Evolutionary Comparison of the Complete Chloroplast Genomes in Convallaria Species and Phylogenetic Study of Asparagaceae

Qi-Xiang Lu; Xiao Chang; Jing Gao; Xue Wu; Jing Wu; Zhe-Chen Qi; Rui-Hong Wang; Xiao-Ling Yan; Pan Li

doi:10.3390/genes13101724

Evolutionary Comparison of the Complete Chloroplast Genomes in Convallaria Species and Phylogenetic Study of Asparagaceae

Genes (Basel). 2022 Sep 26;13(10):1724. doi: 10.3390/genes13101724.

Authors

Qi-Xiang Lu¹, Xiao Chang¹, Jing Gao¹, Xue Wu¹, Jing Wu², Zhe-Chen Qi^{1

3}, Rui-Hong Wang¹, Xiao-Ling Yan⁴, Pan Li²

Affiliations

¹ Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China.
² The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, and Laboratory of Systematic & Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou 310058, China.
³ Shaoxing Academy of Biomedicine, Zhejiang Sci-Tech University, Shaoxing 312366, China.
⁴ Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai 201602, China.

Abstract

The genus Convallaria (Asparagaceae) comprises three herbaceous perennial species that are widely distributed in the understory of temperate deciduous forests in the Northern Hemisphere. Although Convallaria 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 Convallaria species (two of C. keiskei Miq., two of C. majalis L., and one of C. montana 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 Convallaria 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 (petA-psbJ, psbI-trnS and ccsA-ndhD) were identified as valuable molecular markers. Phylogenetic analysis of the family Asparagaceae using 48 cp genome sequences supported the monophyly of Convallaria, which formed a sister clade to the genus Rohdea. 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 Convallaria.

Keywords: Asparagaceae; Convallaria; chloroplast genome; comparative analysis; phylogenomics.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Asparagaceae* / genetics
Convallaria* / genetics
Genome, Chloroplast* / genetics
Phylogeny
RNA, Transfer / genetics

Substances

RNA, Transfer

Grants and funding

This research was funded by the National Natural Science Foundation of China, grant number 31700321, 31970225; The Special Fund for Scientific Research of Shanghai Landscaping & City Appearance Administrative Bureau, grant numbers G212405, G222403; National Wild Plant Germplasm Resource Center, grant number ZWGX1902; Special Fundamental Work of the Ministry of Science and Technology, grant number 2014FY120400; the Natural Science Foundation of Zhejiang Province, grant number LY21C030008, the Open Fund of Shaoxing Academy of Biomedicine of Zhejiang Sci-Tech University, grant number SXAB202020, and the Science Foundation of Zhejiang Sci-Tech University, grant number 19042144-Y.