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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The first complete mitochondrial genome of Bactrocera tsuneonis (Miyake) (Diptera: Tephritidae) by next-generation sequencing and its phylogenetic implications.
TL;DR: This is the first report of the complete mitochondrial genome of B. tsuneonis, and it can be used in further studies of species diagnosis, evolutionary biology, prevention and control and phylogenetic analyses based on the mitochondrial genome data presented a close genetic relationship between B. Tsuneonis and B. minax.
Journal ArticleDOI
The complete mitogenomes of lobsters and crayfish (Crustacea: Decapoda: Astacidea) reveal surprising differences in closely related taxa and convergences to Priapulida
TL;DR: A huge inversion, involving more than half of the mitogenome, has been found in four freshwater crayfish species of Astacoidea and convergently in one lobster species and suggests a relative ease in the evolution of great similarities in mitochondrial gene order.
Journal ArticleDOI
Recovery and analysis of ancient beetle DNA from subfossil packrat middens using high-throughput sequencing.
Aaron D. Smith,Marcin Jan Kamiński,Marcin Jan Kamiński,Kojun Kanda,Andrew D. Sweet,Andrew D. Sweet,Julio L. Betancourt,Camille A. Holmgren,Elisabeth Hempel,Federica Alberti,Michael Hofreiter +10 more
TL;DR: The results of the first targeted investigation of insect ancient DNA to positively identify subfossil insects to species are reported, which includes the recovery of endogenous content from samples as old as ~ 34,355 ybp.
Journal ArticleDOI
The complete mitochondrial genome of Phyllidiella pustulosa (Cuvier, 1804) (Nudibranchia, Phyllidiidae)
TL;DR: Phylogenetic analysis according to protein coding genes revealed that P. pustulosa has a close relationship with Phyllidia ocellata, the first complete mitochondrial genome record for the genus Phyllidiella.
Journal ArticleDOI
Population diversity of Diaphorina citri (Hemiptera: Liviidae) in China based on whole mitochondrial genome sequences.
Fengnian Wu,Hongyan Jiang,G. Andrew C. Beattie,Paul Holford,Jianchi Chen,Christopher M. Wallis,Zheng Zheng,Xiaoling Deng,Yijing Cen +8 more
TL;DR: Mitogenome sequences analyses revealed two major phylogenetic groups of ACP present in China as well as a possible unique group present currently in Pakistan and the USA.
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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