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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Mitochondrial phylogenomics and genome rearrangements in the barklice (Insecta: Psocodea)
Kazunori Yoshizawa,Kevin P. Johnson,Andrew D. Sweet,Izumi Yao,Rodrigo Lopes Ferreira,Stephen L. Cameron +5 more
TL;DR: The tree estimated from the mitochondrial genomic data was well resolved, strongly supported, and in agreement with previously estimated phylogenies, and provided the first robust support for the family Prionoglarididae, as its monophyly was uncertain in previous morphological and molecular studies.
Journal ArticleDOI
Characterization and comparative analysis of six complete mitochondrial genomes from ectomycorrhizal fungi of the Lactarius genus and phylogenetic analysis of the Agaricomycetes
TL;DR: This study provides the first report of mitogenomes from Lactarius and promotes further understanding of the genetics, evolution, and phylogenetic relationships of this important ectomycorrhizal fungal genus.
Journal ArticleDOI
Complete mitochondrial genomes of Anopheles stephensi and An. dirus and comparative evolutionary mitochondriomics of 50 mosquitoes
You Jin Hao,Yi Lin Zou,Yi Ran Ding,Wenyue Xu,Zhen Tian Yan,Xu-Dong Li,Wen Bo Fu,Ting Jing Li,Bin Chen +8 more
TL;DR: This is the first comprehensive study of mosquito mitogenomes, which are effective for mosquito phylogeny at various taxonomic levels and strongly support the monophyly of subgenera Cellia, Anopheles, Keterszia and Nyssorhynchus.
Journal ArticleDOI
Shotgun assembly of the assassin bug Brontostoma colossus mitochondrial genome (Heteroptera, Reduviidae).
Arthur Kocher,Maria Kamilari,Maria Kamilari,Emeline Lhuillier,Eric Coissac,Julie Péneau,Jérôme Chave,Jérôme Murienne +7 more
TL;DR: A phylogenetic analysis based on 55 true bug mitogenomes confirmed that B. colossus belongs to Reduviidae, but contradicted a widely accepted hypothesis, highlighting the limits of phylogenetic analyses based on mitochondrial data only.
Journal ArticleDOI
Mitochondrial Genome Sequence of the Scabies Mite Provides Insight into the Genetic Diversity of Individual Scabies Infections
Ehtesham Mofiz,Ehtesham Mofiz,Torsten Seemann,Melanie Bahlo,Melanie Bahlo,Deborah C. Holt,Bart J. Currie,Katja Fischer,Anthony T. Papenfuss +8 more
TL;DR: The mitochondrial genome of the scabies mite is described and a new de novo assembly pipeline based on a bait-and-reassemble strategy which produced a 14 kilobase mitochondrial genome sequence assembly is developed, supporting earlier findings that only limited genetic differences may separate some human and animal varieties.
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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