Chisholm SW, Olson RJ, Zettler ER, Goericke R, Waterbury JB, Welschmeyer NA: A novel free-living prochlorophyte abundant in the oceanic euphotic zone. Nature. 1988, 334: 340-343. 10.1038/334340a0.
Article
Google Scholar
Partensky F, Hess WR, Vaulot D: Prochlorococcus, a marine photosynthetic prokaryote of global significance. Microbiol Mol Biol Rev. 1999, 63: 106-127.
PubMed Central
CAS
PubMed
Google Scholar
Partensky F, Garczarek L: Prochlorococcus: advantages and limits of minimalism. Ann Rev Mar Sci. 2010, 2: 305-331. 10.1146/annurev-marine-120308-081034.
Article
PubMed
Google Scholar
Moore LR, Rocap G, Chisholm SW: Physiology and molecular phylogeny of coexisting Prochlorococcus ecotypes. Nature. 1998, 393: 464-467. 10.1038/30965.
Article
CAS
PubMed
Google Scholar
García-Fernández JM, de Marsac NT, Diez J: Streamlined regulation and gene loss as adaptive mechanisms in Prochlorococcus for optimized nitrogen utilization in oligotrophic environments. Microbiol Mol Biol Rev. 2004, 68: 630-638. 10.1128/MMBR.68.4.630-638.2004.
Article
PubMed Central
PubMed
Google Scholar
Kettler GC, Martiny AC, Huang K, Zucker J, Coleman ML, Rodrigue S, Chen F, Lapidus A, Ferriera S, Johnson J, et al.: Patterns and implications of gene gain and loss in the evolution of Prochlorococcus. PLoS Genet. 2007, 3: e231-10.1371/journal.pgen.0030231.
Article
PubMed Central
PubMed
Google Scholar
Dufresne A, Garczarek L, Partensky F: Accelerated evolution associated with genome reduction in a free-living prokaryote. Genome Biol. 2005, 6: 1-10.
Article
Google Scholar
Marais GB, Calteau A, Tenaillon O: Mutation rate and genome reduction in endosymbiotic and free-living bacteria. Genetica. 2008, 134: 205-210. 10.1007/s10709-007-9226-6.
Article
PubMed
Google Scholar
Hu J, Blanchard JL: Environmental sequence data from the sargasso Sea reveal that the characteristics of genome reduction in Prochlorococcus Are Not a harbinger for an escalation in genetic drift. Mol Biol Evol. 2009, 26: 5-13.
Article
PubMed
Google Scholar
Luo H, Friedman R, Tang J, Hughes AL: Genome reduction by deletion of paralogs in the marine cyanobacterium Prochlorococcus. Mol Biol Evol. 2011, 28: 2751-2760. 10.1093/molbev/msr081.
Article
PubMed Central
CAS
PubMed
Google Scholar
Grote J, Thrash JC, Huggett MJ, Landry ZC, Carini P, Giovannoni SJ, Rappé MS: Streamlining and core genome conservation among highly divergent members of the SAR11 clade. mBio. 2012, 3 (5): e00252–12-
Article
PubMed Central
PubMed
Google Scholar
Liu W, Fang L, Li M, Li S, Guo S, Luo R, Feng Z, Li B, Zhou Z, Shao G, et al.: Comparative genomics of mycoplasma: analysis of conserved essential genes and diversity of the Pan-genome. PLoS One. 2012, 7 (4): e35698-10.1371/journal.pone.0035698.
Article
PubMed Central
CAS
PubMed
Google Scholar
Pál C, Papp B, Hurst LD: Highly expressed genes in yeast evolve slowly. Genetics. 2001, 158: 927-931.
PubMed Central
PubMed
Google Scholar
Drummond DA, Bloom JD, Adami C, Wilke CO, Arnold FH: Why highly expressed proteins evolve slowly. Proc Natl Acad Sci USA. 2005, 102: 14338-14343. 10.1073/pnas.0504070102.
Article
PubMed Central
CAS
PubMed
Google Scholar
Brawand D, Soumillon M, Necsulea A, Julien P, Csardi G, Harrigan P, Weier M, Liechti A, Aximu-Petri A, Kircher M, et al.: The evolution of gene expression levels in mammalian organs. Nature. 2011, 478: 343-348. 10.1038/nature10532.
Article
CAS
PubMed
Google Scholar
Whitehead A, Crawford DL: Neutral and adaptive variation in gene expression. Proc Natl Acad Sci USA. 2006, 103: 5425-5430. 10.1073/pnas.0507648103.
Article
PubMed Central
CAS
PubMed
Google Scholar
Drummond DA, Wilke CO: Mistranslation-induced protein misfolding as a dominant constraint on coding-sequence evolution. Cell. 2008, 134: 341-352. 10.1016/j.cell.2008.05.042.
