Abstract
Benincasa hispida (wax gourd) is an important Cucurbitaceae crop, with enormous economic and medicinal importance. Here, we report the de novo assembly and annotation of the complete chloroplast genome of wax gourd with 156,758 bp in total. The quadripartite structure of the chloroplast genome comprises a large single-copy (LSC) region with 86,538 bp and a small single-copy (SSC) region with 18,060 bp, separated by a pair of inverted repeats (IRa and IRb) with 26,080 bp each. Comparison analyses among B. hispida and three other species from Benincaseae presented a significant conversion regarding nucleotide content, genome structure, codon usage, synonymous and non-synonymous substitutions, putative RNA editing sites, microsatellites, and oligonucleotide repeats. The LSC and SSC regions were found to be much more varied than the IR regions through a divergent analysis of the species within Benincaseae. Notable IR contractions and expansions were observed, suggesting a difference in genome size, gene duplication and deletion, and the presence of pseudogenes. Intronic gene sequences, such as trnR-UCU–atpA and atpH–atpI, were observed as highly divergent regions. Two types of phylogenetic analysis based on the complete cp genome and 72 genes suggested sister relationships between B. hispida with the Citrullus, Lagenaria, and Cucumis. Variations and consistency with previous studies regarding phylogenetic relationships are discussed. The cp genome of B. hispida provides valuable genetic information for the detection of molecular markers, research on taxonomic discrepancies, and the inference of the phylogenetic relationships of Cucurbitaceae.
Highlights
We de novo assembled its complete chloroplast genome and the data were submitted to National Center for Biotechnology Information (NCBI) under accession number MW362306 after a thorough check for correctness
We found that none of the π values of the coding sequences (CDSs) genes exceeded 0.05 and that the intergenic spacer (IGS) were more divergent than the gene regions, which was consistent with the aforementioned analysis
We sequenced and reported the complete chloroplast genome of Benincasa hispida and performed comparative analyses with three other, closely related species selected from the Benincaseae but distinct enough to obtain reasonable results, providing valuable genetic data for phylogeographic and population genetic investigation [50,51]
Summary
Cucurbitaceae is a moderately large family of about 130 genera and 900 species [1]. Because of their economic importance in temperate regions, species of the Cucurbitaceae family have a long and close association with human beings [2]. Familiar edible and medicinal fruits, such as cucumber (Cucumis sativus), melon (Cucumis melo), watermelon (Citrullus lanatus), bottle gourd (Lagenaria siceraria), pumpkin, and squash (Cucurbita spp.). Are the main crops of Cucurbitaceae [3]. The early molecular phylogeny of Cucurbitaceae was reconstructed using five chloroplast markers, which weakly support two subfamilies of Cucurbitoideae and Nhandiroboideae [4].
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