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
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Five new mitogenomes of Phylloscopus (Passeriformes, Phylloscopidae): Sequence, structure, and phylogenetic analyses.
TL;DR: Gene order and genome organization information is useful to understand evolutionary relationships among Phylloscopus species and provide genetic markers for species identification, population genetics, and phylogeographic studies of birds.
Journal ArticleDOI
Species delimitation and mitogenome phylogenetics in the subterranean genus Pseudoniphargus (Crustacea: Amphipoda)
TL;DR: The results show that the current distribution pattern of Pseudoniphargus resulted from a complex admix of relatively ancient vicariance events and several episodes of long- distance dispersal.
Journal ArticleDOI
The mitogenomes of two saprophytic Boletales species (Coniophora) reveals intron dynamics and accumulation of plasmid-derived and non-conserved genes.
Peng Wu,Zhijie Bao,Wenying Tu,Lijiao Li,Chuan Xiong,Xin Jin,Ping Li,Mingying Gui,Wenli Huang,Qiang Li +9 more
TL;DR: In this article, the complete mitogenomes of two saprophytic Boletales species, Coniophora olivacea, and C. puteana, were assembled and compared with mitogenome of ectomycorrhizal Boletsales.
Journal ArticleDOI
First complete female mitochondrial genome in four bivalve species genus Donax and their phylogenetic relationships within the Veneroida order.
Jenyfer Fernández-Pérez,Ana Nantón,Francisco J. Ruiz-Ruano,Juan Pedro M. Camacho,Josefina Méndez +4 more
TL;DR: The complete female mitochondrial genomes of the four species vary in size from 17,044 to 17,365 bp, and encode 13 protein-coding genes (including the atp8 gene), 2 rRNAs and 22 tRNAs, all located on the same strand as discussed by the authors.
Journal ArticleDOI
Towards a comprehensive picture of alloacceptor tRNA remolding in metazoan mitochondrial genomes
Abdullah H. Sahyoun,Martin Hölzer,Frank Jühling,Christian Höner zu Siederdissen,Marwa Al-Arab,Kifah Tout,Manja Marz,Martin Middendorf,Peter F. Stadler,Matthias Bernt +9 more
TL;DR: Novel methods to detect tRNA remolding in large-scale data sets and apply them to survey tRNAs remolding throughout animal evolution are described.
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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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
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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.
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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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