Abstract
BackgroundSpecies in the genus Armillaria (fungi, basidiomycota) are well-known as saprophytes and pathogens on plants. Many of them cause white-rot root disease in diverse woody plants worldwide. Mitochondrial genomes (mitogenomes) are widely used in evolutionary and population studies, but despite the importance and wide distribution of Armillaria, the complete mitogenomes have not previously been reported for this genus. Meanwhile, the well-supported phylogeny of Armillaria species provides an excellent framework in which to study variation in mitogenomes and how they have evolved over time.ResultsHere we completely sequenced, assembled, and annotated the circular mitogenomes of four species: A. borealis, A. gallica, A. sinapina, and A. solidipes (116,443, 98,896, 103,563, and 122,167 bp, respectively). The variation in mitogenome size can be explained by variable numbers of mobile genetic elements, introns, and plasmid-related sequences. Most Armillaria introns contained open reading frames (ORFs) that are related to homing endonucleases of the LAGLIDADG and GIY-YIG families. Insertions of mobile elements were also evident as fragments of plasmid-related sequences in Armillaria mitogenomes. We also found several truncated gene duplications in all four mitogenomes.ConclusionsOur study showed that fungal mitogenomes have a high degree of variation in size, gene content, and genomic organization even among closely related species of Armillara. We suggest that mobile genetic elements invading introns and intergenic sequences in the Armillaria mitogenomes have played a significant role in shaping their genome structure. The mitogenome changes we describe here are consistent with widely accepted phylogenetic relationships among the four species.
Highlights
Species in the genus Armillaria are well-known as saprophytes and pathogens on plants
We report the complete sequences of the mitogenomes of A. borealis, A. gallica, A. sinapina, and A. solidipes, and describe their organization, gene content and a comparative analysis
Among free-standing open reading frame (ORF), we found two possible homing endonuclease genes in A. sinapina, the first was located between rnl and nad4 (LAGLIDADG) and the second was between atp6 and cox3 (GIY-YIG)
Summary
Species in the genus Armillaria (fungi, basidiomycota) are well-known as saprophytes and pathogens on plants. Mitochondrial genomes (mitogenomes) are widely used in evolutionary and population studies, but despite the importance and wide distribution of Armillaria, the complete mitogenomes have not previously been reported for this genus. The genus Armillaria consists of common saprophytic and pathogenic fungi that belong to the basidiomycete family Physalacriaceae. Armillaria mitogenome in natural populations is inherited uniparentally, the potential for transient cytoplasmic mixing, heteroplasmy, and recombination exists with each mating event [9]. No Armillaria mitogenomes, have been completely annotated and described previously. We report the complete sequences of the mitogenomes of A. borealis, A. gallica, A. sinapina, and A. solidipes, and describe their organization, gene content and a comparative analysis
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