Complete chloroplast genome sequencing and comparative analysis reveals changes to the chloroplast genome after allopolyploidization in Cucumis
Allopolyploids undergo ‘genomic shock’ leading to large genetic and epigenetic modifications. Previous studies 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 to study cytonuclear variation. Here, we report the chloroplast genome of allotetraploid C. ×hytivus and its diploid parents via sequencing and comparative analysis. The obtained chloroplast genomes ranged in length from 154,673 to 155,760 bp, and their gene contents, gene orders, and GC contents were similar to each other. Comparative genome analysis support chloroplast maternally inheritance. However, we identified 51 Indels and 292 SNPs genetic variation of chloroplast genome in allopolyploid C. ×hytivus relative to its female parent C. hystrix. Nine intergenic regions with rich variation were identified through comparative chloroplast genome analysis in the Cucumis subgenus. 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.