Tomitani A, Knoll AH, Cavanaugh CM, Ohno T. The evolutionary diversification of Cyanobacteria: molecular-phylogenetic and paleontological perspectives. Proc Natl Acad Sci USA. 2006;103:5442–7.
Schirrmeister BE, Gugger M, Donoghue PCJ. Cyanobacteria and the Great Oxidation Event: evidence from genes and fossils. Palaeontology. 2015;58:769–85.
Fischer WW, Hemp J, Johnson JE. Evolution of oxygenic photosynthesis. Annu Rev Earth Planet Sci. 2016;44:647–83.
Soo RM, Hemp J, Parks DH, Fischer WW, Hugenholtz P. On the origins of oxygenic photosynthesis and aerobic respiration in Cyanobacteria. Science. 2017;355:1436–40.
Biller SJ, Berube PM, Lindell D, Chisholm SW. Prochlorococcus: the structure and function of collective diversity. Nat Rev Microbiol. 2015;13:13–27.
Sánchez-Baracaldo P. Origin of marine planktonic Cyanobacteria. Sci Rep. 2015;5:14–17.
Shang JL, Chen M, Hou S, Li T, Yang YW, Li Q, et al. Genomic and transcriptomic insights into the survival of the subaerial cyanobacterium Nostoc flagelliforme in arid and exposed habitats. Environ Microbiol. 2019;21:845–63.
Chrismas NAM, Anesio AM, Śanchez-Baracaldo P. The future of genomics in polar and alpine Cyanobacteria. FEMS Microbiol Ecol. 2018;94:fiy032.
Kashtan N, Roggensack SE, Rodrigue S, Thompson JW, Biller SJ, Coe A, et al. Single-cell genomics reveals hundreds of coexisting subpopulations in wild Prochlorococcus. Science. 2014;344:416–20.
Larsson J, Celepli N, Ininbergs K, Dupont CL, Yooseph S, Bergman B, et al. Picocyanobacteria containing a novel pigment gene cluster dominate the brackish water Baltic Sea. ISME J. 2014;8:1892–903.
Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol. 2012;19:455–77.
Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 2015;25:1043–55.
Gurevich A, Saveliev V, Vyahhi N, Tesler G. QUAST: quality assessment tool for genome assemblies. Bioinformatics. 2013;29:1072–5.
Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics. 2014;30:2068–9.
Mistry J, Finn RD, Eddy SR, Bateman A, Punta M. Challenges in homology search: HMMER3 and convergent evolution of coiled-coil regions. Nucleic Acids Res. 2013;41:e121.
Wu M, Scott AJ. Phylogenomic analysis of bacterial and archaeal sequences with AMPHORA2. Bioinformatics. 2012;28:1033–4.
Capella-Gutierrez S, Silla-Martinez JM, Gabaldon T. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics. 2009;25:1972–3.
Waterhouse RM, Seppey M, Simão FA, Manni M, Ioannidis P, Klioutchnikov G, et al. BUSCO applications from quality assessments to gene prediction and phylogenomics. Mol Biol Evol. 2018;35:543–8.
Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 2013;30:772–80.
Miller MA, Pfeiffer W, Schwartz T. Creating the CIPRES Science Gateway for inference of large phylogenetic trees. In: Proceedings of the Gateway Computing Environments Workshop (GCE). New Orleans (LA): IEEE; 2010. pp 1–8.
Nguyen L-T, Schmidt HA, von Haeseler A, Minh BQ. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol. 2015;32:268–74.
Di Rienzi SC, Sharon I, Wrighton KC, Koren O, Hug LA, Thomas BC, et al. The human gut and groundwater harbor non-photosynthetic bacteria belonging to a new candidate phylum sibling to Cyanobacteria. Elife. 2013;2:e01102.
Matheus Carnevali PB, Schulz F, Castelle CJ, Kantor RS, Shih PM, Sharon I, et al. Hydrogen-based metabolism as an ancestral trait in lineages sibling to the Cyanobacteria. Nat Commun. 2019;10:1–16.
Letunic I, Bork P. Interactive Tree Of Life (iTOL) v4: recent updates and new developments. Nucleic Acids Res. 2019;47:W256–9.
Tung HoLS, Ané C. A linear-time algorithm for Gaussian and non-Gaussian trait evolution models. Syst Biol. 2014;63:397–408.
Benjamini Y, Hochberg Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc Ser B. 1995;57:289–300.
Gan F, Bryant DA. Adaptive and acclimative responses of Cyanobacteria to far-red light. Environ Microbiol. 2015;17:3450–65.
Revell LJ. phytools: an R package for phylogenetic comparative biology (and other things). Methods Ecol Evol. 2012;3:217–23.
Levy A, Salas Gonzalez I, Mittelviefhaus M, Clingenpeel S, Herrera Paredes S, Miao J, et al. Genomic features of bacterial adaptation to plants. Nat Genet. 2018;50:138–50.
Zhu Q, Kosoy M, Dittmar K. HGTector: an automated method facilitating genome-wide discovery of putative horizontal gene transfers. BMC Genom. 2014;15:717.
