Multichromosomal structure of the onion mitochondrial genome and a transcript analysis

Abstract

The structures of plant mitochondrial genomes are more complex than those of animals. One of the reasons for this is that plant mitochondrial genomes typically have many long and short repeated sequences and intra- and intermolecular recombination may create various DNA molecules in this organelle. Recombination may sometimes create a novel gene that causes cytoplasmic male sterility (CMS). The onion has several cytoplasm types, with some causing CMS while others do not. The complete mitochondrial genome sequence of the onion was reported for an inbred line with CMS-S cytoplasm; however, the number of differences between onion strains remains unclear, and studies on purified mitochondrial DNA (mtDNA) have not yet been performed. Furthermore, analyses of transcripts in the mitochondrial genome have not been conducted. In the present study, we examined the mitochondrial genome of the onion variety "Momiji-3" (Allium cepa L.) possessing CMS-S-type cytoplasm using next-generation sequencing (NGS). The "Momiji-3" mitochondrial genome mainly exists as three circles as a result of recombination through repeated sequences and we herein succeeded for the first time in visualizing its structure using pulsed field gel electrophoresis (PFGE). The ability to clarify the structure of the mitochondrial genome is rare in plant mitochondria; therefore, "Momiji-3" represents a good example for elucidating complex plant mitochondrial genomes. We also mapped transcript data to the mitochondrial genome in order to identify the RNA-editing positions in all gene-coding regions and estimate the expression levels of genes. We identified 635 editing positions in gene-coding regions. Start and stop codons were created by RNA editing in six genes (nad1, nad4L, atp6, atp9, ccmFC, and orf725). The transcript amounts of novel open reading frames (ORFs) were all markedly lower than those of functional genes. These results suggest that a new functional gene was not present in the mitochondrial genome of "Momiji-3", and that the candidate gene for CMS is orf725, as previously reported.

Mitochondrial Genome of Fagus sylvatica L. as a Source for Taxonomic Marker Development in the Fagales

“…Because of the highly dynamic structure of mitochondrial genomes of angiosperms, alignments of complete mitochondrial genome sequences make sense only in very closely related individuals. Recombination activities involving repeated sequences may generate subgenomic forms and extensive structural variation of angiosperm mitochondrial genomes even within the same species [ 11 , 12 , 14 , 15 , 17 , 19 , 26 , 29 , 30 , 31 , 32 , 33 , 34 ].…”

“…The mitochondrial genome sequences of angiosperms generally have one or more pairs of large nontandem repeats (interspersed repeats) that can act as sites for inter- and intramolecular recombination, leading to multiple alternative arrangements (isoforms; including subgenomic forms) within a species [ 19 ]. Although plant mitochondrial genomes are often assembled and displayed as circular maps, plant mitochondrial DNA (mtDNA) does most likely not exist as one large circular DNA molecule but mostly as a complex and dynamic collection of linear DNA with combinations of smaller circular and branched DNA molecules [ 12 , 14 , 15 , 17 , 19 , 26 , 29 , 30 , 31 , 32 , 33 , 34 ].…”

Omics approaches inAlliumresearch: Progress and way ahead

“…The mitochondrial genome of the CMS-S-type onion variety “Momiji-3” was characterized which have a multi-chromosomal structure resulting from recombination events. Examination of transcript data revealed RNA editing at 635 positions, and a candidate gene for CMS in “Momiji-3” was also found to be orf725 ( Tsujimura et al, 2019 ) . Similarly, Kim, Yang & Kim (2019) compared the mitochondrial genome of two recently diverged cytoplasms—male-fertile and male-sterile CMS-T-like cytoplasms and obtained almost identical sequences.…”

Peer Review #1 of "The sugarcane mitochondrial genome: assembly, phylogenetics and transcriptomics (v0.1)"

“…Unlike in eukaryotic genomes, splice sites were clustered at genomic loci (Figure 4, Supplemental Table S3) and almost 50% of splice sites were within coding regions. Recently (Tsujimura et al, 2018) reported on the three mitochondrial chromosomes of Allium cepa (onion) CMS line Momiji-3. However, unlike in sugarcane the mitochondrial sub-circles of onion can combine into a master circle through recombination at long repeats.…”

“…Indeed, though the plant mitochondrial genome structure is often portrayed as a circle, micrograph studies reveal that the true physical structure of the mitogenome appears to be a variety of circles, linear molecules, and complex branching structures (Backert, Nielsen & Börner1997;Backert & Börner 2000). While many plant species appear have a single master circle representation of their mitochondrial genome, others are composed of more than a hundred circular chromosomes (Sloan et al, 2012) and two independent chromosomes as in Allium cepa (Tsujimura et al, 2018). The precise mechanism of how plant mitochondria replicate and maintain their DNA is not yet fully understood (Cupp & Nielsen 2014) but it is hypothesized that recombination-dependent replication plays a role, giving a functional role to the repeat sequences often observed in mitochondria (Gualberto et al, 2014).…”