Mobile genetic elements explain size variation in the mitochondrial genomes of four closely-related Armillaria species
2019 | journal article. A publication with affiliation to the University of Göttingen.
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Mobile genetic elements explain size variation in the mitochondrial genomes of four closely-related Armillaria species
Kolesnikova, A. I.; Putintseva, Y. A.; Simonov, E. P.; Biriukov, V. V.; Oreshkova, N. V.; Pavlov, I. N. & Sharov, V. V. et al. (2019)
BMC Genomics, 20(1) art. 351. DOI: https://doi.org/10.1186/s12864-019-5732-z
Documents & Media
12864_2019_Article_5732.pdf2.27 MBAdobe PDFTandem repeats detected in four Armillaria mitogenomes using Tandem Repeats Finder14.73 kBMicrosoft Excel XMLMicrosatellite or simples equence repeat (SSR) loci in four Armillaria mitogenomes11.49 kBMicrosoft Excel XMLComparison of codon usage of 14 oxidative phosphorylation genes and the codon-anticodon recognition pattern of tRNA genes identified in A. borealis, A. gallica, A. sinapina, and A. solidipes. The number of plus signs indicates the presence and numbers of the respective tRNA gene17.64 kBMicrosoft Excel XMLClassification of introns in mitogenomes of four Armillaria species9.97 kBMicrosoft Excel XMLMapping Armillaria transcriptome reads on mitogenomes14.31 kBMicrosoft Word XMLNames and accession numbers for 21 Basidiomycota species downloaded from GenBank and used for phylogenetic analysis9 kBMicrosoft Excel XML
Details
- Authors
- Kolesnikova, Anna I.; Putintseva, Yuliya A.; Simonov, Evgeniy P.; Biriukov, Vladislav V.; Oreshkova, Natalya V.; Pavlov, Igor N.; Sharov, Vadim V.; Kuzmin, Dmitry A.; Anderson, James B.; Krutovsky, Konstantin V.
- Abstract
- Background Species 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. Results Here 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. Conclusions Our 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.
- Issue Date
- 2019
- Journal
- BMC Genomics
- Organization
- Fakultät für Forstwissenschaften und Waldökologie ; Büsgen-Institut ; Abteilung Forstgenetik und Forstpflanzenzüchtung
- Extent
- 14
- Language
- English