CyanoPATH: a knowledgebase of genome-scale functional repertoire for toxic cyanobacterial blooms.

Journal Article (Journal Article)

CyanoPATH is a database that curates and analyzes the common genomic functional repertoire for cyanobacteria harmful algal blooms (CyanoHABs) in eutrophic waters. Based on the literature of empirical studies and genome/protein databases, it summarizes four types of information: common biological functions (pathways) driving CyanoHABs, customized pathway maps, classification of blooming type based on databases and the genomes of cyanobacteria. A total of 19 pathways are reconstructed, which are involved in the utilization of macronutrients (e.g. carbon, nitrogen, phosphorus and sulfur), micronutrients (e.g. zinc, magnesium, iron, etc.) and other resources (e.g. light and vitamins) and in stress resistance (e.g. lead and copper). These pathways, comprised of both transport and biochemical reactions, are reconstructed with proteins from NCBI and reactions from KEGG and visualized with self-created transport/reaction maps. The pathways are hierarchical and consist of subpathways, protein/enzyme complexes and constituent proteins. New cyanobacterial genomes can be annotated and visualized for these pathways and compared with existing species. This set of genomic functional repertoire is useful in analyzing aquatic metagenomes and metatranscriptomes in CyanoHAB research. Most importantly, it establishes a link between genome and ecology. All these reference proteins, pathways and maps and genomes are free to download at http://www.csbg-jlu.info/CyanoPATH.

Full Text

Duke Authors

Cited Authors

  • Du, W; Li, G; Ho, N; Jenkins, L; Hockaday, D; Tan, J; Cao, H

Published Date

  • July 2021

Published In

Volume / Issue

  • 22 / 4

Start / End Page

  • bbaa375 -

PubMed ID

  • 33320930

Electronic International Standard Serial Number (EISSN)

  • 1477-4054

International Standard Serial Number (ISSN)

  • 1467-5463

Digital Object Identifier (DOI)

  • 10.1093/bib/bbaa375

Language

  • eng