A comparative analysis of the complete chloroplast genome sequences of four peanut botanical varieties.

Juan Wang,Shihua Shan,Chunjuan Li,Xiaobo Zhao,Caixia Yan

doi:10.7717/peerj.5349

Abstract

BackgroundArachis hypogaea L. is an economically important oilseed crop worldwide comprising six botanical varieties. In this work, we characterized the chloroplast (cp) genome sequences of the four widely distributed peanut varieties.MethodsThe cp genome data of these four botanical varieties (var. hypogaea, var. hirsuta, var. fastigiata, and var. vulgaris) were obtained by next-generation sequencing. These high-throughput sequencing reads were then assembled, annotated, and comparatively analyzed.ResultsThe total cp genome lengths of the studied A. hypogaea varieties were 156,354 bp (var. hypogaea), 156,878 bp (var. hirsuta), 156,718 bp (var. fastigiata), and 156,399 bp (var. vulgaris). Comparative analysis of theses cp genome sequences revealed that their gene content, gene order, and GC content were highly conserved, with only a total of 46 single nucleotide polymorphisms and 26 insertions/deletions identified. Most of the variations were restricted to non-coding sequences, especially, the trnI-GAU intron region was detected to be highly variable and will be useful for future evolutionary studies.DiscussionThe four cp genome sequences acquired here will provide valuable genetic resources for distinguishing A. hypogaea botanical varieties and determining their evolutionary relationship.

Highlights

Cultivated peanut (Arachis hypogaea L.) is one of the most important oilseed crops that is mainly planted in China, India, USA, and Argentina (Hammons, 1994; Grabiele et al, 2012; Bertioli et al, 2016)
And validation of cp genomes More than 1 GB raw sequencing data per sample was generated from high-throughput sequencing
For each of the assembled cp genome sequences, a .sqn file that was generated by the Sequin software, submitted to GenBank and acquired the following accession numbers: MG814006 for var. fastigiata, MG814007 for var. hirsuta, MG814008 for var. hypogaea, and MG814009 for var. vulgaris

Summary

Introduction

Cultivated peanut (Arachis hypogaea L.) is one of the most important oilseed crops that is mainly planted in China, India, USA, and Argentina (Hammons, 1994; Grabiele et al, 2012; Bertioli et al, 2016). How to cite this article Wang et al (2018), A comparative analysis of the complete chloroplast genome sequences of four peanut botanical varieties. With the help of genetic markers that include two non-coding cpDNA regions (trnTR-trnS and trnT-trnY), Grabiele et al (2012) found that the six peanut botanical varieties were very likely to have a single genetic origin, the fine evolutionary relationship between these varieties remains to be resolved. We characterized the chloroplast (cp) genome sequences of the four widely distributed peanut varieties. Results: The total cp genome lengths of the studied A. hypogaea varieties were 156,354 bp Discussion: The four cp genome sequences acquired here will provide valuable genetic resources for distinguishing A. hypogaea botanical varieties and determining their evolutionary relationship

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Conclusion