Article
PubMed Central
CAS
PubMed
Google Scholar
Rocap G, Larimer FW, Lamerdin J, Malfatti S, Chain P, Ahlgren NA, Arellano A, Coleman M, Hauser L, Hess WR, et al.: Genome divergence in two Prochlorococcus ecotypes reflects oceanic niche differentiation. Nature. 2003, 424: 1042-1047. 10.1038/nature01947.
Article
CAS
PubMed
Google Scholar
Marioni JC, Mason CE, Mane SM, Stephens M, Gilad Y: RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays. Genome Res. 2008, 18: 1509-1517. 10.1101/gr.079558.108.
Article
PubMed Central
CAS
PubMed
Google Scholar
Wang Z, Gerstein M, Snyder M: RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet. 2009, 10: 57-63. 10.1038/nrg2484.
Article
PubMed Central
CAS
PubMed
Google Scholar
Cho B-K, Zengler K, Qiu Y, Park YS, Knight EM, Barrett CL, Gao Y, Palsson BO: The transcription unit architecture of the Escherichia coli genome. Nat Biotech. 2009, 27: 1043-1049. 10.1038/nbt.1582.
Article
CAS
Google Scholar
Passalacqua KD, Varadarajan A, Ondov BD, Okou DT, Zwick ME, Bergman NH: Structure and complexity of a bacterial transcriptome. J Bacteriol. 2009, 191: 3203-3211. 10.1128/JB.00122-09.
Article
PubMed Central
CAS
PubMed
Google Scholar
Wurtzel O, Sapra R, Chen F, Zhu Y, Simmons BA, Sorek R: A single-base resolution map of an archaeal transcriptome. Genome Res. 2010, 20: 133-141. 10.1101/gr.100396.109.
Article
PubMed Central
CAS
PubMed
Google Scholar
Vijayan V, Jain IH, O'Shea EK: A high resolution map of a cyanobacterial transcriptome. Genome Biol. 2011, 12 (5): R47-10.1186/gb-2011-12-5-r47.
Article
PubMed Central
PubMed
Google Scholar
Moore LR, Coe A, Zinser ER, Saito MA, Sullivan MB, Lindell D, Frois-Moniz K, Waterbury J, Chisholm SW: Culturing the marine cyanobacterium Prochlorococcus. Limnol Oceanogr Meth. 2007, 5: 353-362.
Article
CAS
Google Scholar
Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B: Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods. 2008, 5: 621-628. 10.1038/nmeth.1226.
Article
CAS
PubMed
Google Scholar
Taboada B, Ciria R, Martinez-Guerrero CE, Merino E: ProOpDB: prokaryotic operon DataBase. Nucleic Acids Res. 2012, 40: D627-D631. 10.1093/nar/gkr1020.
Article
PubMed Central
CAS
PubMed
Google Scholar
Steglich C, Futschik ME, Lindell D, Voss B, Chisholm SW, Hess WR: The challenge of regulation in a minimal photoautotroph: Non-coding RNAs in Prochlorococcus. PLoS Genet. 2008, 4 (8): e1000173-10.1371/journal.pgen.1000173.
Article
PubMed Central
PubMed
Google Scholar
Steglich C, Lindell D, Futschik M, Rector T, Steen R, Chisholm SW: Short RNA half-lives in the slow-growing marine cyanobacterium Prochlorococcus. Genome Biol. 2010, 11: R54-10.1186/gb-2010-11-5-r54.
Article
PubMed Central
PubMed
Google Scholar
Holtzendorff J, Partensky F, Mella D, Lennon J-F, Hess WR, Garczarek L: Genome streamlining results in loss of robustness of the circadian clock in the marine cyanobacterium Prochlorococcus marinus PCC 9511. J Biol Rhythms. 2008, 23: 187-199. 10.1177/0748730408316040.
Article
CAS
PubMed
Google Scholar
Mary I, Vaulot D: Two-component systems in Prochlorococcus MED4: Genomic analysis and differential expression under stress. FEMS Microbiol Lett. 2003, 226: 135-144. 10.1016/S0378-1097(03)00587-1.
Article
CAS
PubMed
Google Scholar
Memon D, Singh AK, Pakrasi HB, Wangikar PP: A global analysis of adaptive evolution of operons in cyanobacteria. Antonie Van Leeuwenhoek. 2013, 103 (2): 331-346. 10.1007/s10482-012-9813-0.
