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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The complete mitochondrial genome of the grooved carpet shell, Ruditapes decussatus (Bivalvia, Veneridae)
Fabrizio Ghiselli,Liliana Milani,Mariangela Iannello,Emanuele Procopio,Peter L. Chang,Sergey V. Nuzhdin,Marco Passamonti +6 more
TL;DR: The complete mitochondrial genome of the grooved carpet shell, Ruditapes decussatus, also known as the European clam, is reported for the first time, and is more genetically similar to species of the Genus Paphia than to the congeneric Ruditape philippinarum, a finding that bolsters the already-proposed need of a taxonomic revision.
Journal ArticleDOI
Complete mitogenome of tea green leafhopper, Empoasca onukii (Hemiptera: Cicadellidae) from Anshun, Guizhou Province in China
TL;DR: The complete mitogenome of E. onukii can provide essential DNA molecular data for further phylogenetic and evolutionary analysis and showed that it is closely related to E. vitis with high bootstrap value supported.
Journal ArticleDOI
Mitochondrial Genome Polymorphisms in the Human Pathogenic Fungus Cryptococcus neoformans.
Yue Wang,Jianping Xu +1 more
TL;DR: A dynamic evolution of mitochondrial genomes in this important human fungal pathogen is revealed and the combined mitogenome exon-based phylogeny and intron distributions suggested that clades VNI, VNII and VNB could be further divided into sub-clades.
Journal ArticleDOI
Mitochondrial genome plasticity among species of the nematode genus Meloidogyne (Nematoda: Tylenchina)
TL;DR: A comparison of the mt genome architecture in plant-parasitic nematodes and phylogenetic analyses support that Pratylenchus is the most recent ancestor of root-knot nematode species, M. javanica.
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Mitochondrial genome of the Christmas tree worm Spirobranchus giganteus (Annelida: Serpulidae) reveals a high substitution rate among annelids.
TL;DR: It is shown that mitochondrial gene order rearrangements can directly correlate to variations in gene length, consistent with a faster rate of mitochondrial sequence evolution in S. giganteus.
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.
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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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