CANT-HYD: A Curated Database of Phylogeny-Derived Hidden Markov Models for Annotation of Marker Genes Involved in Hydrocarbon Degradation

Many pathways for hydrocarbon degradation have been discovered, yet there are no dedicated tools to identify and predict the hydrocarbon degradation potential of microbial genomes and metagenomes. Here we present the Calgary approach to ANnoTating HYDrocarbon degradation genes (CANT-HYD), a database...

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Detalles Bibliográficos
Autores principales: Khot, Varada, Zorz, Jackie, Gittins, Daniel A., Chakraborty, Anirban, Bell, Emma, Bautista, María A., Paquette, Alexandre J., Hawley, Alyse K., Novotnik, Breda, Hubert, Casey R. J., Strous, Marc, Bhatnagar, Srijak
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2022
Materias:
Microbiology
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8767102/
https://www.ncbi.nlm.nih.gov/pubmed/35069469
http://dx.doi.org/10.3389/fmicb.2021.764058
Descripción
Sumario:Many pathways for hydrocarbon degradation have been discovered, yet there are no dedicated tools to identify and predict the hydrocarbon degradation potential of microbial genomes and metagenomes. Here we present the Calgary approach to ANnoTating HYDrocarbon degradation genes (CANT-HYD), a database of 37 HMMs of marker genes involved in anaerobic and aerobic degradation pathways of aliphatic and aromatic hydrocarbons. Using this database, we identify understudied or overlooked hydrocarbon degradation potential in many phyla. We also demonstrate its application in analyzing high-throughput sequence data by predicting hydrocarbon utilization in large metagenomic datasets from diverse environments. CANT-HYD is available at https://github.com/dgittins/CANT-HYD-HydrocarbonBiodegradation.

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