Analyses of the complete genome and gene expression of chloroplast of sweet potato [Ipomoea batata

Lang Yan,Yizheng Zhang,Changhe Wei,Xuemei Tan,Xuedan Li,Xianjun Lai,Genlou Sun

doi:10.1371/journal.pone.0124083

Lang Yan, Yizheng Zhang + Show 5 more

Open Access

https://doi.org/10.1371/journal.pone.0124083

Copy DOI

Journal: PloS one	Publication Date: Apr 15, 2015
Citations: 45	License type: CC BY 4.0

Affiliation: Sichuan University, Sichuan Agricultural University

Abstract

Sweet potato [Ipomoea batatas (L.) Lam] ranks among the top seven most important food crops cultivated worldwide and is hexaploid plant (2n=6x=90) in the Convolvulaceae family with a genome size between 2,200 to 3,000 Mb. The genomic resources for this crop are deficient due to its complicated genetic structure. Here, we report the complete nucleotide sequence of the chloroplast (cp) genome of sweet potato, which is a circular molecule of 161,303 bp in the typical quadripartite structure with large (LSC) and small (SSC) single-copy regions separated by a pair of inverted repeats (IRs). The chloroplast DNA contains a total of 145 genes, including 94 protein-encoding genes of which there are 72 single-copy and 11 double-copy genes. The organization and structure of the chloroplast genome (gene content and order, IR expansion/contraction, random repeating sequences, structural rearrangement) of sweet potato were compared with those of Ipomoea (L.) species and some basal important angiosperms, respectively. Some boundary gene-flow and gene gain-and-loss events were identified at intra- and inter-species levels. In addition, by comparing with the transcriptome sequences of sweet potato, the RNA editing events and differential expressions of the chloroplast functional-genes were detected. Moreover, phylogenetic analysis was conducted based on 77 protein-coding genes from 33 taxa and the result may contribute to a better understanding of the evolution progress of the genus Ipomoea (L.), including phylogenetic relationships, intraspecific differentiation and interspecific introgression.

Highlights

Chloroplasts are photosynthetic intracellular organelles and have their own genome of a circular double-stranded DNA molecule [1]
As for the diversification relationship and evolutionary status of sweet potato in Convolvulaceae, this study mainly focused on the monophyletic tribe Ipomoeeae which consists of ca. 650–900 species distributed throughout the tropics and subtropics of the world [17]
We assembled, annotated and analyzed the complete chloroplast sequence of sweet potato (Ipomoea batatas). This cp genome was compared to other available Ipomoea (L.) cp genomes and some basal important angiosperms

Summary

Introduction

Chloroplasts (cp) are photosynthetic intracellular organelles and have their own genome of a circular double-stranded DNA molecule [1]. Since the first complete cp genome of liverwort (Marchantia polymorpha) was sequenced and characterized in 1986, more than 320 chloroplast genomes spanning 268 distinct organisms have been deposited in GOBASE The Complete Genome and Gene Expression of Chloroplast of Sweet Potato. Along with the evolutionary process of the angiosperm species, cp genomes undergo recombination and rearrangements that resulted in deviations from the general rules. In the previous comparative studies, gene loss-and-gain events and indels in the intergenic regions of cp genomes are identified in independent plant groups and have great potentials in addressing phylogenetic questions at both high and low taxonomic levels [7,8,9,10,11]. Cp genome sequences have been used to trace the evolutionary history of the plant kingdom, including phylogenetic relationships, intraspecific differentiation and interspecific introgression [2]

Methods

Findings

Discussion

Conclusion