Evolutionary Comparison of the Complete Chloroplast Genomes in <i>Convallaria</i> Species and Phylogenetic Study of Asparagaceae.

The genus <i>Convallaria</i> (Asparagaceae) comprises three herbaceous perennial species that are widely distributed in the understory of temperate deciduous forests in the Northern Hemisphere. Although <i>Convallaria</i> species have high medicinal and horticultural values, studies related to the phylogenetic analysis of this genus are few. In the present study, we assembled and reported five complete chloroplast (cp) sequences of three <i>Convallaria</i> species (two of <i>C. keiskei</i> Miq., two of <i>C. majalis</i> L., and one of <i>C. montana</i> Raf.) using Illumina paired-end sequencing data. The cp genomes were highly similar in overall size (161,365-162,972 bp), and all consisted of a pair of inverted repeats (IR) regions (29,140-29,486 bp) separated by a large single-copy (LSC) (85,183-85,521 bp) and a small single-copy (SSC) region (17,877-18,502 bp). Each cp genome contained the same 113 unique genes, including 78 protein-coding genes, 30 transfer RNA genes, and 4 ribosomal RNA genes. Gene content, gene order, AT content and IR/SC boundary structure were nearly identical among all of the <i>Convallaria</i> cp genomes. However, their lengths varied due to contraction/expansion at the IR/LSC borders. Simple sequence repeat (SSR) analyses indicated that the richest SSRs are A/T mononucleotides. Three highly variable regions (<i>petA</i>-<i>psbJ</i>, <i>psbI</i>-<i>trnS</i> and <i>ccsA</i>-<i>ndhD</i>) were identified as valuable molecular markers. Phylogenetic analysis of the family Asparagaceae using 48 cp genome sequences supported the monophyly of <i>Convallaria</i>, which formed a sister clade to the genus <i>Rohdea</i>. Our study provides a robust phylogeny of the Asparagaceae family. The complete cp genome sequences will contribute to further studies in the molecular identification, genetic diversity, and phylogeny of <i>Convallaria</i>.