Improving the coverage of the cyanobacterial phylum using diversity-driven genome sequencing

Patrick M. Shih, Dongying Wu, Amel Latifi, Seth D. Axen, David P. Fewer, Emmanuel Talla, Alexandra Calteau, Fei Cai, Nicole Tandeau De Marsac, Rosmarie Rippka, Michael Herdman, Kaarina Sivonen, Therese Coursin, Thierry Laurent, Lynne Goodwin, Matt Nolan, Karen W. Davenport, Cliff S. Han, Edward M. Rubin, Jonathan A EisenTanja Woyke, Muriel Gugger, Cheryl A. Kerfeld

Research output: Contribution to journalArticle

402 Scopus citations

Abstract

The cyanobacterial phylum encompasses oxygenic photosynthetic prokaryotes of a great breadth of morphologies and ecologies; they play key roles in global carbon and nitrogen cycles. The chloroplasts of all photosynthetic eukaryotes can trace their ancestry to cyanobacteria. Cyanobacteria also attract considerable interest as platforms for "green" biotechnology and biofuels. To explore the molecular basis of their different phenotypes and biochemical capabilities, we sequenced the genomes of 54 phylogenetically and phenotypically diverse cyanobacterial strains. Comparison of cyanobacterial genomes reveals the molecular basis for many aspects of cyanobacterial ecophysiological diversity, as well as the convergence of complex morphologies without the acquisition of novel proteins. This phylum-wide study highlights the benefits of diversity-driven genome sequencing, identifying more than 21,000 cyanobacterial proteins with no detectable similarity to known proteins, and foregrounds the diversity of lightharvesting proteins and gene clusters for secondary metabolite biosynthesis. Additionally, our results provide insight into the distribution of genes of cyanobacterial origin in eukaryotic nuclear genomes. Moreover, this study doubles both the amount and the phylogenetic diversity of cyanobacterial genome sequence data. Given the exponentially growing number of sequenced genomes, this diversity-driven study demonstrates the perspective gained by comparing disparate yet related genomes in a phylum-wide context and the insights that are gained from it.

Original languageEnglish (US)
Pages (from-to)1053-1058
Number of pages6
JournalProceedings of the National Academy of Sciences of the United States of America
Volume110
Issue number3
DOIs
StatePublished - Jan 15 2013

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Shih, P. M., Wu, D., Latifi, A., Axen, S. D., Fewer, D. P., Talla, E., Calteau, A., Cai, F., Tandeau De Marsac, N., Rippka, R., Herdman, M., Sivonen, K., Coursin, T., Laurent, T., Goodwin, L., Nolan, M., Davenport, K. W., Han, C. S., Rubin, E. M., ... Kerfeld, C. A. (2013). Improving the coverage of the cyanobacterial phylum using diversity-driven genome sequencing. Proceedings of the National Academy of Sciences of the United States of America, 110(3), 1053-1058. https://doi.org/10.1073/pnas.1217107110