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 mitogenome of Achalarus lyciades (Lepidoptera: Hesperiidae).
TL;DR: A complete mitochondrial genome of a skipper butterfly Achalarus lyciades (Hesperiidae, Eudaminae) is obtained from next generation sequencing reads and its gene order is typical for mitogenomes of Lepidoptera.
Journal ArticleDOI
Next-generation sequencing yields the complete mitogenome of massive coral, Porites lutea (Cnidaria: Poritidae)
TL;DR: The complete mitogenome sequence of massive coral, Porites lutea, has been sequenced by next-generation sequencing method and provides essential and important DNA molecular data for further phylogenetic and evolutionary analysis for stony coral.
Journal ArticleDOI
The mitochondrial genome of the dung beetle, Copris tripartitus, with mitogenomic comparisons within Scarabaeidae (Coleoptera).
TL;DR: Phylogenetic analysis of the 32 species within the Scarabaeidae strongly supported the Onthophagini as non-monophyletic group and placed Coprini as a sister tribe to the group composed of Dichotomiini, Phanaeini, and Eurysternini with lower nodal supports.
Journal ArticleDOI
The complete mitochondrial genome of a medicinal insect, Hydrillodes repugnalis (Lepidoptera: Noctuoidea: Erebidae), and related phylogenetic analysis.
Mingsheng Yang,Lu Song,Yuxia Shi,Yanjun Yin,Yueying Wang,Peipei Zhang,Jiaqin Chen,Lijiao Lou,Xiaomeng Liu +8 more
TL;DR: Phylogenetic analyses showed that H. repugnalis is nested into the Erebidae clade, consistently being sister to the Aganainae, and mitochondrial genome analysis showed that the motif "ATGATAA" between atp8 and atp6, and the motif 'ATACTAA' are commonly present in noctuoid mitogenomes.
Journal ArticleDOI
Phylotranscriptomic Insights into the Diversification of Endothermic Thunnus Tunas.
Adam Ciezarek,Owen G. Osborne,Oliver N. Shipley,Oliver N. Shipley,Edward J. Brooks,Sean R. Tracey,Jaime D. McAllister,Luke D. Gardner,Michael J.E. Sternberg,Barbara A. Block,Vincent Savolainen +10 more
TL;DR: It is found that parallel selection on standing genetic variation is associated with the evolution of endothermy in bluefin tunas, and phylogenetic techniques illustrate that the eight Thunnus species are genetically distinct, but found evidence of mitochondrial genome introgression across two species.
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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