Comparative Chloroplast Genome Analysis of Wax Gourd (Benincasa hispida) with Three Benincaseae Species, Revealing Evolutionary Dynamic Patterns and Phylogenetic Implications

doi:10.3390/genes13030461

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	Comparative Chloroplast Genome Analysis of Wax Gourd (Benincasa hispida) with Three Benincaseae Species, Revealing Evolutionary Dynamic Patterns and Phylogenetic Implications
	Song, Weicai; Chen, Zimeng; He, Li; Feng, Qi; Zhang, Hongrui; Du, Guilin; Shi, Chao; Wang, Shuo
	2022
发表期刊	GENES
卷号	13 期号:3 页码:461
摘要	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.
关键词	Benincasa hispida chloroplast genome comparative analysis divergence region phylogenetic CUCURBITACEAE SEQUENCES PLANTS ANNOTATION EXTRACT FAMILY FRUITS GENES TOOLS
DOI	10.3390/genes13030461
收录类别	SCI
WOS记录号	WOS:000775289300001
引用统计
文献类型	期刊论文
条目标识符	http://ir.kib.ac.cn/handle/151853/74689
专题	中国科学院昆明植物研究所
推荐引用方式 GB/T 7714	Song, Weicai,Chen, Zimeng,He, Li,et al. Comparative Chloroplast Genome Analysis of Wax Gourd (Benincasa hispida) with Three Benincaseae Species, Revealing Evolutionary Dynamic Patterns and Phylogenetic Implications[J]. GENES,2022,13(3):461.
APA	Song, Weicai.,Chen, Zimeng.,He, Li.,Feng, Qi.,Zhang, Hongrui.,...&Wang, Shuo.(2022).Comparative Chloroplast Genome Analysis of Wax Gourd (Benincasa hispida) with Three Benincaseae Species, Revealing Evolutionary Dynamic Patterns and Phylogenetic Implications.GENES,13(3),461.
MLA	Song, Weicai,et al."Comparative Chloroplast Genome Analysis of Wax Gourd (Benincasa hispida) with Three Benincaseae Species, Revealing Evolutionary Dynamic Patterns and Phylogenetic Implications".GENES 13.3(2022):461.

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