title: Bioinformatics analysis of plant orthologous introns: identification of an intronic tRNA-like sequence.
abstract: Orthologous introns have identical positions relative to the coding sequence in orthologous genes of different species. By analyzing the complete genomes of five plants we generated a database of 40,512 orthologous intron groups of dicotyledonous plants, 28,519 orthologous intron groups of angiosperms, and 15,726 of land plants (moss and angiosperms). Multiple sequence alignments of each orthologous intron group were obtained using the Mafft algorithm. The number of conserved regions in plant introns appeared to be hundreds of times fewer than that in mammals or vertebrates. Approximately three quarters of conserved intronic regions among angiosperms and dicots, in particular, correspond to alternatively-spliced exonic sequences. We registered only a handful of conserved intronic ncRNAs of flowering plants. However, the most evolutionarily conserved intronic region, which is ubiquitous for all plants examined in this study, including moss, possessed multiple structural features of tRNAs, which caused us to classify it as a putative tRNA-like ncRNA. Intronic sequences encoding tRNA-like structures are not unique to plants. Bioinformatics examination of the presence of tRNA inside introns revealed an unusually long-term association of four glycine tRNAs inside the Vac14 gene of fish, amniotes, and mammals.
authors.affiliation: Faculty of Biology and Soil Science, St. Petersburg State University, St. Petersburg 199034, Russia; Program in Bioinformatics and Proteomics/Genomics, University of Toledo, Health Science Campus, Toledo, OH 43614, USA. Electronic address: akkuratov.evgeny@gmail.com.
authors.forename: Evgeny E
authors.initials: EE
authors.lastname: Akkuratov
authors.affiliation: Program in Bioinformatics and Proteomics/Genomics, University of Toledo, Health Science Campus, Toledo, OH 43614, USA; Department of Bioengineering, University of Toledo, Main Campus, Toledo, OH 43606, USA. Electronic address: lorraine.walters@rockets.utoledo.edu.
authors.forename: Lorraine
authors.initials: L
authors.lastname: Walters
authors.affiliation: Program in Bioinformatics and Proteomics/Genomics, University of Toledo, Health Science Campus, Toledo, OH 43614, USA. Electronic address: asahaman@ucalgary.ca.
authors.forename: Arnab
authors.initials: A
authors.lastname: Saha-Mandal
authors.affiliation: Department of Biological Sciences, University of Toledo, Main Campus, Toledo, OH 43606, USA. Electronic address: sushant43606@yahoo.com.
authors.forename: Sushant
authors.initials: S
authors.lastname: Khandekar
authors.affiliation: Department of Medicine, University of Toledo, Health Science Campus, Toledo, OH 43614, USA. Electronic address: erin.crawford@utoledo.edu.
authors.forename: Erin
authors.initials: E
authors.lastname: Crawford
authors.affiliation: Department of Mathematics and Statistics, Bowling Green State University, Bowling Green, OH 43403, USA. Electronic address: zirbel@bgsu.edu.
authors.forename: Craig L
authors.initials: CL
authors.lastname: Zirbel
authors.affiliation: Department of Biological Sciences, University of Toledo, Main Campus, Toledo, OH 43606, USA. Electronic address: scott.leisner@utoledo.edu.
authors.forename: Scott
authors.initials: S
authors.lastname: Leisner
authors.affiliation: Department of Medicine, University of Toledo, Health Science Campus, Toledo, OH 43614, USA. Electronic address: ashwin.prakash@jhmi.edu.
authors.forename: Ashwin
authors.initials: A
authors.lastname: Prakash
authors.affiliation: Department of Medicine, University of Toledo, Health Science Campus, Toledo, OH 43614, USA. Electronic address: lvfedorova3@gmail.com.
authors.forename: Larisa
authors.initials: L
authors.lastname: Fedorova
authors.affiliation: Program in Bioinformatics and Proteomics/Genomics, University of Toledo, Health Science Campus, Toledo, OH 43614, USA; Department of Medicine, University of Toledo, Health Science Campus, Toledo, OH 43614, USA. Electronic address: Alexei.fedorov@utoledo.edu.
authors.forename: Alexei
authors.initials: A
authors.lastname: Fedorov
mesh_terms: D000465:Algorithms; D000818:Animals; D017360:Arabidopsis / Q000235:genetics / Q000254:growth & development; D001483:Base Sequence; D044002:Bryophyta / Q000235:genetics; D019295:Computational Biology / Q000379:methods; D017124:Conserved Sequence; D030541:Databases, Genetic; D035264:Flowers / Q000235:genetics; D018745:Genome, Plant; D006801:Humans; D007438:Introns; D019684:Magnoliopsida / Q000235:genetics*; D051379:Mice; D008969:Molecular Sequence Data; D012275:Oryza / Q000235:genetics; D010802:Phylogeny; D032107:Populus / Q000235:genetics; D018749:RNA, Plant / Q000737:chemistry; D012343:RNA, Transfer / Q000235:genetics; D027843:Vitis / Q000235:genetics
chemical_list: D018749:RNA, Plant; D012343:RNA, Transfer
keywords: Computational biology; Genomics; MALAT1; mascRNA