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

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.

The Complete Plastid Genome of Artocarpus camansi: A High Degree of Conservation of the Plastome Structure in the Family Moraceae

“…The most abundant amino acid was leucine, with 2523 codons, that is, approximately 10.94% of the total number of codons, whereas, excluding stop codons, cysteine was the least abundant one (270 codons, 1.17% of the total number). A prevalence of leucine and reduced quantities of cysteine were also observed by Somaratne et al [57] in their evaluation of the plastid genome of species of the bush clover genus Lespedeza. The most abundant codon was ATT, which encodes isoleucine.…”

Comparative Genomics and Phylogenetic Analyses of Christia vespertilionis and Urariopsis brevissima in the Tribe Desmodieae (Fabaceae: Papilionoideae) Based on Complete Chloroplast Genomes

“…The typical angiosperm cp genome is a circular, double-stranded DNA molecule with a quadripartite structure composed of a large single copy region (LSC), a small single copy region (SSC), and a pair of inverted repeats (IRs) [ 12 ]. In contrast with nuclear genomes, cp genomes in Fabaceae are uniparentally inherited and largely conserved in gene content, organization, and structure [ 13 , 14 ]. Due to its stable uniparental inheritance, the cp genome can be of great value for discriminating between closely related species and understanding their evolutionary relationships [ 15 , 16 , 17 ].…”

Transcriptome and Comparative Chloroplast Genome Analysis of Vincetoxicum versicolor: Insights Into Molecular Evolution and Phylogenetic Implication

“…As an important evolutionary feature, the codon usage pattern has been widely investigated in plant chloroplast genomes ( Gao et al, 2018 ; Somaratne et al, 2019 ; Yang et al, 2019a ). To explore the codon usage pattern in the chloroplast genomes of the Vincetoxicum and Cynanchum species, we calculated the number of codons and RSCU of protein-coding genes in the four chloroplast genomes using Mega X ( Supplementary Table 4 ).…”