Open Access
Open access
PeerJ, volume 6, pages e5963

First steps towards mitochondrial pan-genomics: detailed analysis of Fusarium graminearum mitogenomes

Balázs Brankovics 1, 2, 3
Tomasz Kulik 4
Jakub Sawicki 4
Katarzyna Bilska 4
Hao Zhang 5
G. Sybren de Hoog 2, 3
Theo AJ van der Lee 1
Cees Waalwijk 1
Anne D. van Diepeningen 1, 2
Show full list: 9 authors
2
 
Westerdijk Fungal Biodiversity Institute, Utrecht, Netherlands
5
 
State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agriculture Sciences, Beijing, P.R. China
Publication typeJournal Article
Publication date2018-12-19
Journal: PeerJ
scimago Q1
SJR0.623
CiteScore4.7
Impact factor2.3
ISSN21678359
PubMed ID:  30588394
General Biochemistry, Genetics and Molecular Biology
General Medicine
General Agricultural and Biological Sciences
General Neuroscience
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.

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