Article
CAS
PubMed
Google Scholar
Klein MG, Zwart P, Bagby SC, Cai F, Chisholm SW, Heinhorst S, Cannon GC, Kerfeld CA: Identification and structural analysis of a novel carboxysome shell protein with implications for metabolite transport. J Mol Biol. 2009, 392: 319-333. 10.1016/j.jmb.2009.03.056.
Article
CAS
PubMed
Google Scholar
Sorek R, Cossart P: Prokaryotic transcriptomics: a new view on regulation, physiology and pathogenicity. Nat Rev Genet. 2010, 11: 9-16.
Article
CAS
PubMed
Google Scholar
Gardner PP, Daub J, Tate JG, Nawrocki EP, Kolbe DL, Lindgreen S, Wilkinson AC, Finn RD, Griffiths-Jones S, Eddy SR, Bateman A: Rfam: updates to the RNA families database. Nucleic Acids Res. 2009, 37: D136-D140. 10.1093/nar/gkn766.
Article
PubMed Central
CAS
PubMed
Google Scholar
Tagwerker C, Dupont CL, Karas BJ, Ma L, Chuang RY, Benders GA, Ramon A, Novotny M, Montague MG, Venepally P, et al.: Sequence analysis of a complete 1.66 Mb Prochlorococcus marinus MED4 genome cloned in yeast. Nucleic Acids Res. 2012, 40 (20): 10375-10383. 10.1093/nar/gks823.
Article
PubMed Central
CAS
PubMed
Google Scholar
Naville M, Ghuillot-Gaudeffroy A, Marchais A, Gautheret D: ARNold: a web tool for the prediction of Rho-independent transcription terminators. RNA Biol. 2011, 8: 11-13. 10.4161/rna.8.1.13346.
Article
CAS
PubMed
Google Scholar
Waldbauer JR, Rodrigue S, Coleman ML, Chisholm SW: Transcriptome and proteome dynamics of a light–dark synchronized bacterial cell cycle. PLoS One. 2012, 7: e43432-10.1371/journal.pone.0043432.
Article
PubMed Central
CAS
PubMed
Google Scholar
Zhang R, Lin Y: DEG 5.0, a database of essential genes in both prokaryotes and eukaryotes. Nucleic Acids Res. 2009, 37: D455-D458. 10.1093/nar/gkn858.
Article
PubMed Central
CAS
PubMed
Google Scholar
Wall DP, Hirsh AE, Fraser HB, Kumm J, Giaever G, Eisen MB, Feldman MW: Functional genomic analysis of the rates of protein evolution. Proc Natl Acad Sci USA. 2005, 102: 5483-5488. 10.1073/pnas.0501761102.
Article
PubMed Central
CAS
PubMed
Google Scholar
Drummond DA, Raval A, Wilke CO: A single determinant dominates the rate of yeast protein evolution. Mol Biol Evol. 2006, 23: 327-337.
Article
CAS
PubMed
Google Scholar
Tatusov RL, Galperin MY, Natale DA, Koonin EV: The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res. 2000, 28: 33-36. 10.1093/nar/28.1.33.
Article
PubMed Central
CAS
PubMed
Google Scholar
Shi T, Falkowski PG: Genome evolution in cyanobacteria: the stable core and the variable shell. Proc Natl Acad Sci USA. 2008, 105: 2510-2515. 10.1073/pnas.0711165105.
Article
PubMed Central
CAS
PubMed
Google Scholar
Banerjee T, Ghosh TC: Gene expression level shapes the amino acid usages in Prochlorococcus marinus MED4. J Biomol Struct Dyn. 2006, 23: 547-553. 10.1080/07391102.2006.10507079.
Article
CAS
PubMed
Google Scholar
Mulkidjanian AY, Koonin EV, Makarova KS, Mekhedov SL, Sorokin A, Wolf YI, Dufresne A, Partensky F, Burd H, Kaznadzey D, et al.: The cyanobacterial genome core and the origin of photosynthesis. Proc Natl Acad Sci USA. 2006, 103: 13126-13131. 10.1073/pnas.0605709103.
Article
PubMed Central
CAS
PubMed
Google Scholar
Zinser ER, Lindell D, Johnson ZI, Futschik ME, Steglich C, Coleman ML, Wright MA, Rector T, Steen R, McNulty N, et al.: Choreography of the transcriptome, photophysiology, and cell cycle of a minimal photoautotroph, prochlorococcus. PLoS One. 2009, 4: e5135-10.1371/journal.pone.0005135.
Article
PubMed Central
PubMed
Google Scholar
Moore LR, Ostrowski M, Scanlan DJ, Feren K, Sweetsir T: Ecotypic variation in phosphorus-acquisition mechanisms within marine picocyanobacteria. Aquat Microb Ecol. 2005, 39: 257-269.
