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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Whole-genome sequence of the oriental lung fluke Paragonimus westermani.
Harald Oey,Martha Zakrzewski,Kanwar Narain,K Rekha Devi,Takeshi Agatsuma,Sujeevi Nawaratna,Sujeevi Nawaratna,Geoffrey N. Gobert,Geoffrey N. Gobert,Malcolm K. Jones,Mark A. Ragan,Donald P. McManus,Lutz Krause,Lutz Krause +13 more
TL;DR: The generated assembly of the P. westermani genome represents the first Paragonimus genome sequence and will facilitate future molecular studies of this important, but neglected, parasite group.
Journal ArticleDOI
Solenodon genome reveals convergent evolution of venom in eulipotyphlan mammals
Nicholas R. Casewell,Daniel Petras,Daniel Petras,Daren C. Card,Daren C. Card,Vivek Suranse,Alexis M. Mychajliw,Alexis M. Mychajliw,Alexis M. Mychajliw,David Richards,David Richards,Ivan Koludarov,Laura-Oana Albulescu,Julien Slagboom,Benjamin-Florian Hempel,Neville M Ngum,Rosalind J. Kennerley,Jorge L. Brocca,Gareth Whiteley,Robert A. Harrison,Fiona M.S. Bolton,Jordan Debono,Freek J. Vonk,Jessica Alföldi,Jeremy Johnson,Elinor K. Karlsson,Elinor K. Karlsson,Kerstin Lindblad-Toh,Kerstin Lindblad-Toh,Ian R. Mellor,Roderich D. Süssmuth,Bryan G. Fry,Sanjaya Kuruppu,Wayne C. Hodgson,Jeroen Kool,Todd A. Castoe,Ian Barnes,Kartik Sunagar,Eivind A. B. Undheim,Eivind A. B. Undheim,Samuel T. Turvey +40 more
TL;DR: It is demonstrated that venom has evolved independently on at least 4 occasions in eulipotyphlans, and that molecular components of these venoms have also evolved convergently, with kallikrein-1 proteins coopted as toxins in both solenodons and shrews following their divergence over 70 million years ago.
Journal ArticleDOI
A mitochondrial genome phylogeny of Mytilidae (Bivalvia: Mytilida).
TL;DR: Divergence time analysis with a molecular clock indicated that lineage splitting among the major subfamilies of Mytilidae occurred in the Mesozoic period, coinciding with high diversification rates of marine fauna during that time.
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The complete mitochondrial genome of Scutopus ventrolineatus (Mollusca: Chaetodermomorpha) supports the Aculifera hypothesis
TL;DR: Phylogenetic analyses of mitochondrial sequences showed strong among-lineage rate heterogeneity that produced long-branch attraction biases and the reconstructed phylogenetic tree based on combined mitochondrial and nuclear sequence data recovered monophyletic Aplacophora, Aculifera, and Conchifera.
Journal ArticleDOI
Characterization and comparison of the mitochondrial genomes from two Lyophyllum fungal species and insights into phylogeny of Agaricomycetes.
TL;DR: Phylogenetic analysis based on a combined mitochondrial gene dataset resulted in a well-supported topology, wherein the two Lyophyllum species were most closely related to Tricholoma matsutake.
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.
Journal ArticleDOI
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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