Complete chloroplast genome sequencing and comparative analysis reveals changes to the chloroplast genome after allopolyploidization in Cucumis

Allopolyploids undergo “genomic shock” leading to significant genetic and epigenetic modifications. Previous studies have mainly focused on nuclear changes, while little is known about the inheritance and changes of organelle genome in allopolyploidization. The synthetic allotetraploid Cucumis ×hytivus, which is generated via hybridization between C. hystrix and C. sativus, is a useful model system for studying cytonuclear variation. Here, we report the chloroplast genome of allotetraploid C. ×hytivus and its diploid parents via sequencing and comparative analysis. The size of the obtained chloroplast genomes ranged from 154 673 to 155 760 bp, while their gene contents, gene orders, and GC contents were similar to each other. Comparative genome analysis supports chloroplast maternal inheritance. However, we identified 51 indels and 292 SNP genetic variants in the chloroplast genome of the allopolyploid C. ×hytivus relative to its female parent C. hystrix. Nine intergenic regions with rich variation were identified through comparative analysis of the chloroplast genomes within the subgenus Cucumis. The phylogenetic network based on the chloroplast genome sequences clarified the evolution and taxonomic position of the synthetic allotetraploid C. ×hytivus. The results of this study provide us with an insight into the changes of organelle genome after allopolyploidization, and a new understanding of the cytonuclear evolution.The accepted manuscript in pdf format is listed with the files at the bottom of this page. The presentation of the authors' names and (or) special characters in the title of the manuscript may differ slightly between what is listed on this page and what is listed in the pdf file of the accepted manuscript; that in the pdf file of the accepted manuscript is what was submitted by the author