Gaby John Christian, Buckley Daniel H
Department of Crop and Soil Sciences, Cornell University, Ithaca, NY 14853, USA.
Database (Oxford). 2014 Feb 5;2014:bau001. doi: 10.1093/database/bau001. Print 2014.
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/buckley/nifh.htm.
我们描述了一个有助于分析固氮生物进化与生态的固氮酶基因序列数据库。该数据库包含32954条与系统发育树及相关序列元数据相链接的比对固氮酶nifH序列。数据库包括185个链接的多基因条目，其中有全长nifH、nifD、nifK和16S核糖体RNA（rRNA）基因序列。多基因条目所支持的进化分析证实了古菌和细菌之间固氮酶基因的古老水平转移，并提供证据表明nifH与nifDK酶核心具有不同的水平基因转移历史。进一步分析表明，固氮酶聚类I和聚类III中的谱系在nifD内具有不同的替换率，这表明nifD在这两个谱系中受到不同的选择压力。最后，我们发现，在通常用于定义微生物物种的序列差异值上，nifH和16S rRNA基因的遗传差异并不具有很好的相关性，因为16S rRNA基因序列差异小于3%的菌株，其nifH的差异可能高达23%。nifH数据库有多种用途，包括系统发育和进化分析、引物/探针的设计与评估以及固氮酶序列多样性评估。数据库网址：http://www.css.cornell.edu/faculty/buckley/nifh.htm 。
