Comparative analysis of chloroplast genomes of five Robinia species: Genome comparative and evolution analysis

Abstract

The black locust (Robinia pseudoacacia) is widely distributed, and has strong drought resistance and salt tolerance. These characteristics make it the best type of tree for landscaping and resource conservation in China. In this study, the chloroplast genomes of five black locusts were identified de novo and the evolutionary relationship among these black locusts and their taxonomic statuses in leguminous plants were determined. The chloroplast structures of the five black locusts were typical and had four parts, including two single copy regions (large and small single copy sections) and a pair of inverted repeats (IRs). Genome sizes were between 155,364 bp and 155,655 bp; the genome of R. pseudoacacia var. decaisneana was the smallest, while that of R. pseudoacacia var. tortuosa was the largest. The genomes contained 124–130 protein-coding genes; R. pseudoacacia var. tortuosa had the fewest, while R. hispida and R. pseudoacacia var. decaisneana had the most. In this study, eight to ten genes from chloroplast genomes contained introns. Nine genes from the chloroplast genomes of R. pseudoacacia and R. pseudoacacia f. unifolia contained introns that had lost the trnL-CAA gene via evolution, while eight chloroplast genes of R. pseudoacacia var. tortuosa contained introns that had lost the trnL-CAA and psaA genes. Among them, the rpoC1 gene had the longest introns at 2828 bp, and rps12+ had the smallest introns at only 533 bp. There were various amplification phenomena in the IR region among the five black locusts. Most of the protein-coding genes of the five black locusts had a high degree of codon preference. To determine the phylogenetic positions of the five black locusts, we conducted a systematic evolutionary analysis using common protein-coding genes in chloroplast sequences from 34 species of leguminous plants and 12 other species. The results showed that the relationship between Robinia and Acacia ligulata was the most distant among those of the leguminous plants, and the relationship between Robinia and Lotus japonicus was the closest. The chloroplast protein-coding genes in different black locusts were relatively conservative by evolutionary selection pressure analysis standards. These results are important for our understanding of their photosynthetic mechanisms and evolution, and the transgenic engineering of their chloroplasts.