Likuan Liu, Yifan Wang, Haoyu Liu, Tianyu Zhao, Jianfen Ma, Haotian Wang, Kaidi Su, Jinping Li
This study provides valuable insights into the chloroplast genomic structure, codon usage patterns, and SSR distribution of M. squamosa, contributing to genomic evolution studies and taxonomic revision within the Tamaricaceae family.
BACKGROUND: Myricaria squamosa Desv., a perennial shrub of the Tamaricaceae family, holds significant ecological, medicinal and economic values on the Qinghai-Tibet Plateau.
METHODS: This study performed chloroplast whole-genome sequencing of M. squamosa and analyzed its genomic characteristics, codon usage bias, and phylogenetic relationships.
RESULTS: The M. squamosa chloroplast genome spans 154,689 bp, with a GC content of 36.3%. A total of 129 functional genes were annotated, including 84 protein-coding genes, 37 transport RNA (tRNA) genes, and eight ribosomal RNA (rRNA) genes. Structural analysis revealed that contraction and expansion of the inverted repeat (IR) boundaries in Tamaricaceae species primarily involve the rps19 and ycf1 genes. We identified 214 simple sequence repeat (SSR) loci. Comparative genomic analysis indicated higher variability in the large single-copy (LSC) and small single-copy (SSC) regions compared to the IR regions, and greater divergence in intergenic spacers than in protein-coding regions. All protein-coding sequences contain a total of 26,045 codons, with leucine (2750) being the most frequent, and a pronounced preference for adenine/thymine (A/T) endings. Phylogenetic reconstruction revealed that M. squamosa is most closely related to Myricaria laxiflora.
CONCLUSIONS: This study provides valuable insights into the chloroplast genomic structure, codon usage patterns, and SSR distribution of M. squamosa, contributing to genomic evolution studies and taxonomic revision within the Tamaricaceae family.