Buchfink B, Xie C, Huson DH. Fast and sensitive protein alignment using DIAMOND. Nat Methods. 2014;12:59–60.
Csurös M. Count: evolutionary analysis of phylogenetic profiles with parsimony and likelihood. Bioinformatics. 2010;26:1910–2.
Enright AJ. An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res. 2002;30:1575–84.
Komárek J. A polyphasic approach for the taxonomy of Cyanobacteria: principles and applications. Eur J Phycol. 2016;51:346–53.
Komárek J, Kaštovský J, Mareš J, Johansen JR. Taxonomic classification of cyanoprokaryotes (Cyanobacterial genera) 2014, using a polyphasic approach. Preslia. 2014;86:295–335.
Ponce-Toledo RI, Deschamps P, López-García P, Zivanovic Y, Benzerara K, Moreira D. An early-branching freshwater Cyanobacterium at the origin of plastids. Curr Biol. 2017;27:386–91.
de Vries J, Archibald JM. Endosymbiosis: did plastids evolve from a freshwater Cyanobacterium? Curr Biol. 2017;27:R103–5.
Dagan T, Roettger M, Stucken K, Landan G, Koch R, Major P, et al. Genomes of stigonematalean Cyanobacteria (subsection V) and the evolution of oxygenic photosynthesis from prokaryotes to plastids. Genome Biol Evol. 2013;5:31–44.
Shih PM, Wu D, Latifi A, Axen SD, Fewer DP, Talla E, et al. Improving the coverage of the cyanobacterial phylum using diversity-driven genome sequencing. Proc Natl Acad Sci USA. 2013;110:1053–8.
Sánchez-Baracaldo P, Raven JA, Pisani D, Knoll AH. Early photosynthetic eukaryotes inhabited low-salinity habitats. Proc Natl Acad Sci USA. 2017;114:E7737–45.
FitzJohn RG, Maddison WP, Otto SP. Estimating trait-dependent speciation and extinction rates from incompletely resolved phylogenies. Syst Biol. 2009;58:595–611.
Monk JM, Charusanti P, Aziz RK, Lerman JA, Premyodhin N, Orth JD, et al. Genome-scale metabolic reconstructions of multiple Escherichia coli strains highlight strain-specific adaptations to nutritional environments. Proc Natl Acad Sci USA. 2013;110:20338–43.
Tripp HJ, Bench SR, Turk KA, Foster RA, Desany BA, Niazi F, et al. Metabolic streamlining in an open-ocean nitrogen-fixing cyanobacterium. Nature. 2010;464:90–4.
Scanlan DJ, Ostrowski M, Mazard S, Dufresne A, Garczarek L, Hess WR, et al. Ecological genomics of marine Picocyanobacteria. Microbiol Mol Biol Rev. 2009;73:249–99.
Poulton NJ, Acinas SG, Lauro FM, Cavicchioli R, Swan BK, Hanson NW, et al. Prevalent genome streamlining and latitudinal divergence of planktonic bacteria in the surface ocean. Proc Natl Acad Sci USA. 2013;110:11463–8.
Bentkowski P, Van Oosterhout C, Ashby B, Mock T. The effect of extrinsic mortality on genome size evolution in prokaryotes. ISME J. 2017;11:1011–8.
Steele JH, Brink KH, Scott BE. Comparison of marine and terrestrial ecosystems: suggestions of an evolutionary perspective influenced by environmental variation. ICES J Mar Sci. 2019;76:50–9.
Philippot L, Andersson SGE, Battin TJ, Prosser JI, Schimel JP, Whitman WB, et al. The ecological coherence of high bacterial taxonomic ranks. Nat Rev Microbiol. 2010;8:523–9.
Luo H, Csűros M, Hughes AL, Moran MA. Evolution of divergent life history strategies in marine Alphaproteobacteria. MBio. 2013;4:1–8.
Whitton BA (editor). Ecology of Cyanobacteria II. Dordrecht, Netherlands: Springer; 2012.
Yoshihara S, Katayama M, Geng X, Ikeuchi M. Cyanobacterial phytochrome-like PixJ1 holoprotein shows novel reversible photoconversion between blue- and green-absorbing forms. Plant Cell Physiol. 2004;45:1729–37.
Bhaya D, Takahashi A, Grossman AR. Light regulation of type IV pilus-dependent motility by chemosensor-like elements in Synechocystis PCC6803. Proc Natl Acad Sci USA. 2001;98:7540–5.
Yang Y, Lam V, Adomako M, Simkovsky R, Jakob A, Rockwell NC, et al. Phototaxis in a wild isolate of the cyanobacterium Synechococcus elongatus. Proc Natl Acad Sci USA. 2018;115:E12378–87.
Kehoe DM, Gutu A. Responding to color: the regulation of complementary chromatic adaptation. Annu Rev Plant Biol. 2006;57:127–50.
Sánchez-Baracaldo P, Bianchini G, Di Cesare A, Callieri C, Chrismas NAM. Insights Into the evolution of Picocyanobacteria and Phycoerythrin Genes (mpeBA and cpeBA). Front Microbiol. 2019;10:45.
