The Complete Chloroplast Genomes of Two Lespedeza Species: Insights into Codon Usage Bias, RNA Editing Sites, and Phylogenetic Relationships in Desmodieae (Fabaceae: Papilionoideae).

Yamuna Somaratne,Liang Zhao,Sheng-Quan Xu,Wen-Qiang Wang,De-Long Guan

doi:10.3390/plants9010051

Abstract

The genus Lespedeza (tribe: Desmodieae) consists of about 40 species that have high medicinal and economic value. However, in this genus, using morphological characters, the species identification is quite complicated, which can be solved by the analysis of the complete chloroplast genomes. As primary organelle genomes, the complete genome sequences of chloroplasts (cp) provide unique molecular information to study the divergence of species, RNA editing, and phylogeny. Therefore, to the best of our knowledge, for the first time, we sequenced the complete cp genomes of two representative Lespedeza species: Lespedeza davurica and Lespedeza cuneata. The cp genomes of both the species were found to be 149,010 bp in length, exhibiting the typical angiosperm chloroplast structure containing four regions. The Lespedeza cp genomes showed similar conserved gene contents, order, and orientations with a total GC content of 35.0%. A total of 128 genes, including 83 protein-coding genes, 37 tRNAs, and eight rRNAs, were identified from each genome. Unique molecular features of the two Lespedeza cp genome sequences were obtained by performing the analysis of repeats, sequence divergence, codon usage, and predicting the RNA editing sites in addition to phylogenetic analysis with other key genera in tribe Desmodieae. Using the two datasets, the phylogenetic relationship of Lespedeza species among Deasmodieae was discovered, suggesting that whole cp genomes provided useful information for phylogenetic studies of these species.

Highlights

Lespedeza is a genus in the tribe Desmodieae, which belongs to the subfamily Papilionoideae of the family Fabaceae, and this genus comprises nearly 40 species distributed mainly in eastern Asia and eastern North America [1]
52.2% of the complete chloroplast genomes consisted of protein‐coding genes (77,868 bp), 6.1% consisted of rRNAs (9062 bp), and 1.8%
The analysis revealed that the GC content of the cp genome of both the species was 35.0% and the inverted repeats (IRs) regions exhibited highest GC content (42.2%) followed by the large single-copy (LSC) regions (32.5%) and small single-copy (SSC)

Summary

Introduction

Lespedeza is a genus in the tribe Desmodieae, which belongs to the subfamily Papilionoideae of the family Fabaceae, and this genus comprises nearly 40 species distributed mainly in eastern Asia and eastern North America [1]. These plants grow as shrubs or trailing vines and can be either annual or perennial. Due to the structure of the plants and their inflorescences, some species like Lespedeza bicolor, are used as ornamental plants The leaves of these plants can be used as forage and for soil enrichment, and its deep root system is useful to prevent soil erosion. The high adaptability to drought and good forage quality of L. davurica are Plants 2020, 9, 51; doi:10.3390/plants9010051 www.mdpi.com/journal/plants

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