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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Complete Mitochondrial Genome of Dinorhynchus dybowskyi (Hemiptera: Pentatomidae: Asopinae) and Phylogenetic Analysis of Pentatomomorpha Species.
TL;DR: The complete mitochondrial genome (mitogenome) of Dinorhynchus dybowskyi was sequenced using the next-generation sequencing technology, and the results support the monophyly of five superfamilies Aradoidea, PentatomoideA, Pyrrhocoroidesa, Lygaeoidea), and Coreoidesa.
Journal ArticleDOI
Signatures of the Evolution of Parthenogenesis and Cryptobiosis in the Genomes of Panagrolaimid Nematodes.
Philipp H. Schiffer,Philipp H. Schiffer,Etienne Danchin,Ann M. Burnell,Christopher J. Creevey,Simon Wong,Ilona Dix,Georgina O’Mahony,Bridget A. Culleton,Corinne Rancurel,Gary Stier,Elizabeth A. Martínez-Salazar,Aleksandra Marconi,Urmi Trivedi,Michael Kroiher,Michael A. S. Thorne,Einhard Schierenberg,Thomas Wiehe,Mark Blaxter +18 more
TL;DR: This work sequenced and compared the genomes and transcriptomes of parthenogenetic and outcrossing panagrolaimid species, including cryptobionts and non-cryptobiont species, finding systems that may contribute to cryptobiosis.
Journal ArticleDOI
Complete mitochondrial genome of Bactrocera arecae (Insecta: Tephritidae) by next-generation sequencing and molecular phylogeny of Dacini tribe.
TL;DR: The whole mitogenome of B. arecae will serve as a useful dataset for studying the genetics, systematics and phylogenetic relationships of the many species of Bactrocera genus in particular, and tephritid fruit flies in general.
Journal ArticleDOI
Positive diversifying selection is a pervasive adaptive force throughout the Drosophila radiation.
Francesco Cicconardi,Paolo Marcatili,Wolfgang Arthofer,Birgit C. Schlick-Steiner,Florian M. Steiner +4 more
TL;DR: This study, one of the largest and most comprehensive ones on genome-wide positive diversifying selection to date, shows that positive diversification selection has promoted species-specific differentiation among evolutionary lineages throughout the Drosophila radiation.
Journal ArticleDOI
Mitogenomics reveals phylogenetic relationships of Arcoida (Mollusca, Bivalvia) and multiple independent expansions and contractions in mitochondrial genome size.
TL;DR: The results suggest that tandem repeats might facilitate intraspecific mitochondrial genome size variation, and that inverted repeats, which could be derived from transposons, might be responsible for mitochondrial genome expansions and contractions.
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: 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
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