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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Morphological and genetic evidence for early Holocene cattle management in northeastern China.
Hucai Zhang,Johanna L. A. Paijmans,Johanna L. A. Paijmans,Fengqin Chang,Xiaohong Wu,Guangjie Chen,Chuzhao Lei,Xiujuan Yang,Zhenyi Wei,Daniel G. Bradley,Ludovic Orlando,Terry O'Connor,Michael Hofreiter,Michael Hofreiter +13 more
TL;DR: The data suggest that the first attempts to manage cattle in northern China predate the introduction of domestic cattle that gave rise to the current stock by several thousand years.
Journal ArticleDOI
Evolution of mitochondrial gene order in Annelida.
Anne Weigert,Anja Golombek,Michael Gerth,Francine Schwarz,Torsten H. Struck,Christoph Bleidorn +5 more
TL;DR: It is demonstrated that the supposedly highly conserved mitochondrial gene order suggested for Annelida is restricted to Pleistoannelida, representing the ground pattern of this group and the first mitochondrial genomes in AnnelIDA that encode genes on both strands are reported.
Journal ArticleDOI
The elusive nature of adaptive mitochondrial DNA evolution of an arctic lineage prone to frequent introgression.
José Melo-Ferreira,Joana Vilela,Miguel Fonseca,Miguel Fonseca,Rute R. da Fonseca,Rute R. da Fonseca,Pierre Boursot,Paulo C. Alves,Paulo C. Alves +8 more
TL;DR: Adaptation impacted the evolution of hare mtDNA and may have influenced the occurrence and consequences of the many reported cases of massive mtDNA introgression, suggesting that the origin of adaptation remains elusive.
Journal ArticleDOI
Mitogenomics at the base of Metazoa.
Hans-Jürgen Osigus,Michael Eitel,Michael Eitel,Matthias Bernt,Alexander Donath,Bernd Schierwater,Bernd Schierwater +6 more
TL;DR: The results of these analyses illustrate the value of mitogenomics and support previously known topologies between animal phyla but also identify several problematic taxa, which are sensitive to long branch artifacts or missing data.
Journal ArticleDOI
ORDER within the chaos: Insights into phylogenetic relationships within the Anomura (Crustacea: Decapoda) from mitochondrial sequences and gene order rearrangements.
Mun Hua Tan,Han Ming Gan,Yin Peng Lee,Stuart M. Linton,Frédéric Grandjean,Marlise Ladvocat Bartholomei-Santos,Adam D. Miller,Christopher M. Austin,Christopher M. Austin +8 more
TL;DR: The value of MGOs as a source of novel synapomorphies for independently reinforcing tree-based relationships and for shedding light on relationships among challenging groups such as the Aegloidea and Lomisoidea that were unresolved in phylogenetic reconstructions is demonstrated.
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: 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
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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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