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A comprehensive aligned nifH gene database: a multipurpose tool for studies of nitrogen-fixing bacteria

机译：全面的整合nifH基因数据库：研究固氮细菌的多功能工具

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We describe a nitrogenase gene sequence database that facilitates analysis of the evolution and ecology of nitrogen-fixing organisms. The database contains 32 954 aligned nitrogenase nifH sequences linked to phylogenetic trees and associated sequence metadata. The database includes 185 linked multigene entries including full-length nifH, nifD, nifK and 16S ribosomal RNA (rRNA) gene sequences. Evolutionary analyses enabled by the multigene entries support an ancient horizontal transfer of nitrogenase genes between Archaea and Bacteria and provide evidence that nifH has a different history of horizontal gene transfer from the nifDK enzyme core. Further analyses show that lineages in nitrogenase cluster I and cluster III have different rates of substitution within nifD, suggesting that nifD is under different selection pressure in these two lineages. Finally, we find that that the genetic divergence of nifH and 16S rRNA genes does not correlate well at sequence dissimilarity values used commonly to define microbial species, as stains having 3% sequence dissimilarity in their 16S rRNA genes can have up to 23% dissimilarity in nifH. The nifH database has a number of uses including phylogenetic and evolutionary analyses, the design and assessment of primers/probes and the evaluation of nitrogenase sequence diversity. Database URL: http://www.css.cornell.edu/faculty/buckleyifh.htm
机译：我们描述了一个固氮酶基因序列数据库，可促进固氮生物的进化和生态分析。该数据库包含32 954个比对的固氮酶nifH序列，这些序列链接到系统树和相关的序列元数据。该数据库包括185个链接的多基因条目，包括全长nifH，nifD，nifK和16S核糖体RNA（rRNA）基因序列。由多基因条目支持的进化分析支持古细菌和细菌之间古老的水平转移氮酶基因，并提供了证据，表明nifH与nifDK酶核心的水平基因转移历史不同。进一步的分析表明，硝化酶簇I和簇III中的谱系在nifD中具有不同的取代率，这表明nifD在这两个谱系中处于不同的选择压力下。最后，我们发现nifH和16S rRNA基因的遗传差异在通常用于定义微生物物种的序列差异值上没有很好的相关性，因为在其16S rRNA基因中具有<3％序列差异的污渍可以具有高达23％的差异在nifH中。 nifH数据库具有许多用途，包括系统发育和进化分析，引物/探针的设计和评估以及固氮酶序列多样性的评估。数据库网址：http://www.css.cornell.edu/faculty/buckleyifh.htm

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