Multichromosomal structure of the onion mitochondrial genome and a transcript analysis

Area of Science:

• Plant molecular biology
• Genomics
• Organelle genetics

Background:

• Plant mitochondrial genomes are notably complex due to extensive repetitive sequences and recombination.
• Cytoplasmic male sterility (CMS) in onions is linked to mitochondrial genome variations, but differences between strains and transcript analyses are underexplored.
• Previous studies reported the onion mitochondrial genome sequence but lacked detailed structural and transcriptomic analyses.

Purpose of the Study:

• To elucidate the complex mitochondrial genome structure of the onion variety "Momiji-3" with CMS-S cytoplasm.
• To identify RNA-editing sites and analyze gene expression within the mitochondrial genome.
• To investigate the role of specific genes, such as orf725, in CMS.

Main Methods:

• Next-generation sequencing (NGS) for whole-genome analysis.
• Pulsed field gel electrophoresis (PFGE) for visualizing mitochondrial genome structure.
• Transcriptome mapping to identify RNA-editing sites and gene expression levels.

Main Results:

• The "Momiji-3" mitochondrial genome was visualized as three main circular molecules, revealing its complex structure.
• 635 RNA-editing sites were identified in gene-coding regions, with six genes showing editing that created start/stop codons.
• Novel open reading frames (ORFs) exhibited low transcript levels, and orf725 was confirmed as a candidate gene for CMS.

Conclusions:

• The study provides the first visualization of the "Momiji-3" onion mitochondrial genome structure, offering insights into complex plant mitochondrial genomics.
• RNA editing significantly impacts gene function in the onion mitochondrial genome, creating functional start and stop codons.
• The candidate gene for cytoplasmic male sterility (CMS) in "Momiji-3" is likely orf725, with no evidence of newly evolved functional genes.