenetic analysis based on 28 species (25 Rosales + 3 outgroups) revealed that B. nivea forms a clade with other Boehmeria species with 98% bootstrap support, supporting their close phylogenetic affinity. CONCLUSIONS: The complete chloroplast genome of B. nivea assembled in this study provides comprehensive genomic resources for understanding the structural characteristics and evolutionary patterns of Urticaceae plants. The identified SSR markers and highly variable regions offer valuable tools for ramie germplasm identification, genetic diversity analysis, and molecular breeding.