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

BMC Genomics

James B. Anderson¹  Vladislav V. Biriukov²  Dmitry A. Kuzmin²  Konstantin V. Krutovsky²  Yuliya A. Putintseva²  Natalya V. Oreshkova²  Vadim V. Sharov²  Anna I. Kolesnikova²  Evgeniy P. Simonov³  Igor N. Pavlov⁴ 

[1] Department of Biology, University of Toronto;Laboratory of Forest Genomics, Genome Research and Education Center, Institute of Fundamental Biology and Biotechnology, Siberian Federal University;Laboratory of Genomic Research and Biotechnology, Federal Research Center “Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Sciences”;Laboratory of Reforestation, Mycology and Plant Pathology, V. N. Sukachev Institute of Forest, Siberian Branch of Russian Academy of Sciences;

关键词: Armillaria;    Duplications;    Evolution;    GIY-YIG;    Homing endonucleases;    Introns;   

DOI  :  10.1186/s12864-019-5732-z

来源: DOAJ

【 摘 要 】

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.

【 授权许可】

Unknown