Ting CS, Rocap G, King J, Chisholm SW. Cyanobacterial photosynthesis in the oceans: the origins and significance of divergent light-harvesting strategies. Trends Microbiol. 2002;10:134–42.
Gan F, Zhang S, Rockwell NC, Martin SS, Lagarias JC, Bryant DA. Extensive remodeling of a cyanobacterial photosynthetic apparatus in far-red light. Science. 2014;345:1312–7.
Thiel V, Tank M, Bryant DA. Diversity of chlorophototrophic bacteria revealed in the Omics Era. Annu Rev Plant Biol. 2018;69:21–49.
Kühl M, Trampe E, Mosshammer M, Johnson M, Larkum AWD, Frigaard N-U, et al. Substantial near-infrared radiation-driven photosynthesis of chlorophyll f-containing Cyanobacteria in a natural habitat. Elife. 2020;9:e50871.
Oren A. Microbial life at high salt concentrations: phylogenetic and metabolic diversity. Saline Syst. 2008;4:1–13.
Sääf A, Baars L, von Heijne G. The internal repeats in the Na+/Ca 2+ exchanger-related Escherichia coli protein YrbG have opposite membrane topologies. J Biol Chem. 2001;276:18905–7.
Price GD, Woodger FJ, Badger MR, Howitt SM, Tucker L. Identification of a SulP-type bicarbonate transporter in marine Cyanobacteria. Proc Natl Acad Sci USA. 2004;101:18228–33.
Sakamoto T, Inoue-Sakamoto K, Bryant DA. A novel nitrate/nitrite permease in the marine cyanobacterium Synechococcus sp. strain PCC 7002. J Bacteriol. 1999;181:7363–72.
Carrieri D, Wawrousek K, Eckert C, Yu J, Maness PC. The role of the bidirectional hydrogenase in Cyanobacteria. Bioresour Technol. 2011;102:8368–77.
Tamagnini P, Axelsson R, Lindberg P, Oxelfelt F, Wunschiers R, Lindblad P. Hydrogenases and hydrogen metabolism of Cyanobacteria. Microbiol Mol Biol Rev. 2002;66:1–20.
Huisman J, Codd GA, Paerl HW, Ibelings BW, Verspagen JMH, Visser PM. Cyanobacterial blooms. Nat Rev Microbiol. 2018;16:471–83.
Ben Fekih I, Zhang C, Li YP, Zhao Y, Alwathnani HA, Saquib Q, et al. Distribution of arsenic resistance genes in prokaryotes. Front Microbiol. 2018;9:2473.
Fürst-Jansen JMR, de Vries S, de Vries J. Evo-physio: on stress responses and the earliest land plants. J Exp Bot. 2020;71:3254–69.
Murik O, Oren N, Shotland Y, Raanan H, Treves H, Kedem I, et al. What distinguishes Cyanobacteria able to revive after desiccation from those that cannot: the genome aspect. Environ Microbiol. 2017;19:535–50.
Gul N, Poolman B. Functional reconstitution and osmoregulatory properties of the ProU ABC transporter from Escherichia coli. Mol Membr Biol. 2013;30:138–48.
Pathak J, Ahmed H, Singh PR, Singh SP, Häder D-P, Sinha RP. Mechanisms of photoprotection in Cyanobacteria. In: Mishra AK, Tiwari DN, Rai AN. editors. Cyanobacteria. Cambridge: Academic Press; 2019. pp. 145–171.
Meulenbroek EM, Peron Cane C, Jala I, Iwai S, Moolenaar GF, Goosen N, et al. UV damage endonuclease employs a novel dual-dinucleotide flipping mechanism to recognize different DNA lesions. Nucleic Acids Res. 2013;41:1363–71.
Richardson EJ, Bacigalupe R, Harrison EM, Weinert LA, Lycett S, Vrieling M, et al. Gene exchange drives the ecological success of a multi-host bacterial pathogen. Nat Ecol Evol. 2018;2:1468–78.
Wiedenbeck J, Cohan FM. Origins of bacterial diversity through horizontal genetic transfer and adaptation to new ecological niches. FEMS Microbiol Rev. 2011;35:957–76.
Smillie CS, Smith MB, Friedman J, Cordero OX, David LA, Alm EJ. Ecology drives a global network of gene exchange connecting the human microbiome. Nature. 2011;480:241–4.
Sheppard SK, Guttman DS, Fitzgerald JR. Population genomics of bacterial host adaptation. Nat Rev Genet. 2018;19:1–17.
Oliveira PH, Touchon M, Rocha EPC. Regulation of genetic flux between bacteria by restriction-modification systems. Proc Natl Acad Sci USA. 2016;113:5658–63.
Jain R, Rivera MC, Lake JA. Horizontal gene transfer among genomes: the complexity hypothesis. Proc Natl Acad Sci USA. 1999;96:3801–6.
Pál C, Papp B, Lercher MJ. Adaptive evolution of bacterial metabolic networks by horizontal gene transfer. Nat Genet. 2005;37:1372–5.
Source: Ecology - nature.com
