Comparative Analyses of Chloroplast Genomes of Cucurbitaceae Species: Lights into Selective Pressures and Phylogenetic Relationships.

Xiao Zhang,Tao Zhou,Yuemei Zhao,Guifang Zhao,Miaomiao Ju,Jingjing Sun,Jia Yang

doi:10.3390/molecules23092165

Abstract

Cucurbitaceae is the fourth most important economic plant family with creeping herbaceous species mainly distributed in tropical and subtropical regions. Here, we described and compared the complete chloroplast genome sequences of ten representative species from Cucurbitaceae. The lengths of the ten complete chloroplast genomes ranged from 155,293 bp (C. sativus) to 158,844 bp (M. charantia), and they shared the most common genomic features. 618 repeats of three categories and 813 microsatellites were found. Sequence divergence analysis showed that the coding and IR regions were highly conserved. Three protein-coding genes (accD, clpP, and matK) were under selection and their coding proteins often have functions in chloroplast protein synthesis, gene transcription, energy transformation, and plant development. An unconventional translation initiation codon of psbL gene was found and provided evidence for RNA editing. Applying BI and ML methods, phylogenetic analysis strongly supported the position of Gomphogyne, Hemsleya, and Gynostemma as the relatively original lineage in Cucurbitaceae. This study suggested that the complete chloroplast genome sequences were useful for phylogenetic studies. It would also determine potential molecular markers and candidate DNA barcodes for coming studies and enrich the valuable complete chloroplast genome resources of Cucurbitaceae.

Highlights

As the fourth most economically important plant family, Cucurbitaceae consists of 115 proposed genera with approximately 960 species distributed in tropical and subtropical areas [1]
The comparative analyses of whole chloroplast genomes (CPGs) from ten species of Cucurbitaceae showed that the sizes of 10 CPGs ranged from 155,293 bp (C. sativus) to 158,844 bp (M. charantia), with an average CPG
The large single-copy region (LSC) region and IR region had a significant correlational relationship with the overall genome size, and each of the structural regions of the CPGs were not correlated with each other (Figure 2)

Summary

Introduction

As the fourth most economically important plant family, Cucurbitaceae consists of 115 proposed genera with approximately 960 species distributed in tropical and subtropical areas [1]. The vast majority of these plants are annual vines and woody lianas, and only a small proportion are shrubs and trees [2]. Especially melon (Cucumis melo), watermelon (Citrullus lanatus), bottle gourd (Lagenaria siceraria), pumpkin (Cucurbita pepo), and cucumber (Cucumis sativus), are the basis for industries [3]. Their fruits are edible, and used by humans mostly as durable containers, fishnet floats, and musical instruments [4]. Flavonoids and saponins contained in Gynostemma pentaphyllum [5] have radical scavenging and antiproliferative properties [6], and cucurbitane-type compounds extracted from Hemsleya amabilis and Hemsleya carnosiflora exert anti-inflammatory

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Discussion

Conclusion