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

Varada Khot, Jackie Zorz, Daniel A. Gittins, Anirban Chakraborty, Emma Bell, María A. Bautista, Alexandre J. Paquette, Alyse K. Hawley, Breda Novotnik, Casey R.J. Hubert, Marc Strous, Srijak Bhatnagar

Research output: Contribution to journalJournal Articlepeer-review

18 Citations (Scopus)

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.

Original languageEnglish
Article number764058
JournalFrontiers in Microbiology
Volume12
DOIs
Publication statusPublished - 7 Jan. 2022

Keywords

  • Hidden Markov Models
  • Marker genes
  • gene annotation
  • hydrocarbon cycling
  • hydrocarbon degradation

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