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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Gene Family Evolution Reflects Adaptation to Soil Environmental Stressors in the Genome of the Collembolan Orchesella cincta
Anna Faddeeva-Vakhrusheva,Martijn F.L. Derks,Seyed Yahya Anvar,Valeria Agamennone,Wouter Suring,Sandra Smit,Nico M. van Straalen,Dick Roelofs +7 more
TL;DR: A draft genome of an O. cincta reference strain is presented, containing 20,249 genes, and several lineage-specific genes, expanded gene families, and horizontally transferred genes, associated with altered gene expression as a consequence of genetic adaptation to metal stress are identified.
Journal ArticleDOI
Complete mitochondrial genomes and nuclear ribosomal RNA operons of two species of Diplostomum (Platyhelminthes: Trematoda): a molecular resource for taxonomy and molecular epidemiology of important fish pathogens
TL;DR: Complete sequences of the mt genome and rRNA operon of two species of Diplostomum provide a valuable resource for novel genetic markers for species delineation and large-scale molecular epidemiology and disease ecology studies based on the most accessible life-cycle stages of eye flukes.
Journal ArticleDOI
Valuing museum specimens: high‐throughput DNA sequencing on historical collections of New Guinea crowned pigeons (Goura)
Guillaume Besnard,Joris A. M. Bertrand,Joris A. M. Bertrand,Boris Delahaie,Yann Bourgeois,Yann Bourgeois,Emeline Lhuillier,Christophe Thébaud +7 more
TL;DR: This study confirms the power of using next-generation sequencing methods to investigate the evolutionary history of species for which access to fresh samples is limited but museum collections are available.
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Deep-level phylogeny of Cicadomorpha inferred from mitochondrial genomes sequenced by NGS
Nan Song,Wanzhi Cai,Hu Li +2 more
TL;DR: The phylogenetic reconstructions congruently recovered the monophyly of each superfamily within Cicadomorpha and the hypothesis (Membracoidea + (CicadoideA’+’Cercopoidea) was strongly supported under the heterogeneous CAT model.
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Molecular phylogeny of Polyneoptera (Insecta) inferred from expanded mitogenomic data.
TL;DR: A phylogenetic reconstruction for this group of insects based on expanded mitochondrial genome data is presented, demonstrating that model selection, data treatment, and outgroup choice can have significant effects on the reconstructed phylogenetic relationships of Polyneoptera.
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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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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