Journal ArticleDOI
MITOS: Improved de novo metazoan mitochondrial genome annotation
Matthias Bernt,Alexander Donath,Frank Jühling,Frank Jühling,Fabian Externbrink,Catherine Florentz,Guido Fritzsch,Joern Pütz,Martin Middendorf,Peter F. Stadler +9 more
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TLDR
The MITOS pipeline is designed to compute a consistent de novo annotation of the mitogenomic sequences and it is shown that the results of MITOS match RefSeq and MitoZoa in terms of annotation coverage and quality.About:
This article is published in Molecular Phylogenetics and Evolution.The article was published on 2013-11-01. It has received 3323 citations till now. The article focuses on the topics: RefSeq.read more
Citations
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Armless mitochondrial tRNAs in Enoplea (Nematoda)
TL;DR: Three lines of computational evidence support that minimal functional mt-tRNAs are indeed minimal functional, and the persistence of these sequence elements throughout several genome rearrangements that place them between different flanking genes is persistence.
Journal ArticleDOI
Fifteen shades of green: The evolution of Bufotes toads revisited.
Christophe Dufresnes,Glib Mazepa,Daniel Jablonski,Ricardo Caliari Oliveira,Tom Wenseleers,D. A. Shabanov,Markus Auer,Raffael Ernst,Claudia Koch,Héctor E. Ramírez-Chaves,Héctor E. Ramírez-Chaves,Kevin P. Mulder,Kevin P. Mulder,Kevin P. Mulder,Evgeniy Simonov,Arthur Tiutenko,Dmytro Kryvokhyzha,Paul Louis Wennekes,Oleksandr Zinenko,Oleksiy V. Korshunov,Awadh M. Al-Johany,Evgeniy A. Peregontsev,Rafaqat Masroor,Caroline Betto-Colliard,Mathieu Denoël,Leo J. Borkin,Dmitriy V. Skorinov,Roza A. Pasynkova,Lyudmila F. Mazanaeva,Juriy Rosanov,Sylvain Dubey,Spartak N. Litvinchuk +31 more
TL;DR: Across the radiation of Palearctic green toads, a stepwise progression of reproductive isolation through time is pinpointed, with a threshold below which hybridizability is irrespective of divergence, above which species barely admix and eventually evolve different mating calls, or can successfully cross-breed through allopolyploidization.
Journal ArticleDOI
Tropical ancient DNA reveals relationships of the extinct Bahamian giant tortoise Chelonoidis alburyorum
Christian Kehlmaier,Axel Barlow,Alexander K. Hastings,Melita Vamberger,Johanna L. A. Paijmans,David W. Steadman,Nancy A. Albury,Richard Franz,Michael Hofreiter,Uwe Fritz +9 more
TL;DR: In this article, the authors reconstructed the near-complete mitochondrial genome of an extinct giant tortoise from the Bahamas (Chelonoidis alburyorum) using an approximately 1, 000-year-old humerus from a water-filled sinkhole (blue hole) on Great Abaco Island.
Journal ArticleDOI
Phylogeny, evolution and mitochondrial gene order rearrangement in scale worms (Aphroditiformia, Annelida).
Yanjie Zhang,Jin Sun,Greg W. Rouse,Helena Wiklund,Fredrik Pleijel,Hiromi Watanabe,Chong Chen,Pei-Yuan Qian,Jian-Wen Qiu +8 more
TL;DR: This study provided more evidence for reconstruction of the phylogeny of Aphroditiformia, provided evidence to refute the assumption that mitochondrial gene order in Errantia is conserved, and indicated that the deep-sea extreme environment may have affected the mitochondrial genome evolution rate and gene order arrangement in Polynoidae.
Journal ArticleDOI
Mitogenomic phylogenetics of the bank vole Clethrionomys glareolus, a model system for studying end-glacial colonization of Europe
TL;DR: The mtDNA phylogeny of the bank vole Clethrionomys glareolus is revisited based on Sanger and next-generation Illumina sequencing of 32 complete mitochondrial genomes and finds little evidence of pervasive effects of deviation from neutrality on bank voles mtDNA phylogeography.
References
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Basic Local Alignment Search Tool
TL;DR: A new approach to rapid sequence comparison, basic local alignment search tool (BLAST), directly approximates alignments that optimize a measure of local similarity, the maximal segment pair (MSP) score.
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tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence.
Todd M. Lowe,Sean R. Eddy +1 more
TL;DR: A program is described, tRNAscan-SE, which identifies 99-100% of transfer RNA genes in DNA sequence while giving less than one false positive per 15 gigabases.
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NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins
TL;DR: The National Center for Biotechnology Information Reference Sequence (RefSeq) database provides a non-redundant collection of sequences representing genomic data, transcripts and proteins that pragmatically includes sequence data that are currently publicly available in the archival databases.
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Biopython: freely available Python tools for computational molecular biology and bioinformatics
Peter J. A. Cock,Tiago Antao,Jeffrey T. Chang,Brad Chapman,Cymon J. Cox,Andrew Dalke,Iddo Friedberg,Thomas Hamelryck,Frank Kauff,Bartosz Wilczyński,Michiel J. L. de Hoon +10 more
TL;DR: Biopython includes modules for reading and writing different sequence file formats and multiple sequence alignments, dealing with 3D macro molecular structures, interacting with common tools such as BLAST, ClustalW and EMBOSS, accessing key online databases, as well as providing numerical methods for statistical learning.
Journal ArticleDOI
Automatic annotation of organellar genomes with DOGMA
TL;DR: The Dual Organellar GenoMe Annotator (DOGMA) automates the annotation of organellar genomes and allows the use of BLAST searches against a custom database, and conservation of basepairing in the secondary structure of animal mitochondrial tRNAs to identify and annotate genes.
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