A database for ITS2 sequences from nematodes

Workentine, M. L.; Chen, R.; Zhu, S.; Gavriliuc, S.; Shaw, N.; de Rijke, J.; Redman, E. M.; Avarmenko, R. W.; Wit, J.; Poissant, J.; Gilleard, J. S.

doi:10.1101/689695

bioRxiv · 10.1101/689695

A database for ITS2 sequences from nematodes

Workentine, M. L.·Chen, R.·Zhu, S.·Gavriliuc, S.·Shaw, N.·de Rijke, J.·Redman, E. M.·Avarmenko, R. W.·Wit, J.·Poissant, J.·Gilleard, J. S.

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Abstract

Marker gene surveys have a wide variety of applications in species identification, population genetics, and molecular epidemiology. As these methods expand to new types of organisms and additional markers beyond 16S and 18S rRNA genes, comprehensive databases are a critical requirement for proper analysis of these data. Here we present an ITS2 rDNA database for maker gene surveys of both free-living and parasitic nematode populations and the software used to build the database. This is an important resource for researchers working on nematodes and also provides a tool to create ITS2 databases for any given taxonomy.\n\nAvailability and ImplementationThe database is available as an interactive web app at https://cooperia.chgi.ucalgary.ca/Nematode_ITS2/. The full database can also be downloaded from zenodo https://doi.org/10.5281/zenodo.3235802, and the open source software used to create the database, markerDB is available at https://github.com/ucvm/markerDB/releases/latest.

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Workentine, M. L., Chen, R., Zhu, S., Gavriliuc, S., Shaw, N., de Rijke, J., Redman, E. M., Avarmenko, R. W., Wit, J., Poissant, J., Gilleard, J. S.. 2019-07-02. A database for ITS2 sequences from nematodes. https://doi.org/10.1101/689695

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