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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Characterization and comparative analysis of the complete mitochondrial genome of Azygia hwangtsiyui Tsin, 1933 (Digenea), the first for a member of the family Azygiidae.
TL;DR: Phylogenetic analysis based on concatenated amino acid sequences of twelve protein-coding genes reveals that A. hwangtsiyui is placed in a separate clade, suggesting that it has no close relationship with any other trematode family.
Journal ArticleDOI
Signatures of mitonuclear coevolution in a warbler species complex.
Silu Wang,Silu Wang,Madelyn J. Ore,Madelyn J. Ore,Else K. Mikkelsen,Else K. Mikkelsen,Julie A. Lee-Yaw,Julie A. Lee-Yaw,David P. L. Toews,Sievert Rohwer,Darren E. Irwin +10 more
TL;DR: In this paper, the authors investigate the possibility that divergent mitonuclear coadaptation could facilitate speciation in two hybridizing species of warbler, Setophaga occidentalis and S. townsendi, in western North America.
Journal ArticleDOI
Characterization of the complete mitochondrial genome of Rhinogobius leavelli (Perciformes: Gobiidae: Gobionellinae) and its phylogenetic analysis for Gobionellinae
Fubin Zhang,Yanjun Shen +1 more
TL;DR: The complete mitochondrial genome of R. leavelli was determined and it was placed in a well-supported monophyletic cluster with the other five Rhinogobius species in Gobionellinae and the phylogenetic position of RhinOGobius was closer to Tridentiger.
Journal ArticleDOI
Mitochondrial Genome Assemblies of Elysia timida and Elysia cornigera and the Response of Mitochondrion-Associated Metabolism during Starvation.
Cessa Rauch,Gregor Christa,Gregor Christa,Jan de Vries,Jan de Vries,Christian Woehle,Sven B. Gould +6 more
TL;DR: It is speculated that kleptoplasts might aid in the rerouting or recycling of reducing power independent of, yet maybe improved by, photosynthesis.
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The complete mitochondrial genome of the conifer needle endophyte, Phialocephala scopiformis DAOMC 229536 confirms evolutionary division within the fungal Phialocephala fortinii s.l. - Acephala appalanata species complex.
TL;DR: The mt genome of the conifer needle endophyte, Phialocephala scopiformis DAOMC 229536 is described, representing the 10th complete mt genome for the order Helotiales (containing >3800 species), and how large-scale genomic patterns can be used to confirm lineages within fungal species complexes are shown.
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
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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