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

Authors
  • Khot, Varada1
  • Zorz, Jackie1
  • Gittins, Daniel A.2
  • Chakraborty, Anirban2
  • Bell, Emma2
  • Bautista, María A.2
  • Paquette, Alexandre J.1
  • Hawley, Alyse K.1
  • Novotnik, Breda1
  • Hubert, Casey R. J.2
  • Strous, Marc1
  • Bhatnagar, Srijak2
  • 1 Energy Bioengineering and Geomicrobiology Group, Department of Geoscience, University of Calgary, Calgary, AB , (Canada)
  • 2 Energy Bioengineering and Geomicrobiology Group, Department of Biological Sciences, University of Calgary, Calgary, AB , (Canada)
Type
Published Article
Journal
Frontiers in Microbiology
Publisher
Frontiers Media SA
Publication Date
Jan 07, 2022
Volume
12
Identifiers
DOI: 10.3389/fmicb.2021.764058
Source
Frontiers
Keywords
Disciplines
  • Microbiology
  • Methods
License
Green

Abstract

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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