微生物基因数据库在氮循环功能基因注释中的应用

Application of microbial gene databases in the annotation of nitrogen cycle functional genes

摘要:

氮循环是微生物和化学过程介导的生物地球化学循环。利用基因测序技术研究环境中参与氮循环的微生物群落、微生物及功能基因，是环境基因组学和微生物生态学的重要研究热点。近年来，各种类型的数据库被开发并应用到功能分析中。本文结合时下最新研究成果，聚焦由微生物引起的同化硝酸盐还原作用、异化硝酸盐还原作用、反硝化作用、固氮作用、硝化作用(包括完全氨氧化作用)和厌氧氨氧化作用等6种无机氮循环途径的功能基因，对比了National Center for Biotechnology Information (NCBI)、Integrated Microbial Genomes (IMG)、Universal Protein (UniProt)、Kyoto Encyclopedia of Genes and Genomes (KEGG)、Protein Families (Pfam)、Functional Gene (FunGene)、Clusters of Orthologous Groups (COG)和NCycDB等数据库的设计理念和功能特点，并结合环境介质、表征基因、分析方法和比对方法等影响因素，分析了以上数据库在氮循环功能基因注释中的选择及应用方式，展望了未来氮循环基因数据库的发展方向，以期为研究人员了解氮循环基因家族和选择合适的数据分析平台提供参考。

Abstract:

Nitrogen cycle is a biogeochemical cycle mediated by both abiotic and biotic processes. The important research hotspot in environmental genomics and microbial ecology is to use gene sequencing technology to study microbial communities, microorganisms and functional genes involved in the nitrogen cycle in the environment. In recent years, various types of databases are developed and applied to functional analysis. Combining with the latest research results, we focus here on the functional genes of six inorganic nitrogen cycle pathways driven by microorganisms, containing assimilation nitrate reduction, dissimilation nitrate reduction, denitrification, nitrogen fixation, nitrification (including complete ammonia oxidation) and anaerobic ammonia oxidation. we compare the design concepts and functional characteristics of databases such as National Center for Biotechnology Information (NCBI), Integrated Microbial Genomes (IMG), Universal Protein (UniProt), Kyoto Encyclopedia of Genes and Genomes (KEGG), Protein Families (Pfam), Functional Gene (FunGene), Clusters of Orthologous Groups (COG) and NCycDB. Also, we statistically analyze the selection and application of the above databases in the annotation of nitrogen cycle functional genes, combining with the influence factors such as environmental media, characteristic genes, analysis methods and comparison methods, and prospected the future development direction of the nitrogen cycle gene databases. It is expected to provide reference for researchers to understand the nitrogen cycle gene family and choose an appropriate data analysis platform.