Phenotyping in the era of genomics: MaTrics—a digital character matrix to document mammalian phenotypic traits

Media type: E-Article
Title: Phenotyping in the era of genomics: MaTrics—a digital character matrix to document mammalian phenotypic traits
Contributor: Stefen, Clara; Wagner, Franziska; Asztalos, Marika; Giere, Peter; Grobe, Peter; Hiller, Michael; Hofmann, Rebecca; Jähde, Maria; Lächele, Ulla; Lehmann, Thomas; Ortmann, Sylvia; Peters, Benjamin; Ruf, Irina; Schiffmann, Christian; Thier, Nadja; Unterhitzenberger, Gabriele; Vogt, Lars; Rudolf, Matthias; Wehner, Peggy; Stuckas, Heiko
imprint: Springer Science and Business Media LLC, 2022
Published in: Mammalian Biology
Language: English
DOI: 10.1007/s42991-021-00192-5
ISSN: 1616-5047; 1618-1476
Keywords: Animal Science and Zoology ; Ecology, Evolution, Behavior and Systematics
Origination:
Footnote:
Description: <jats:title>Abstract</jats:title><jats:p>A new and uniquely structured matrix of mammalian phenotypes,<jats:italic>MaTrics</jats:italic>(<jats:italic><jats:underline>Ma</jats:underline></jats:italic><jats:italic>mmalian</jats:italic><jats:italic><jats:underline>Tr</jats:underline></jats:italic><jats:italic>aits for Comparative Genom</jats:italic><jats:italic><jats:underline>ics</jats:underline></jats:italic>) in a digital form is presented. By focussing on mammalian species for which genome assemblies are available,<jats:italic>MaTrics</jats:italic>provides an interface between mammalogy and comparative genomics.</jats:p><jats:p><jats:italic>MaTrics</jats:italic>was developed within a project aimed to find genetic causes of phenotypic traits of mammals using<jats:italic>Forward Genomics.</jats:italic>This approach requires genomes and comprehensive and recorded information on homologous phenotypes that are coded as discrete categories in a matrix.<jats:italic>MaTrics</jats:italic>is an evolving online resource providing information on phenotypic traits in numeric code; traits are coded either as absent/present or with several states as multistate. The state record for each species is linked to at least one reference (e.g., literature, photographs, histological sections, CT scans, or museum specimens) and so<jats:italic>MaTrics</jats:italic>contributes to digitalization of museum collections. Currently,<jats:italic>MaTrics</jats:italic>covers 147 mammalian species and includes 231 characters related to structure, morphology, physiology, ecology, and ethology and available in a machine actionable NEXUS-format*. Filling<jats:italic>MaTrics</jats:italic>revealed substantial knowledge gaps, highlighting the need for phenotyping efforts. Studies based on selected data from<jats:italic>MaTrics</jats:italic>and using<jats:italic>Forward Genomics</jats:italic>identified associations between genes and certain phenotypes ranging from lifestyles (e.g., aquatic) to dietary specializations (e.g., herbivory, carnivory). These findings motivate the expansion of phenotyping in<jats:italic>MaTrics</jats:italic>by filling research gaps and by adding taxa and traits. Only databases like<jats:italic>MaTrics</jats:italic>will provide machine actionable information on phenotypic traits, an important limitation to genomics.<jats:italic>MaTrics</jats:italic>is available within the data repository Morph·D·Base (<jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="http://www.morphdbase.de">www.morphdbase.de</jats:ext-link>).</jats:p>

Search in field:

Recently searched for: