Abstract
There is a gradual shift from representing a species’ genome by a single reference genome sequence to a pan-genome representation. Pan-genomes are the abstract representations of the genomes of all the strains that are present in the population or species. In this study, we employed a pan-genomic approach to analyze the intraspecific mitochondrial genome diversity of Fusarium graminearum. We present an improved reference mitochondrial genome for F. graminearum with an intron-exon annotation that was verified using RNA-seq data. Each of the 24 studied isolates had a distinct mitochondrial sequence. Length variation in the F. graminearum mitogenome was found to be largely due to variation of intron regions (99.98%). The “intronless” mitogenome length was found to be quite stable and could be informative when comparing species. The coding regions showed high conservation, while the variability of intergenic regions was highest. However, the most important variable parts are the intron regions, because they contain approximately half of the variable sites, make up more than half of the mitogenome, and show presence/absence variation. Furthermore, our analyses show that the mitogenome of F. graminearum is recombining, as was previously shown in F. oxysporum, indicating that mitogenome recombination is a common phenomenon in Fusarium. The majority of mitochondrial introns in F. graminearum belongs to group I introns, which are associated with homing endonuclease genes (HEGs). Mitochondrial introns containing HE genes may spread within populations through homing, where the endonuclease recognizes and cleaves the recognition site in the target gene. After cleavage of the “host” gene, it is replaced by the gene copy containing the intron with HEG. We propose to use introns unique to a population for tracking the spread of the given population, because introns can spread through vertical inheritance, recombination as well as via horizontal transfer. We demonstrate how pooled sequencing of strains can be used for mining mitogenome data. The usage of pooled sequencing offers a scalable solution for population analysis and for species level comparisons studies. This study may serve as a basis for future mitochondrial genome variability studies and representations.
Highlights
One of the most ideal markers for monitoring the distribution and spread of populations is the mitochondrial genome (Harrison, 1989; Taylor, 1986)
The re-sequencing of the mitochondrial genome of F. graminearum strain PH-1 revealed two SNPs compared to the most recent published mitogenome assembly (HG970331.1) of the strain that was based on generation sequencing reads (King et al, 2015)
Intraspecific mitochondrial genome length variations are mainly due to intron presence/absence variation, using ‘‘intronless’’ length—subtracting the length of the intron regions from the total mitogenome length—could be a valuable information when comparing species
Summary
One of the most ideal markers for monitoring the distribution and spread of populations is the mitochondrial genome (Harrison, 1989; Taylor, 1986). Due to its high copy number within individual cells, the mitochondrial genome is easy to access. The marker that was selected was a mitochondrial gene, cytochrome c oxidase I—COI or cox (Hebert et al, 2003). In Fusarium the use of cox was abandoned as a barcoding region, because the frequent presence of introns in the gene made this region impractical for PCR amplification (Gilmore et al, 2009). The difficulty in obtaining mitochondrial sequence, due to introns, lead to a general shift of interest from the mitochondrial to the nuclear genomes in fungi. De novo assembly of mitochondrial sequences from NGS data is not confounded by the presence of nuclear mitochondrial DNA segments (NUMTs), while NUMTs are known to cause problems in PCR-based barcoding (Song et al, 2008)
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