Comparative analysis of Fusarium mitochondrial genomes reveals a highly variable region that encodes an exceptionally large open reading frame

Alreedy, Rasha M.; Malireddy, Rahul; Dillman, Casey B.; Kennell, John C.

doi:10.1016/j.fgb.2011.11.008

Cited by 64 publications

(101 citation statements)

References 71 publications

(117 reference statements)

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“…The mt genomes of F. circinatum [GenBank accession number JX910419], F. verticillioides [22], and F. fujikuroi [GenBank accession number JX910420] represent circular molecules with sizes of respectively 67 106, 53 753 and 46 927 base pairs (bp), whereas those of F. graminearum, F. oxysporum and F. solani are 95 676, 34 476 bp and 62 978 bp, respectively [19,22]. The average GC content of the three GFC genomes were 31.4%, 32.6% and 32.4%, respectively, which fall within the range of what was found for the other Fusarium mt genomes [22].…”

Section: Resultsmentioning

confidence: 99%

“…It is thus not surprising that mt genomes have been used in various phylogenetic and comparative studies to resolve and/or determine evolutionary relationships between or among eukaryotes at all taxonomic levels e.g [10,11]. In the fungi, partial or whole mt genome sequence data have been used to resolve relationships among various members of the Basidiomycota [12-14], and in the Ascomycota among classes such as Schizosaccharomycetes [15], Dothideomycetes [16], Eurotiomycetes [17], as well as Sordariomycetes [18-22]. …”

Section: Introductionmentioning

confidence: 99%

“…In fact, the fully annotated mt genome for only one member of the GFC, Fusarium verticillioides (Saccardo) Nirenberg, is currently available in the public domain [22]. Because of the limited information available on the structure and evolution of mt DNAs in the GFC, the first objective of this study was, therefore, to fully characterize the mt genomes for a representative set of species.…”

Section: Introductionmentioning

confidence: 99%

“…Britz, Coutinho, Wingfield and Marasas, which is the causal agent of pine pitch canker [38] and representative of the “American” Clade; Fusarium fujikuroi Nirenberg, which is the causal agent of Bakanae disease of rice [39] and representative of the “Asian” Clade; and F. verticillioides that causes seed, root, stalk and ear rot of maize [40] and that is representative of the “African” Clade [22]. To achieve our first objective, a comparative genomic approach was used to predict and annotate genes and repeat elements in the GFC species, which allowed subsequent comparisons with those described previously within Fusarium [19,22,41] and the Sordariomycetes [18,20,21]. The second objective of this study was to determine whether the mt genomes of these fungi have any value in resolving the higher-level evolutionary relationships in the GFC.…”

Section: Introductionmentioning

confidence: 99%

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Evidence for inter-specific recombination among the mitochondrial genomes of Fusarium species in the Gibberella fujikuroi complex

et al. 2013

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BackgroundThe availability of mitochondrial genomes has allowed for the resolution of numerous questions regarding the evolutionary history of fungi and other eukaryotes. In the Gibberella fujikuroi species complex, the exact relationships among the so-called “African”, “Asian” and “American” Clades remain largely unresolved, irrespective of the markers employed. In this study, we considered the feasibility of using mitochondrial genes to infer the phylogenetic relationships among Fusarium species in this complex. The mitochondrial genomes of representatives of the three Clades (Fusarium circinatum, F. verticillioides and F. fujikuroi) were characterized and we determined whether or not the mitochondrial genomes of these fungi have value in resolving the higher level evolutionary relationships in the complex.ResultsOverall, the mitochondrial genomes of the three species displayed a high degree of synteny, with all the genes (protein coding genes, unique ORFs, ribosomal RNA and tRNA genes) in identical order and orientation, as well as introns that share similar positions within genes. The intergenic regions and introns generally contributed significantly to the size differences and diversity observed among these genomes. Phylogenetic analysis of the concatenated protein-coding dataset separated members of the Gibberella fujikuroi complex from other Fusarium species and suggested that F. fujikuroi (“Asian” Clade) is basal in the complex. However, individual mitochondrial gene trees were largely incongruent with one another and with the concatenated gene tree, because six distinct phylogenetic trees were recovered from the various single gene datasets.ConclusionThe mitochondrial genomes of Fusarium species in the Gibberella fujikuroi complex are remarkably similar to those of the previously characterized Fusarium species and Sordariomycetes. Despite apparently representing a single replicative unit, all of the genes encoded on the mitochondrial genomes of these fungi do not share the same evolutionary history. This incongruence could be due to biased selection on some genes or recombination among mitochondrial genomes. The results thus suggest that the use of individual mitochondrial genes for phylogenetic inference could mask the true relationships between species in this complex.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Evidence for inter-specific recombination among the mitochondrial genomes of Fusarium species in the Gibberella fujikuroi complex

et al. 2013

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“…There were four major clades: clade A includes four F. oxysporum strains, clade B includes F. circinatum (31 proteins) and F. verticillioides (21 proteins) (Al-Reedy et al 2012;Fourie et al 2013), clade C contains F. culmorum (60 proteins), F. gerlachii (53 proteins), and F. graminearum (50 proteins) (Cuomo et al 2007;Kulik et al 2016aKulik et al , 2016b, and clade D contains F. solani (30 proteins) (Al-Reedy et al 2012) (Figure 1). All 10 Fusarium mitogenomes encode 15 typical protein-coding genes, but they encode different numbers of LAGLIDADG endonucleases, GIY-YIG endonucleases, and hypothetical proteins.…”

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confidence: 99%

Complete mitogenome of the high ethanol production fungus Fusarium oxysporum Mh2-2

Zeng

Liu

Lin

et al. 2017

Mitochondrial DNA Part B

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Comparative analysis of the complete mitochondrial genomes of four cordyceps fungi

Zhong

Jin

Zhou

et al. 2022

Ecology and Evolution

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Cordyceps is a large group of entomogenous, medicinally important fungi. In this study, we sequenced, assembled, and annotated the entire mitochondrial genome of Ophiocordyceps xuefengensis , in addition to comparing it against other three complete cordyceps mitogenomes that were previously published. Comparative analysis indicated that the four complete mitogenomes are all composed of circular DNA molecules, although their sizes significantly differ due to high variability in intron and intergenic region sizes in the Ophiocordyceps sinensis and O . xuefengensis mitogenomes. All mitogenomes contain 14 conserved genes and two ribosomal RNA genes, but varying numbers of tRNA introns. The Ka/Ks ratios for all 14 PCGs and rps3 were all less than 1, indicating that these genes have been subject to purifying selection. Phylogenetic analysis was conducted using concatenated amino acid and nucleotide sequences of the 14 PCGs and rps3 using two different methods (Maximum Likelihood and Bayesian analysis), revealing highly supported relationships between O . xuefengensis and other Ophiocordyceps species, in addition to a close relationship with O . sinensis . Further, the analyses indicated that cox1 and rps3 play important roles in population differentiation. These mitogenomes will allow further study of the population genetics, taxonomy, and evolutionary biology of medicinally important cordyceps species.

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Comparative analysis of Fusarium mitochondrial genomes reveals a highly variable region that encodes an exceptionally large open reading frame

Cited by 64 publications

References 71 publications

Evidence for inter-specific recombination among the mitochondrial genomes of Fusarium species in the Gibberella fujikuroi complex

Evidence for inter-specific recombination among the mitochondrial genomes of Fusarium species in the Gibberella fujikuroi complex

Complete mitogenome of the high ethanol production fungus Fusarium oxysporum Mh2-2

Comparative analysis of the complete mitochondrial genomes of four cordyceps fungi

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