title: Improving the coverage of the cyanobacterial phylum using diversity-driven genome sequencing.
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 light-harvesting 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.
authors.affiliation: US Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA.
authors.forename: Patrick M
authors.initials: PM
authors.lastname: Shih
authors.forename: Dongying
authors.initials: D
authors.lastname: Wu
authors.forename: Amel
authors.initials: A
authors.lastname: Latifi
authors.forename: Seth D
authors.initials: SD
authors.lastname: Axen
authors.forename: David P
authors.initials: DP
authors.lastname: Fewer
authors.forename: Emmanuel
authors.initials: E
authors.lastname: Talla
authors.forename: Alexandra
authors.initials: A
authors.lastname: Calteau
authors.forename: Fei
authors.initials: F
authors.lastname: Cai
authors.forename: Nicole
authors.initials: N
authors.lastname: Tandeau de Marsac
authors.forename: Rosmarie
authors.initials: R
authors.lastname: Rippka
authors.forename: Michael
authors.initials: M
authors.lastname: Herdman
authors.forename: Kaarina
authors.initials: K
authors.lastname: Sivonen
authors.forename: Therese
authors.initials: T
authors.lastname: Coursin
authors.forename: Thierry
authors.initials: T
authors.lastname: Laurent
authors.forename: Lynne
authors.initials: L
authors.lastname: Goodwin
authors.forename: Matt
authors.initials: M
authors.lastname: Nolan
authors.forename: Karen W
authors.initials: KW
authors.lastname: Davenport
authors.forename: Cliff S
authors.initials: CS
authors.lastname: Han
authors.forename: Edward M
authors.initials: EM
authors.lastname: Rubin
authors.forename: Jonathan A
authors.initials: JA
authors.lastname: Eisen
authors.forename: Tanja
authors.initials: T
authors.lastname: Woyke
authors.forename: Muriel
authors.initials: M
authors.lastname: Gugger
authors.forename: Cheryl A
authors.initials: CA
authors.lastname: Kerfeld
mesh_terms: D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D061146:Chlorophyll Binding Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D000458:Cyanobacteria / Q000145:classification* / Q000235:genetics* / Q000378:metabolism; D019143:Evolution, Molecular; D014644:Genetic Variation; D016680:Genome, Bacterial; D045342:Light-Harvesting Protein Complexes / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D008958:Models, Molecular; D008969:Molecular Sequence Data; D005810:Multigene Family; D045331:Photosystem I Protein Complex / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D010802:Phylogeny; D018087:Plastids / Q000235:genetics; D017386:Sequence Homology, Amino Acid
chemical_list: D001426:Bacterial Proteins; D061146:Chlorophyll Binding Proteins; D045342:Light-Harvesting Protein Complexes; D045331:Photosystem I Protein Complex