Accurate annotation of protein-coding genes in mitochondrial genomes

Marwa Al Arab; Christian Höner Zu Siederdissen; Kifah Tout; Abdullah H Sahyoun; Peter F Stadler; Matthias Bernt

doi:10.1016/j.ympev.2016.09.024

Accurate annotation of protein-coding genes in mitochondrial genomes

Mol Phylogenet Evol. 2017 Jan:106:209-216. doi: 10.1016/j.ympev.2016.09.024. Epub 2016 Sep 28.

Authors

Marwa Al Arab¹, Christian Höner Zu Siederdissen², Kifah Tout³, Abdullah H Sahyoun⁴, Peter F Stadler⁵, Matthias Bernt⁶

Affiliations

¹ Bioinformatics Group, Department of Computer Science University of Leipzig, Härtelstraße 16-18, D-04107 Leipzig, Germany; Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstraße 16-18, D-04107 Leipzig, Germany; Doctoral School of Science and Technology, AZM Center for Biotechnology Research, Lebanese University, Tripoli, Lebanon. Electronic address: [email protected].
² Bioinformatics Group, Department of Computer Science University of Leipzig, Härtelstraße 16-18, D-04107 Leipzig, Germany; Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstraße 16-18, D-04107 Leipzig, Germany; Institute for Theoretical Chemistry, University of Vienna, Währingerstraße 17, A-1090 Wien, Austria. Electronic address: [email protected].
³ Doctoral School of Science and Technology, AZM Center for Biotechnology Research, Lebanese University, Tripoli, Lebanon. Electronic address: [email protected].
⁴ Bioinformatics Group, Department of Computer Science University of Leipzig, Härtelstraße 16-18, D-04107 Leipzig, Germany; Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstraße 16-18, D-04107 Leipzig, Germany; Doctoral School of Science and Technology, AZM Center for Biotechnology Research, Lebanese University, Tripoli, Lebanon; TRON - Translational Oncology at the University Medical Center of the Johannes Gutenberg University Mainz gGmbH, Mainz, Germany. Electronic address: [email protected].
⁵ Bioinformatics Group, Department of Computer Science University of Leipzig, Härtelstraße 16-18, D-04107 Leipzig, Germany; Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstraße 16-18, D-04107 Leipzig, Germany; Institute for Theoretical Chemistry, University of Vienna, Währingerstraße 17, A-1090 Wien, Austria; Max Planck Institute for Mathematics in the Sciences, Inselstraße 22, D-04103 Leipzig, Germany; Fraunhofer Institut für Zelltherapie und Immunologie, Perlickstraße 1, D-04103 Leipzig, Germany; Center for Non-Coding RNA in Technology and Health, University of Copenhagen, Grønnegårdsvej 3, DK-1870 Frederiksberg C, Denmark; Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe, NM 87501, United States. Electronic address: [email protected].
⁶ Bioinformatics Group, Department of Computer Science University of Leipzig, Härtelstraße 16-18, D-04107 Leipzig, Germany; Parallel Computing and Complex Systems Group, Department of Computer Science, University of Leipzig, Augustusplatz 10, D-04103 Leipzig, Germany. Electronic address: [email protected].

PMID: 27693569
DOI: 10.1016/j.ympev.2016.09.024

Abstract

Mitochondrial genome sequences are available in large number and new sequences become published nowadays with increasing pace. Fast, automatic, consistent, and high quality annotations are a prerequisite for downstream analyses. Therefore, we present an automated pipeline for fast de novo annotation of mitochondrial protein-coding genes. The annotation is based on enhanced phylogeny-aware hidden Markov models (HMMs). The pipeline builds taxon-specific enhanced multiple sequence alignments (MSA) of already annotated sequences and corresponding HMMs using an approximation of the phylogeny. The MSAs are enhanced by fixing unannotated frameshifts, purging of wrong sequences, and removal of non-conserved columns from both ends. A comparison with reference annotations highlights the high quality of the results. The frameshift correction method predicts a large number of frameshifts, many of which are unknown. A detailed analysis of the frameshifts in nad3 of the Archosauria-Testudines group has been conducted.

Keywords: Annotation; Hidden Markov models; Metazoa; Mitochondrial DNA; Protein coding genes.

MeSH terms

Animals
Base Sequence
Birds / classification
DNA, Mitochondrial / chemistry
DNA, Mitochondrial / classification
DNA, Mitochondrial / metabolism
Databases, Genetic
Frameshift Mutation
Genome, Mitochondrial*
Markov Chains
Mitochondrial Proteins / chemistry
Mitochondrial Proteins / classification
Mitochondrial Proteins / genetics
Mitochondrial Proteins / metabolism
Molecular Sequence Data
Phylogeny
Reptiles / classification
Sequence Alignment

Substances

DNA, Mitochondrial
Mitochondrial Proteins