Mobile genetic elements explain size variation in the mitochondrial genomes of four closely-related Armillaria species.

Autor: Kolesnikova AI; Laboratory of Forest Genomics, Genome Research and Education Center, Institute of Fundamental Biology and Biotechnology, Siberian Federal University, Krasnoyarsk, 660036, Russia.; Laboratory of Genomic Research and Biotechnology, Federal Research Center 'Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Sciences', Krasnoyarsk, 660036, Russia., Putintseva YA; Laboratory of Forest Genomics, Genome Research and Education Center, Institute of Fundamental Biology and Biotechnology, Siberian Federal University, Krasnoyarsk, 660036, Russia., Simonov EP; Laboratory of Genomic Research and Biotechnology, Federal Research Center 'Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Sciences', Krasnoyarsk, 660036, Russia.; Institute of Animal Systematics and Ecology, Siberian Branch of Russian Academy of Sciences, 630091, Novosibirsk, Russia., Biriukov VV; Laboratory of Forest Genomics, Genome Research and Education Center, Institute of Fundamental Biology and Biotechnology, Siberian Federal University, Krasnoyarsk, 660036, Russia.; Laboratory of Genomic Research and Biotechnology, Federal Research Center 'Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Sciences', Krasnoyarsk, 660036, Russia., Oreshkova NV; Laboratory of Forest Genomics, Genome Research and Education Center, Institute of Fundamental Biology and Biotechnology, Siberian Federal University, Krasnoyarsk, 660036, Russia.; Laboratory of Genomic Research and Biotechnology, Federal Research Center 'Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Sciences', Krasnoyarsk, 660036, Russia.; Laboratory of Forest Genetics and Selection, V. N. Sukachev Institute of Forest, Siberian Branch of Russian Academy of Sciences, Krasnoyarsk, 660036, Russia., Pavlov IN; Laboratory of Reforestation, Mycology and Plant Pathology, V. N. Sukachev Institute of Forest, Siberian Branch of Russian Academy of Sciences, Krasnoyarsk, 660036, Russia., Sharov VV; Laboratory of Forest Genomics, Genome Research and Education Center, Institute of Fundamental Biology and Biotechnology, Siberian Federal University, Krasnoyarsk, 660036, Russia.; Laboratory of Genomic Research and Biotechnology, Federal Research Center 'Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Sciences', Krasnoyarsk, 660036, Russia.; Department of High Performance Computing, Institute of Space and Information Technologies, Siberian Federal University, Krasnoyarsk, 660074, Russia., Kuzmin DA; Laboratory of Forest Genomics, Genome Research and Education Center, Institute of Fundamental Biology and Biotechnology, Siberian Federal University, Krasnoyarsk, 660036, Russia.; Department of High Performance Computing, Institute of Space and Information Technologies, Siberian Federal University, Krasnoyarsk, 660074, Russia., Anderson JB; Department of Biology, University of Toronto, Mississauga, ON, l5L 1C6, Canada., Krutovsky KV; Laboratory of Forest Genomics, Genome Research and Education Center, Institute of Fundamental Biology and Biotechnology, Siberian Federal University, Krasnoyarsk, 660036, Russia. konstantin.krutovsky@forst.uni-goettingen.de.; Department of Forest Genetics and Forest Tree Breeding, Georg-August University of Göttingen, 37077, Göttingen, Germany. konstantin.krutovsky@forst.uni-goettingen.de.; Laboratory of Population Genetics, N. I. Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119333, Russia. konstantin.krutovsky@forst.uni-goettingen.de.; Department of Ecosystem Science and Management, Texas A&M University, College Station, TX, 77843-2138, USA. konstantin.krutovsky@forst.uni-goettingen.de.
Jazyk: angličtina
Zdroj: BMC genomics [BMC Genomics] 2019 May 08; Vol. 20 (1), pp. 351. Date of Electronic Publication: 2019 May 08.
DOI: 10.1186/s12864-019-5732-z
Abstrakt: 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.
Databáze: MEDLINE
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