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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A genome-skimmed phylogeny of a widespread bryozoan family, Adeonidae
Russell J. S. Orr,Marianne N. Haugen,Boejrn Berning,Philip E. Bock,Robyn L. Cumming,Wayne K. Florence,Masato Hirose,Emanuela Di Martino,Mali H. Ramsfjell,Maja M. Sannum,Abigail M. Smith,Leandro M. Vieira,Andrea Waeschenbach,Lee Hsiang Liow,Lee Hsiang Liow +14 more
TL;DR: A genome-skimming approach is used to extract sequence information for 15 mitochondrial and 2 ribosomal operon genes from the cheilostome bryozoan family, Adeonidae, whose current systematics is based purely on morphological traits and presents a highly-supported topology based on 17 genes.
Journal ArticleDOI
The complete mitochondrial genome of Porites harrisoni (Cnidaria: Scleractinia) obtained using next-generation sequencing.
Tullia Isotta Terraneo,Tullia Isotta Terraneo,Roberto Arrigoni,Francesca Benzoni,Zac H. Forsman,Michael L. Berumen +5 more
TL;DR: The complete mitochondrial genome of Porites harrisoni was sequenced using ezRAD and Illumina technology and was arranged in 13 protein-coding genes, 2 rRNA, and 2 tRNA genes.
Journal ArticleDOI
Analysis of mitochondrial and chloroplast genomes in two volvocine algae: Eudorina elegans and Eudorina cylindrica (Volvocaceae, Chlorophyta)
TL;DR: An unexpected phylogenetic relationship is revealed, namely, E. elegans is more closely related to Pleodorina starrii than to E. cylindrica, and the synteny analysis of the chloroplast genome indicated that the genus Eudorina may have experienced genomic changes.
Journal ArticleDOI
Past, current, and potential future distributions of unique genetic diversity in a cold-adapted mountain butterfly.
Melissa Minter,Kanchon K. Dasmahapatra,Chris D. Thomas,Michael D. Morecroft,Athayde Tonhasca,Thomas Schmitt,Stefanos Siozios,Jane K. Hill +7 more
TL;DR: The results suggest that historical range expansion and retraction processes by a cold‐ Adapted mountain species caused diversification between populations, resulting in unique genetic diversity which may be at risk if distributions of cold‐adapted species shrink in future.
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The complete mitochondrial genome of Vanessa indica and phylogenetic analyses of the family Nymphalidae.
TL;DR: The most important objective was to completely reconstruct the phylogenetic relationships for family members within Nymphalidae, and the results are significant because they would be useful in further understanding of the evolutionary biology of Nymphaticae.
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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