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

Stefen, C.; Wagner, F.; Asztalos, M.; Giere, P.; Grobe, P.; Hiller, M.; Hofmann, R.; Jaehde, M.; Laechele, U.; Lehmann, T.; Ortmann, S.; Peters, B.; Ruf, I.; Schiffmann, C.; Thier, N.; Unterhitzenberger, G.; Vogt, L.; Rudolf, M.; Wehner, P.; Stuckas, H.

doi:10.1101/2021.01.17.426960

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bioRxiv · 10.1101/2021.01.17.426960

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

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Abstract

A new and uniquely structured matrix of mammalian phenotypes, MaTrics (Mammalian Traits for Comparative Genomics) is presented in a digital form. By focussing on mammalian species for which genome assemblies are available, MaTrics provides an interface between mammalogy and comparative genomics. MaTrics was developed as part of a project to link phenotypic differences between mammals to differences in their genomes using Forward Genomics. Apart from genomes this approach requires information on homologous phenotypes that are numerically encoded (presence-absence; multistate character coding*) in a matrix. MaTrics provides these data, links them to at least one reference (e.g., literature, photographs, histological sections, CT-scans, or museum specimens) and makes them available in a machine actionable NEXUS-format. By making the data computer readable, MatTrics opens a new way for digitizing collections. Currently, MaTrics covers 147 mammalian species and includes 207 characters referring to structure, morphology, physiology, ecology and ethology. Researching these traits revealed substantial knowledge gaps, highlighting the need for substantial phenotyping efforts in the genomic era. Using the trait information documented in MaTrics, previous Forward Genomics screens identified changes in genes that are associated with various phenotypes, ranging from fully-aquatic lifestyle to dietary specializations. These results motivate the continuous expansion of phenotype information, both by filling research gaps or by adding additional taxa and traits. MaTrics is digitally available online within the data repository Morph{middle dot}D{middle dot}Base (www.morphdbase.de).

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Stefen, C., Wagner, F., Asztalos, M., Giere, P., Grobe, P., Hiller, M., Hofmann, R., Jaehde, M., Laechele, U., Lehmann, T., Ortmann, S., Peters, B., Ruf, I., Schiffmann, C., Thier, N., Unterhitzenberger, G., Vogt, L., Rudolf, M., Wehner, P., Stuckas, H.. 2021-01-19. Phenotyping in the era of genomics: MaTrics a digital character matrix to document mammalian phenotypic traits coded numerically. https://doi.org/10.1101/2021.01.17.426960

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