Analysis on the Chloroplast Genome Characteristics and Phylogeny of Polygonatum Verticillatum

Danzeng Jinmei; Zhang Lin; Du Hanyu; Wen Xuemei; Xu Aiguo

doi:10.3969/j.issn.1004-3403.2025.04.002

Abstract：This study employed the Illumina NovaSeq 6000 platform to perform in-depth sequencing,assembly,an-notation,and structural analysis of the chloroplast genome of Polygonatum verticillatum.Comparative and phyloge-netic analyses with chloroplast genomes of other species within the Polygonatum genus revealed the structural charac-teristics of the P.verticillatum chloroplast genome and its evolutionary position within the genus.The results showed that the chloroplast genome of P.verticillatum was 155,973 bp in length,with a GC content of 37.63%,and exhibited a typical quadripartite structure,consisting of a large single-copy region(LSC,84,589 bp),a small single-copy region(SSC,18,554 bp),and two inverted repeat regions(IRa/IRb,each 52,830 bp).A total of 131 genes were annotated and encoded,including 85 protein-coding genes,38 tRNA genes,8 rRNA genes,50 simple sequence repeats(SSRs),and 45 dispersed sequence repeats.Additionally,codon usage preference analysis showed that most codons with high rela-tive synonymous codon usage(RSCU)value in the chloroplast genome of P.verticillatum ended with A or U,consis-tent with the general preference observed in most plants.Boundary analysis on IRregions revealed differences in their expansion and contraction among P.verticillatum and other species within the Polygonatum genus,reflecting genetic diversity among species within the genus.Phylogenetic analysis showed that P.verticillatum formed an independent branch on the evolutionary tree with its close relatives,clearly differentiating from other species within the genus.This study provides significant support for further research on genetic diversity,species identification and evolution-ary adaptation of Polygonatum genus,and lays a genomic foundation for genetic studies,conservation and resource utilization of P.verticillatum.