Improving the coverage of the cyanobacterial phylum using diversity driven genome sequencing
Open accessAbstract
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.
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The clustering of A. platensis YZ with other Arthrospira is highly congruent with previous study on whole cyanobacteria phylum phylogeny.
“which is highly congruent with the findings of previous study on whole cyanobacteria phylum phylogeny.”
From Whole genomic DNA sequencing and comparative genomic analysis of<i>Arthrospira platensis</i>: high genome plasticity and genetic diversity (2016) · cites this paper as [27]
In “Increased Coverage and Diversity of Cyanobacterial Genomes” (page not supplied), the paper reports a cyanobacterial species tree and lists several Arthrospira strains among its taxa. Our copy does not mention A. platensis YZ or state that it clusters with other Arthrospira, so the claimed strain-specific congruence is not established. (LLM, conf=0.82)
Experimental — accuracy not yet measuredDifferent CRISPR loci are highly present in cyanobacterial genomes.
“Different CRISPR loci are highly present in cyanobacterial genomes (Shih et al., 2013; Hou et al., 2019), where they could be a barrier to transformation processes.”
From Characterization of Limnospira platensis PCC 9108 R-M and CRISPR-Cas systems (2024) · cites this paper as Shih et al., 2013
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Self-citationMéjean, A., Mazmouz, R., Mann, S., et al. (2010) · Journal of Bacteriology · doi:10.1128/jb.00704-10 · Cited by 45 · see citing works
Bench, S. R., Ilikchyan, I. N., Tripp, H. J., & Zehr, J. P. (2011) · Frontiers in Microbiology · doi:10.3389/fmicb.2011.00261 · Cited by 43 · see citing works
Zhang, J., Chen, W., & Zhang, C. (2009) · Microbiology · doi:10.1099/mic.0.027540-0 · Cited by 39 · see citing works
Miller, S. R., Wood, A. M., Blankenship, R. E., et al. (2011) · Genome Biology and Evolution · doi:10.1093/gbe/evr060 · Cited by 39 · see citing works
Campbell, E. L., Wong, F. C. Y., & Meeks, J. C. (2003) · Molecular Microbiology · doi:10.1046/j.1365-2958.2003.03320.x · Cited by 37 · see citing works
Nomenclature for membrane-bound light-harvesting complexes of cyanobacteria
Chen, M., Zhang, Y., & Blankenship, R. E. (2007) · Photosynthesis Research · doi:10.1007/s11120-007-9255-0 · Cited by 32 · see citing works
Flagged first, then by citations
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Cited by
Sorted by citations
Parks, D. H., Imelfort, M., Skennerton, C. T., Hugenholtz, P., & Tyson, G. W. (2015) · Genome Research · doi:10.1101/gr.186072.114 · Cited by 12,496 · see citing works
Cyanobacteria and the Great Oxidation Event: evidence from genes and fossils
Schirrmeister, B. E., Gugger, M., & Donoghue, P. C. J. (2015) · Palaeontology · doi:10.1111/pala.12178 · Cited by 304 · see citing works
Self-citationGenomes in turmoil: quantification of genome dynamics in prokaryote supergenomes
Puigbò, P., Lobkovsky, A. E., Kristensen, D. M., Wolf, Y. I., & Koonin, E. V. (2014) · BMC Biology · doi:10.1186/s12915-014-0066-4 · Cited by 232 · see citing works
Intracellular Ca-carbonate biomineralization is widespread in cyanobacteria
Benzerara, K., Skouri-Panet, F., Li, J., Férard, C., Gugger, M., Laurent, T., Couradeau, E., Ragon, M., Cosmidis, J., Menguy, N., et al. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1403510111 · Cited by 264 · see citing works
Self-citationThe Syntrophy hypothesis for the origin of eukaryotes revisited
López-García, P., & Moreira, D. (2020) · Nature Microbiology · doi:10.1038/s41564-020-0710-4 · Cited by 201 · see citing works
Nowicka-Krawczyk, P., Mühlsteinová, R., & Hauer, T. (2019) · Scientific Reports · doi:10.1038/s41598-018-36831-0 · Cited by 185 · see citing works
Genomic Insights into Plastid Evolution
Sibbald, S. J., & Archibald, J. M. (2020) · Genome Biology and Evolution · doi:10.1093/gbe/evaa096 · Cited by 161 · see citing works
Shih, P. M., & Matzke, N. J. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1305813110 · Cited by 151 · see citing works
Self-citationFurmaniak, M. A., Misztak, A. E., Franczuk, M. D., Wilmotte, A., Waleron, M., & Waleron, K. F. (2017) · Frontiers in Microbiology · doi:10.3389/fmicb.2017.02541 · Cited by 121 · see citing works
Photosynthetic Production of Sunscreen Shinorine Using an Engineered Cyanobacterium
Yang, G., Cozad, M. A., Holland, D. A., Zhang, Y., Luesch, H., & Ding, Y. (2018) · ACS Synthetic Biology · doi:10.1021/acssynbio.7b00397 · Cited by 82 · see citing works
Kobayashi, K., Masuda, T., Tajima, N., Wada, H., & Sato, N. (2014) · Genome Biology and Evolution · doi:10.1093/gbe/evu170 · Cited by 65 · see citing works
Harnessing the potential: Advances in cyanobacterial natural product research and biotechnology
Baunach, M., Guljamow, A., Miguel-Gordo, M., & Dittmann, E. (2024) · Natural Product Reports · doi:10.1039/d3np00045a · Cited by 66 · see citing works
Stucken, K., Koch, R., & Dagan, T. (2013) · Biological Research · doi:10.4067/s0716-97602013000400009 · Cited by 52 · see citing works
Spirulina/Arthrospira/Limnospira—Three Names of the Single Organism
Sinetova, M. A., Kupriyanova, E. V., & Los, D. A. (2024) · Foods · doi:10.3390/foods13172762 · Cited by 51 · see citing works
“Several studies have focused on the evolutionary relationship of Arthrospira to taxa other than the type species, Arthrospira jenneri [9,20].”
