Chloroplast whole genome assembly and phylogenetic analysis of Persicaria criopolitana reveals its new taxonomic status

Abstract

Abstract Persicaria criopolitana (Polygonaceae), a dominant annual herb in wetland ecosystems, is ecologically and horticulturally significant. Despite its prevalence, genomic resources for clarifying its phylogenetic relationships and supporting conservation efforts remain limited. The complete chloroplast genome of P. criopolitana was sequenced, assembled, and annotated. Comparative genomic analyses with other Persicaria species were conducted to identify structural variations and evolutionary dynamics. Phylogenetic relationships were reconstructed using maximum-likelihood methods based on whole chloroplast genome sequences. The chloroplast genome (159,427 bp) exhibits a conserved quadripartite structure, encoding 131 genes, including 86 protein-coding, 37 tRNA, and 8 rRNA genes. Key features include: 208 simple sequence repeats (SSRs) were detected, predominantly mononucleotide motifs. A pronounced preference for A/U-ending codons, with leucine as the most frequent amino acid. A 62-bp extension of the ndhF gene into the inverted repeat (IRb) region within the small single-copy (SSC) region.Phylogenetic resolution: P. criopolitana clusters within Persicaria sect. Polygonum, demonstrating distant divergence from sect. Cephalophilon.This study provides the first complete chloroplast genome resource for P. criopolitana, resolving its taxonomic position and revealing adaptive genomic signatures. These findings advance molecular tools for species identification, inform conservation strategies, and elucidate evolutionary mechanisms in Persicaria.