Article
Google Scholar
Avrani S, Wurtzel O, Sharon I, Sorek R, Lindell D: Genomic island variability facilitates Prochlorococcus-virus coexistence. Nature. 2011, 474: 604-608. 10.1038/nature10172.
Article
CAS
PubMed
Google Scholar
He QF, Dolganov N, Bjorkman O, Grossman AR: The high light-inducible polypeptides in Synechocystis PCC6803 - expression and function in high light. J Biol Chem. 2001, 276: 306-314.
Article
CAS
PubMed
Google Scholar
Pál C, Hurst LD: Evidence against the selfish operon theory. Trends Genet. 2004, 20: 232-234.
Article
PubMed
Google Scholar
Price MN, Huang KH, Arkin AP, Alm EJ: Operon formation is driven by co-regulation and not by horizontal gene transfer. Genome Res. 2005, 15: 809-819. 10.1101/gr.3368805.
Article
PubMed Central
CAS
PubMed
Google Scholar
Deana A, Belasco JG: Lost in translation: the influence of ribosomes on bacterial mRNA decay. Genes Dev. 2005, 19: 2526-2533. 10.1101/gad.1348805.
Article
CAS
PubMed
Google Scholar
Thompson AW, Huang K, Saito MA, Chisholm SW: Transcriptome response of high- and low-light-adapted Prochlorococcus strains to changing iron availability. ISME J. 2011, 5: 1580-1594. 10.1038/ismej.2011.49.
Article
PubMed Central
CAS
PubMed
Google Scholar
Pál C, Papp B, Lercher MJ: An integrated view of protein evolution. Nat Rev Genet. 2006, 7: 337-348. 10.1038/nrg1838.
Article
PubMed
Google Scholar
Drummond DA, Wilke CO: The evolutionary consequences of erroneous protein synthesis. Nat Rev Genet. 2009, 10: 715-724. 10.1038/nrg2662.
Article
PubMed Central
PubMed
Google Scholar
Stewart FJ, Sharma AK, Bryant JA, Eppley JM, DeLong EF: Community transcriptomics reveals universal patterns of protein sequence conservation in natural microbial communities. Genome Biol. 2011, 12 (3): R26-10.1186/gb-2011-12-3-r26.
Article
PubMed Central
CAS
PubMed
Google Scholar
Hirsh AE, Fraser HB: Protein dispensability and rate of evolution. Nature. 2001, 411: 1046-1049. 10.1038/35082561.
Article
CAS
PubMed
Google Scholar
Dandekar T, Snel B, Huynen M, Bork P: Conservation of gene order: a fingerprint of proteins that physically interact. Trends Biochem Sci. 1998, 23: 324-328. 10.1016/S0968-0004(98)01274-2.
Article
CAS
PubMed
Google Scholar
Chen Z, Wen B, Wang Q, Tong W, Guo J, Bai X, Zhao J, Sun Y, Tang Q, Lin Z, et al.: Quantitative proteomics reveals the temperature-dependent proteins encoded by a series of cluster genes in Thermoanaerobacter tengcongensis. Mol Cell Proteomics. 2013, 12 (8): 2266-2277. 10.1074/mcp.M112.025817.
Article
PubMed Central
CAS
PubMed
Google Scholar
Langmead B, Salzberg SL: Fast gapped-read alignment with Bowtie 2. Nat Meth. 2012, 9: 357-359. 10.1038/nmeth.1923.
Article
CAS
Google Scholar
Quinlan AR, Hall IM: BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010, 26: 841-842. 10.1093/bioinformatics/btq033.
Article
PubMed Central
CAS
PubMed
Google Scholar
Dehal PS, Joachimiak MP, Price MN, Bates JT, Baumohl JK, Chivian D, Friedland GD, Huang KH, Keller K, Novichkov PS, et al.: MicrobesOnline: an integrated portal for comparative and functional genomics. Nucleic Acids Res. 2010, 38: D396-D400. 10.1093/nar/gkp919.
Article
PubMed Central
CAS
PubMed
Google Scholar
Nagalakshmi U, Wang Z, Waern K, Shou C, Raha D, Gerstein M, Snyder M: The transcriptional landscape of the yeast genome defined by RNA sequencing. Science. 2008, 320: 1344-1349. 10.1126/science.1158441.
Article
PubMed Central
CAS
PubMed
Google Scholar
Besemer J, Borodovsky M: GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses. Nucleic Acids Res. 2005, 33: W451-W454. 10.1093/nar/gki487.
Article
PubMed Central
CAS
PubMed
Google Scholar
Yang Z, Nielsen R: Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models. Mol Biol Evol. 2000, 17: 32-43. 10.1093/oxfordjournals.molbev.a026236.
Article
CAS
PubMed
Google Scholar