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Mol Phylogenet Evol. 2019 Dec 15;144:106710. doi: 10.1016/j.ympev.2019.106710. [Epub ahead of print]

Hidden cases of tRNA gene duplication and remolding in mitochondrial genomes of amphipods.

Author information

1
Laboratory of Molecular Systematics, Limnological Institute, Irkutsk, Russian Federation. Electronic address: elena_romanova@lin.irk.ru.
2
Laboratory of Molecular Systematics, Limnological Institute, Irkutsk, Russian Federation; Faculty of Biology and Soil Studies, Irkutsk State University, Irkutsk, Russian Federation.
3
Belozersky Institute for Physicochemical Biology, Lomonosov Moscow State University, Moscow, Russian Federation; Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russian Federation.

Abstract

The evolution of tRNA genes in mitochondrial (mt) genomes is a complex process that includes duplications, degenerations, and transpositions, as well as a specific process of identity change through mutations in the anticodon (tRNA gene remolding or tRNA gene recruitment). Using amphipod-specific tRNA models for annotation, we show that tRNA duplications are more common in the mt genomes of amphipods than what was revealed by previous annotations. Seventeen cases of tRNA gene duplications were detected in the mt genomes of amphipods, and ten of them were tRNA genes that underwent remolding. The additional tRNA gene findings were verified using phylogenetic analysis and genetic distance analysis. The majority of remolded tRNA genes (seven out of ten cases) were found in the mt genomes of endemic amphipod species from Lake Baikal. All additional mt tRNA genes arose independently in the Baikalian amphipods, indicating the unusual plasticity of tRNA gene evolution in these species assemblages. The possible reasons for the unusual abundance of additional tRNA genes in the mt genomes of Baikalian amphipods are discussed. The amphipod-specific tRNA models developed for MiTFi refine existing predictions of tRNA genes in amphipods and reveal additional cases of duplicated tRNA genes overlooked by using less specific Metazoa-wide models. The application of these models for mt tRNA gene prediction will be useful for the correct annotation of mt genomes of amphipods and probably other crustaceans.

KEYWORDS:

Amphipods; Anticodon; Baikal; Mitochondrial genome; tRNA gene remolding

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