The complete chloroplast genome of Stryphnodendron adstringens (Leguminosae - Caesalpinioideae): comparative analysis with related Mimosoid species

Ueric José Borges De Souza,José Alexandre Felizola Diniz-Filho,Mariana Pires De Campos Telles,Rhewter Nunes,Cíntia Pelegrineti Targueta

doi:10.1038/s41598-019-50620-3

Ueric José Borges De Souza, José Alexandre Felizola Diniz-Filho + Show 3 more

Open Access

https://doi.org/10.1038/s41598-019-50620-3

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Abstract

Stryphnodendron adstringens is a medicinal plant belonging to the Leguminosae family, and it is commonly found in the southeastern savannas, endemic to the Cerrado biome. The goal of this study was to assemble and annotate the chloroplast genome of S. adstringens and to compare it with previously known genomes of the mimosoid clade within Leguminosae. The chloroplast genome was reconstructed using de novo and referenced-based assembly of paired-end reads generated by shotgun sequencing of total genomic DNA. The size of the S. adstringens chloroplast genome was 162,169 bp. This genome included a large single-copy (LSC) region of 91,045 bp, a small single-copy (SSC) region of 19,014 bp and a pair of inverted repeats (IRa and IRb) of 26,055 bp each. The S. adstringens chloroplast genome contains a total of 111 functional genes, including 77 protein-coding genes, 30 transfer RNA genes, and 4 ribosomal RNA genes. A total of 137 SSRs and 42 repeat structures were identified in S. adstringens chloroplast genome, with the highest proportion in the LSC region. A comparison of the S. adstringens chloroplast genome with those from other mimosoid species indicated that gene content and synteny are highly conserved in the clade. The phylogenetic reconstruction using 73 conserved coding-protein genes from 19 Leguminosae species was supported to be paraphyletic. Furthermore, the noncoding and coding regions with high nucleotide diversity may supply valuable markers for molecular evolutionary and phylogenetic studies at different taxonomic levels in this group.

Highlights

The chloroplast, which is considered to have originated from free-living cyanobacteria through endosymbiosis, plays an essential role in photosynthesis and in many processes in plant cells[1,2,3]
For validation, a set of 18,937,635 raw paired-end Illumina reads were well aligned in the chloroplast genome
The pairwise alignments with species close related to S. adstringens showed a high conservation of the general structure of the chromosome and correct arrangement of the chloroplast regions validating the proposed genome (Supplementary Fig. 2A–D)

Summary

Introduction

The chloroplast, which is considered to have originated from free-living cyanobacteria through endosymbiosis, plays an essential role in photosynthesis and in many processes in plant cells[1,2,3] In this evolutionary context, the chloroplast genome of angiosperms exhibit a highly conserved organization with a quadripartite structure, comprising two copies of inverted repeats (IRs), separated by large (LSC) and small (SSC) single-copy regions[4]. The gene order and content of chloroplast genomes are generally highly conserved along plant evolution and the substitution rates are much lower than that of the nuclear genome[12] This fact, coupled with the non-recombinant nature and maternal inheritance in most angiosperms, makes plant chloroplasts genomes valuable sources of genetic markers for analyzing evolutionary relationships at multiple scales, ranging from short-term phylogeographic patterns up to phylogenetic relationships among large clades[13,14]

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