Chloroplast Pan-Genomes and Comparative Transcriptomics Reveal Genetic Variation and Temperature Adaptation in the...

Area of Science:

• Plant genomics
• Crop genetics
• Molecular biology

Background:

• Cucumber nuclear genomes have been extensively studied, but organelle genome information, particularly the chloroplast genome, remains largely unclear.
• The chloroplast genome is highly conserved and valuable for studying plant phylogeny, domestication, and adaptation.

Purpose of the Study:

• To construct the first cucumber chloroplast pan-genome.
• To investigate genetic variations within the cucumber chloroplast genome.
• To explore chloroplast gene expression under temperature stress.

Main Methods:

• Assembly of 50 complete chloroplast genomes from 121 cucumber germplasms.
• Comparative genomics, phylogenetic analysis, haplotype analysis, and population genetic structure analysis.
• Transcriptome analysis to study gene expression under high- and low-temperature stress.

Main Results:

• Fifty complete chloroplast genomes were assembled, exhibiting typical quadripartite structures.
• Indian ecotype cucumbers show greater genetic variation, suggesting untapped genetic resources.
• Phylogenetic analysis identified three distinct cucumber germplasm types.
• Transcriptomic analysis revealed significant upregulation of *matK* under temperature stress and higher editing efficiency of *accD* under heat stress.

Conclusions:

• Cucumber chloroplasts respond to temperature stress by regulating lipid and ribosome metabolism.
• The gene *accD* may play a role in heat tolerance.
• This study provides insights into chloroplast genome variation and adaptation mechanisms in cucumbers.