NCycDB: a curated integrative database for fast and accurate metagenomic profiling of nitrogen cycling genes

Bioinformatics
Qichao TuZhili He

Abstract

The nitrogen (N) cycle is a collection of important biogeochemical pathways in the Earth ecosystem and has gained extensive foci in ecology and environmental studies. Currently, shotgun metagenome sequencing has been widely applied to explore gene families responsible for N cycle processes. However, there are problems in applying publically available orthology databases to profile N cycle gene families in shotgun metagenomes, such as inefficient database searching, unspecific orthology groups and low coverage of N cycle genes and/or gene (sub)families. To solve these issues, this study built a manually curated integrative database (NCycDB) for fast and accurate profiling of N cycle gene (sub)families from shotgun metagenome sequencing data. NCycDB contains a total of 68 gene (sub)families and covers eight N cycle processes with 84 759 and 219 146 representative sequences at 95 and 100% identity cutoffs, respectively. We also identified 1958 homologous orthology groups and included corresponding sequences in the database to avoid false positive assignments due to 'small database' issues. We applied NCycDB to characterize N cycle gene (sub)families in 52 shotgun metagenomes from the Global Ocean Sampling expedition. Further analy...Continue Reading

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Citations

Aug 1, 2019·GigaScience·Muhammad Zohaib AnwarCarsten Suhr Jacobsen
Aug 23, 2020·International Journal of Environmental Research and Public Health·Yueni WuYe Deng
Jan 19, 2021·The Science of the Total Environment·Shiqing NieChengjian Jiang
Jul 16, 2021·Environmental Science and Pollution Research International·Binjie ZhaoQuanfa Zhang

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