The Complete Chloroplast Genomes of Punica granatum and a Comparison with Other Species in Lythraceae.

Ming Yan,Zhaohe Yuan,Yu Ding,Xueqing Zhao,Yan Huo,Jianqing Zhou

doi:10.3390/ijms20122886

Ming Yan, Zhaohe Yuan + Show 4 more

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https://doi.org/10.3390/ijms20122886

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Abstract

Pomegranates (Punica granatum L.) are one of the most popular fruit trees cultivated in arid and semi-arid tropics and subtropics. In this study, we determined and characterized three complete chloroplast (cp) genomes of P. granatum cultivars with different phenotypes using the genome skimming approach. The complete cp genomes of three pomegranate cultivars displayed the typical quadripartite structure of angiosperms, and their length ranged from 156,638 to 156,639 bp. They encoded 113 unique genes and 17 are duplicated in the inverted regions. We analyzed the sequence diversity of pomegranate cp genomes coupled with two previous reports. The results showed that the sequence diversity is extremely low and no informative sites were detected, which suggests that cp genome sequences may be not be suitable for investigating the genetic diversity of pomegranate genotypes. Further, we analyzed the codon usage pattern and identified the potential RNA editing sites. A comparative cp genome analysis with other species within Lythraceae revealed that the gene content and organization are highly conserved. Based on a site-specific model, 11 genes with positively selected sites were detected, and most of them were photosynthesis-related genes and genetic system-related genes. Together with previously released cp genomes of the order Myrtales, we determined the taxonomic position of P. granatum based on the complete chloroplast genomes. Phylogenetic analysis suggested that P. granatum form a single clade with other species from Lythraceae with a high support value. The complete cp genomes provides valuable information for understanding the phylogenetic position of P. gramatum in the order Myrtales.

Highlights

Pomegranates (Punica granatum L.) are an economically important fruit tree of the tropical and subtropical regions of the world
All of them exhibited a typical quadripartite structure, consisting of a pair of IRs separated by a large single copy region (LSC) and a small single copy region (SSC) (Figure 1)
The rps12 is a trans-spliced gene, whose first exon is located in the LSC, while the second and third exons reside in IRs

Summary

Introduction

Pomegranates (Punica granatum L.) are an economically important fruit tree of the tropical and subtropical regions of the world. Pomegranates have showy edible fruit with a high content of anthocyanins and flavonoids [2,3]. It has been well demonstrated that pomegranates are valuable to human health due to high levels of flavonoids and anthocyanins, which are considered potent antioxidants offering protection against heart disease and cancer [4,5]. As important resources for basic research and crop improvement, the genome of P. granatum ‘Taishanhong’ has been determined [7]. This genome will shed new light on the understanding of some unique biological processes and pomegranate breeding. Compared to the nuclear genome, the complete chloroplast genome is a low-cost and efficient way to get valuable genomic resources that can be used to understand evolution at multiple taxonomic levels [8,9] and analyze the population [10] because of its highly conserved structures and comparatively moderate substitution rates [11]

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