TY - JOUR
T1 - CANT-HYD
T2 - A Curated Database of Phylogeny-Derived Hidden Markov Models for Annotation of Marker Genes Involved in Hydrocarbon Degradation
AU - Khot, Varada
AU - Zorz, Jackie
AU - Gittins, Daniel A.
AU - Chakraborty, Anirban
AU - Bell, Emma
AU - Bautista, María A.
AU - Paquette, Alexandre J.
AU - Hawley, Alyse K.
AU - Novotnik, Breda
AU - Hubert, Casey R.J.
AU - Strous, Marc
AU - Bhatnagar, Srijak
N1 - Funding Information:
This work was supported by funds from Genome Canada to GENICE—The microbial genomics for oil spill preparedness in the Canadian Arctic, to CRJH and MS. We acknowledge support from the Canada First Research Excellence Fund to BN and AJP and from the Government of Alberta to VK, JZ, and MS. Additional support for JZ, AJP, and AKH was provided by Natural Sciences and Engineering Research Council of Canada (NSERC).
Publisher Copyright:
Copyright © 2022 Khot, Zorz, Gittins, Chakraborty, Bell, Bautista, Paquette, Hawley, Novotnik, Hubert, Strous and Bhatnagar.
PY - 2022/1/7
Y1 - 2022/1/7
N2 - 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.
AB - 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.
KW - Hidden Markov Models
KW - Marker genes
KW - gene annotation
KW - hydrocarbon cycling
KW - hydrocarbon degradation
UR - http://www.scopus.com/inward/record.url?scp=85123245167&partnerID=8YFLogxK
U2 - 10.3389/fmicb.2021.764058
DO - 10.3389/fmicb.2021.764058
M3 - Journal Article
AN - SCOPUS:85123245167
VL - 12
JO - Frontiers in Microbiology
JF - Frontiers in Microbiology
M1 - 764058
ER -