Moss Phylogeny Reconstruction Using Nucleotide Pangenome of Complete Mitogenome Sequences

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D. V. Goryunov¹, B. E. Nagaev^1,2, M. Yu. Nikolaev², A. V. Alexeevski^1,2,3, and A. V. Troitsky^1*

¹Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia; fax: +7 (495) 939-3181; E-mail: bobr@belozersky.msu.ru

²Lomonosov Moscow State University, Faculty of Bioengineering and Bioinformatics, 119991 Moscow, Russia; E-mail: aba@belozersky.msu.ru

³Scientific Research Institute for System Studies, Russian Academy of Sciences, 117281 Moscow, Russia

^* To whom correspondence should be addressed.

Received July 6, 2015; Revision received September 6, 2015

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Stability of composition and sequence of genes was shown earlier in 13 mitochondrial genomes of mosses (Rensing, S. A., et al. (2008) Science, 319, 64-69). It is of interest to study the evolution of mitochondrial genomes not only at the gene level, but also on the level of nucleotide sequences. To do this, we have constructed a “nucleotide pangenome” for mitochondrial genomes of 24 moss species. The nucleotide pangenome is a set of aligned nucleotide sequences of orthologous genome fragments covering the totality of all genomes. The nucleotide pangenome was constructed using specially developed new software, NPG-explorer (NPGe). The stable part of the mitochondrial genome (232 stable blocks) is shown to be, on average, 45% of its length. In the joint alignment of stable blocks, 82% of positions are conserved. The phylogenetic tree constructed with the NPGe program is in good correlation with other phylogenetic reconstructions. With the NPGe program, 30 blocks have been identified with repeats no shorter than 50 bp. The maximal length of a block with repeats is 140 bp. Duplications in the mitochondrial genomes of mosses are rare. On average, the genome contains about 500 bp in large duplications. The total length of insertions and deletions was determined in each genome. The losses and gains of DNA regions are rather active in mitochondrial genomes of mosses, and such rearrangements presumably can be used as additional markers in the reconstruction of phylogeny.

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KEY WORDS: mosses, phylogeny, pangenome, mitochondrial genome

DOI: 10.1134/S0006297915110152

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