Complete Chloroplast Genome and Comparative Analysis of Entada phaseoloides (Fabaceae)

Abstract

Background: Entada phaseoloides (L.) Merr (Fabaceae) is a large woody climber that is found widely in southern China and other tropical and subtropical areas worldwide. The genus Entada contains ~30 species, and E. phaseoloides is most commonly found in China. The E. phaneroneura and E. pervillei are endangered species. Previous studies had focused on medicinal components, transcriptional regulation, and nuclear genomes. The chloroplast genome of Entada has not been reported, and little is known about the phylogenetic relationships within the Entada. In this study, we performed short-read sequencing of E. phaseoloides and assembled and analyzed its chloroplast genome. Methods: Dry specimen leaves of E. phaseoloides were subjected to DNA extraction and sequenced using the Illumina Novoseq platform. The chloroplast genome was assembled using Get Organelle, annotated using CPGAVAS2 and Geneious Prime. Repeat sequences and SSR analysis were performed using the Reputer and MISA programs, respectively. Phylogenetic analyses were performed using IQTREE and MrBayes software. Result: The complete chloroplast genome of E. phaseoloides is 159,963 bp in length and has a quadripartite structure with large single copy of 89,972 bp and a small single copy of 19,309 bp separated by inverted repeats of 25,341 bp. A total of 112 genes in E. phaseoloides comprised 78 protein-coding genes, 30 transfer RNA genes, and 4 ribosomal RNA genes. The distribution of simple sequence repeats and long repeat sequences was determined. We carried out phylogenetic analysis based on homologous protein-coding genes among 21 species derived from Fabaceae. We found that the phylogeny was largely congruent with prior hypotheses about the position of E. phaseoloides in evolutionary branches. The E. phaseoloides has a closer relationship with the Piptadeniastrum africanum.