BackgroundXu, T., Qin, S., Hu, Y., Song, Z., Ying, J., Li, P., Dong, W., Zhao, F., Yang, H., & Bao, Q. (2016) · DNA Research · doi:10.1093/dnares/dsw023 · Cited by 37 · see citing works
“platensis YZ was clustered together with the other members of genus Arthrospira, which is highly congruent with the findings of previous study on whole cyanobacteria phylum phylogeny.(27) Subclade D of the tree showed that A.”
ResultInorganic Carbon Assimilation in Cyanobacteria: Mechanisms, Regulation, and Engineering
Hagemann, M., Song, S., & Brouwer, E. (2021) · Cyanobacteria Biotechnology · doi:10.1002/9783527824908.ch1 · Cited by 33 · see citing works
Highly iterated palindromic sequences (HIPs) and their relationship to DNA methyltransferases
Elhai, J. (2015) · Life · doi:10.3390/life5010921 · Cited by 20 · see citing works
CRISPR-Cas mediated genome engineering of cyanobacteria
Sengupta, A., Liu, D., & Pakrasi, H. B. (2022) · Methods in Enzymology · doi:10.1016/bs.mie.2022.07.023 · Cited by 13 · see citing works
Ohdate, K., Sakata, M., Maeda, K., Sakamaki, Y., Nimura-Matsune, K., Ohbayashi, R., Hess, W. R., & Watanabe, S. (2024) · Frontiers in Microbiology · doi:10.3389/fmicb.2024.1311290 · Cited by 9 · see citing works
Characterization of Limnospira platensis PCC 9108 R-M and CRISPR-Cas systems
Castillo, M., Guevara, G., Baldanta, S., Rodríguez, P. S., Agudo, L., Nogales, J., Carrasco, A. D., Arribas-Aguilar, F., Pérez-Pérez, J., García, J. L., et al. (2024) · Microbiological Research · doi:10.1016/j.micres.2023.127572 · Cited by 7 · see citing works
He, H., Gao, K., Mao, B., Shi, G., Li, Y., & Deng, X. (2025) · Biotechnology Journal · doi:10.1002/biot.70162 · Cited by 4 · see citing works
- Authors
- 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., Eisen, J. A., Woyke, T., Gugger, M., & Kerfeld, C. A.
- Affiliations
- Joint Genome Institute (US)
- Centre National de la Recherche Scientifique (FR)
- University of Helsinki (FI)
- Aix-Marseille University, Laboratoire de Chimie Bactérienne (LCB), Centre National de la Recherche Scientifique (CNRS) Unité Mixte de Recherche (UMR) 7283, 13402 Marseille, France;
- Institut Pasteur, Collection des Cyanobactéries, 75724 Paris Cedex 15, France; and
- Institut Pasteur (FR)
- Los Alamos National Laboratory (US)
- ORCID
- Venue
- Proceedings of the National Academy of Sciences
- Publisher
- National Academy of Sciences
- Published
- 2012-12-31
- Volume
- 110
- Issue
- 3
- Pages
- 1053-1058
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- PMC
- PMC3549136
- OpenAlex
- W2075555781
- Cited by
- 800
- References
- 94
- Citations by year
- 2026: 29 · 2025: 27 · 2024: 42 · 2023: 34 · 2022: 54 · 2021: 67 · 2020: 71 · 2019: 73 · 2018: 66 · 2017: 65 · 2016: 83 · 2015: 79 · 2014: 80 · 2013: 28 · 2012: 1
- FWCI
- 24.19
- Type
- journal article
- Language
- en
- Open access
- green
- europepmc.org
- Locations
- Proceedings of the National Academy of Sciences (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information) (submittedVersion)
- HAL (submittedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- Funders
- National Science Foundation (DEAC02-05CH11231, 0851070)
- U.S. Department of Energy (-AC02-05CH11231, 05CH11231, DE AC02 05CH11231, DE-AC02-)
- Joint Genome Institute (AC02-05CH11231, DE–AC02–05CH11231)
- Agence Nationale de la Recherche (ANR-10-INBS-0001)
- Centre National de la Recherche Scientifique (DE-AC02-05CH11231)
- Office of Science (DEAC02–05CH11231, AC02-05CH11231, DE-AC02)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Photosynthetic Processes and Mechanisms
- Life Sciences › Agricultural and Biological Sciences › Ecology, Evolution, Behavior and Systematics › Biocrusts and Microbial Ecology
- Keywords
- cyanobacteria, novel proteins, light-harvesting proteins, secondary metabolite gene clusters, biofuels
- MeSH terms
- Cyanobacteria, Amino Acid Sequence, Bacterial Proteins, Multigene Family, Models, Molecular, Molecular Sequence Data, Phylogeny, Genetic Variation, Genome, Bacterial, Sequence Homology, Amino Acid, Plastids, Evolution, Molecular, Photosystem I Protein Complex, Light-Harvesting Protein Complexes, Chlorophyll Binding Proteins
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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