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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A mitochondrial genome of Micronectidae and implications for its phylogenetic position.
TL;DR: The results supported the phylogenetic analysis of PCG 12 and PCG12RT in Nepomorpha and showed that the third codon positions of PCGs were not suitable for addressing relationships at the superfamily level in NepOMorpha.
Journal ArticleDOI
The complete mitochondrial genome of the storage mite pest Tyrophagus fanetzhangorum (Acari: Acaridae)
Xuan Su,Yu Fang,Jiao-Yang Xu,Weixi Fang,Xue-Bing Zhan,Ying Fang,Ling-Miao Chu,Rui Feng,Yue-Long Jin,Entao Sun +9 more
TL;DR: The complete mitochondrial genome of Tyrophagus fanetzhangorum is sequenced and a typical set of mt tRNA genes (22 tRNAs) are found and Phylogenetic analysis shows that T. fanetzangorum are more closely related to T. putrescentiae than toT.
Journal ArticleDOI
Full Mitochondrial Genome Sequence of the Sugar Beet Wireworm Limonius californicus (Coleoptera: Elateridae), a Common Agricultural Pest
Alida T. Gerritsen,Daniel D. New,Barrie D. Robison,Arash Rashed,Paul A. Hohenlohe,Larry J. Forney,Mahnaz Rashidi,Cathy M. Wilson,Matthew L. Settles +8 more
TL;DR: The mitochondrial genome sequence of Limonius californicus, a species of click beetle that is an agricultural pest in its larval form, is reported here and contains 13 protein-coding genes, 2 rRNA genes, and 22 tRNA genes.
Journal ArticleDOI
The complete mitochondrial genome of Bombyx lemeepauli (Lepidoptera: Bombycidae) and its phylogenetic relationship.
TL;DR: The complete mitogenome sequence provided here would be useful for further understanding the evolutional position of B. lemeepauli, which is a key species to relate the famous resource insect B. mori and the important insect pest Rondotia menciana.
Journal ArticleDOI
Phylogenomics for Chagas Disease Vectors of the Rhodnius Genus (Hemiptera, Triatominae): What We Learn From Mito-Nuclear Conflicts and Recommendations
Jonathan Filée,Marie Merle,Héloïse Bastide,Florence Mougel,Jean-Michel Berenger,Elaine Folly-Ramos,Carlos Eduardo Almeida,Myriam Harry +7 more
TL;DR: Molecular data consistently supports the clustering of the pictipes and pallescens groups, more related to each other than they are to the prolixus group, and performs separate mitochondrial and nuclear phylogenies and takes advantages of mito-nuclear conflicts in order to have a comprehensive evolutionary vision of this genus.
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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