| URL: | https://blogs.cornell.edu/buckley/nifh-sequence-database/ |
| Full name: | nifH database |
| Description: | We have developed an annotated nifH sequence database for use in studies of nitrogenase diversity and ecology as described in Gaby & Buckley (2014). The database is in ARB format and contains 32,954 aligned nifH sequences with associated metadata. The sequences are organized phylogenetically and a guide tree is available for navigation. The database also contains full length nifH, nifD, nifK, and 16S rRNA gene sequences extracted from the genomes of 185 nitrogen fixing organisms. |
| Year founded: | 2014 |
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| Accessibility: |
Accessible
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| Country/Region: | United States |
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| Data object: |
NA
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| Keywords: |
| University/Institution: | Cornell University |
| Address: | Department of Crop and Soil Sciences, Cornell University, Ithaca, NY 14853, USA |
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| Country/Region: | United States |
| Contact name (PI/Team): | Daniel H. Buckley |
| Contact email (PI/Helpdesk): | dhb28@cornell.edu |
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A comprehensive aligned nifH gene database: a multipurpose tool for studies of nitrogen-fixing bacteria. [PMID: 24501396]
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. |