MamMiBase: a mitochondrial genome database for mammalian phylogenetic studies

Vasconcelos, Ana Tereza Ribeiro de; Guimarães, Ana Carolina Ramos; Castelletti, Carlos Henrique Madeiros; Caruso, Célia Sulzbacher; Ribeiro, Cristina; Yokaichiya, Fabiano; Armôa, Geraldo R. G.; Pereira, Gislaine Da Silva P.; Silva, Israel T. Da; Schrago, Carlos G.; Fernandes, Adélia L. V.; Silveira, Aline R. Da; Carneiro, André G.; Carvalho, Berta; Viana, Carlos Juliano M.; Gramkow, Daniel; Lima, Franklin J.; Corrêa, Luiz Gustavo Guedes; Mudado, Mauricio de Alvarenga; Nehab-Hess, Pablo; Souza, Rangel De; Corrêa, Régis L.; Russo, Carlo

doi:10.1093/bioinformatics/bti326

Cited by 17 publications

(8 citation statements)

References 1 publication

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“…Evolutionary rates in panels A, B, D, and E are estimated using multiple alignments of orthologs from 46 species (Fujita et al 2011) following the procedure in Kumar et al (2009). For panel C, amino acid sequence alignments for mitochondrial proteins were obtained for 28 mammalian species from MamMiBase (Vasconcelos et al 2005) and the evolutionary rate was estimated following Kumar et al (2009). 2011) and may explain some of the inability of current genetic association studies to detect many causal variants, as they are typically not sufficiently powered to detect associations with rare alleles at a majority of the polymorphic sites ).…”

Section: Evolutionary Distributions Of Disease-associated Variantsmentioning

confidence: 99%

Human genomic disease variants: A neutral evolutionary explanation

Dudley¹,

Kim²,

Liu³

et al. 2012

Genome Res.

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Many perspectives on the role of evolution in human health include nonempirical assumptions concerning the adaptive evolutionary origins of human diseases. Evolutionary analyses of the increasing wealth of clinical and population genomic data have begun to challenge these presumptions. In order to systematically evaluate such claims, the time has come to build a common framework for an empirical and intellectual unification of evolution and modern medicine. We review the emerging evidence and provide a supporting conceptual framework that establishes the classical neutral theory of molecular evolution (NTME) as the basis for evaluating disease- associated genomic variations in health and medicine. For over a decade, the NTME has already explained the origins and distribution of variants implicated in diseases and has illuminated the power of evolutionary thinking in genomic medicine. We suggest that a majority of disease variants in modern populations will have neutral evolutionary origins (previously neutral), with a relatively smaller fraction exhibiting adaptive evolutionary origins (previously adaptive). This pattern is expected to hold true for common as well as rare disease variants. Ultimately, a neutral evolutionary perspective will provide medicine with an informative and actionable framework that enables objective clinical assessment beyond convenient tendencies to invoke past adaptive events in human history as a root cause of human disease.

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Section: Evolutionary Distributions Of Disease-associated Variantsmentioning

confidence: 99%

Human genomic disease variants: A neutral evolutionary explanation

Dudley¹,

Kim²,

Liu³

et al. 2012

Genome Res.

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“…For example, AMiGA collects only arthropod mtDNA sequences (10); MamMiBase focuses on mammals (11); HmtDB and Human mtDB on human (12,13); MitoFish on fishes (http://mitofish.aori.u-tokyo.ac.jp/). Only the no longer updated OGRe (14) and the currently non-functional Mitome (15) databases collected complete mtDNAs of all metazoans.…”

Section: Introductionmentioning

confidence: 99%

MitoZoa 2.0: a database resource and search tools for comparative and evolutionary analyses of mitochondrial genomes in Metazoa

Meo

D’Antonio

Griggio

et al. 2011

Nucleic Acids Research

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The MITOchondrial genome database of metaZOAns (MitoZoa) is a public resource for comparative analyses of metazoan mitochondrial genomes (mtDNA) at both the sequence and genomic organizational levels. The main characteristics of the MitoZoa database are the careful revision of mtDNA entry annotations and the possibility of retrieving gene order and non-coding region (NCR) data in appropriate formats. The MitoZoa retrieval system enables basic and complex queries at various taxonomic levels using different search menus. MitoZoa 2.0 has been enhanced in several aspects, including: a re-annotation pipeline to check the correctness of protein-coding gene predictions; a standardized annotation of introns and of precursor ORFs whose functionality is post-transcriptionally recovered by RNA editing or programmed translational frameshifting; updates of taxon-related fields and a BLAST sequence similarity search tool. Database novelties and the definition of standard mtDNA annotation rules, together with the user-friendly retrieval system and the BLAST service, make MitoZoa a valuable resource for comparative and evolutionary analyses as well as a reference database to assist in the annotation of novel mtDNA sequences. MitoZoa is freely accessible at http://www.caspur.it/mitozoa.

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“…Several mitogenome databases are available, including HmtDB [ 13 ], mtDB [ 14 ] and MITOMAP [ 15 ], which focus on a particular taxonomic group for specific analysis. MamMiBase [ 16 ] is a database of all mammalian protein coding genes for phylogenetic analysis. MitoFish is a collection of mitogenomes of fish for similarity studies and for the re-annotation of sequences [ 17 ].…”

Section: Introductionmentioning

confidence: 99%

FMiR: A Curated Resource of Mitochondrial DNA Information for Fish

et al. 2015

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Mitochondrial genome sequences have been widely used for evolutionary and phylogenetic studies. Among vertebrates, fish are an important, diverse group, and their mitogenome sequences are growing rapidly in public repositories. To facilitate mitochondrial genome analysis and to explore the valuable genetic information, we developed the Fish Mitogenome Resource (FMiR) database to provide a workbench for mitogenome annotation, species identification and microsatellite marker mining. The microsatellites are also known as simple sequence repeats (SSRs) and used as molecular markers in studies on population genetics, gene duplication and marker assisted selection. Here, easy-to-use tools have been implemented for mining SSRs and for designing primers to identify species/habitat specific markers. In addition, FMiR can analyze complete or partial mitochondrial genome sequence to identify species and to deduce relational distances among sequences across species. The database presently contains curated mitochondrial genomes from 1302 fish species belonging to 297 families and 47 orders reported from saltwater and freshwater ecosystems. In addition, the database covers information on fish species such as conservation status, ecosystem, family, distribution and occurrence downloaded from the FishBase and IUCN Red List databases. Those fish information have been used to browse mitogenome information for the species belonging to a particular category. The database is scalable in terms of content and inclusion of other analytical modules. The FMiR is running under Linux operating platform on high performance server accessible at URL http://mail.nbfgr.res.in/fmir.

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MamMiBase: a mitochondrial genome database for mammalian phylogenetic studies

Abstract: MamMiBase is available at http://www.mammibase.lncc.br

Cited by 17 publications

References 1 publication

Human genomic disease variants: A neutral evolutionary explanation

Human genomic disease variants: A neutral evolutionary explanation

MitoZoa 2.0: a database resource and search tools for comparative and evolutionary analyses of mitochondrial genomes in Metazoa

FMiR: A Curated Resource of Mitochondrial DNA Information for Fish

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