Detection of the extra tRNA genes in mitochondrial genomes of amphipods using lineage-specific models

  • Romanova E.V. 1
  • Bukin Y.S. 1, 2
  • Mikhailov K.V. 3, 4
  • Logacheva M.D. 3, 4
  • Aleoshin V.V. 3, 4
  • Sherbakov D.Yu. 1, 2
  • 1 Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Ulan-Batorskaya Str., 3, Irkutsk, 664033, Russia
    2 Faculty of Biology and Soil Studies, Irkutsk State University, Sukhe-Bator Str., 5, Irkutsk, 664011, Russia
    3 Belozersky Institute for Physicochemical Biology, Lomonosov Moscow State University, Moscow, Leninskye gory, house 1, building 40, 119992, Russia
    4 Institute for Information Transmission Problems, Bolshoy Karetny per. 19, building 1, Moscow, 127051, Russia
Keywords: tRNA gene, mitochondrial genome, tRNA gene remolding, amphipods, Baikal

Abstract

We developed and applied models for tRNA genes prediction in mitochondrial (mt) genomes of amphipods. Using these models, we refined annotation of available mt genomes of amphipod species by finding 16 new tRNA genes in total. Phylogenetic inference and genetic distance analysis allowed to verify these findings and to identify cases of tRNA gene remolding. The majority remolded tRNA genes (seven out of ten) were found in mt genomes of Baikalian amphipods. The effectivity of amphipod-specific models for tRNA genes prediction in MiTFi program implies potential usefulness of other lineage-specific tRNA models for correct annotation of mt genomes of other organisms.
Published
2020-09-07
Section
Articles