Skip to main content
SpringerLink
Log in

Phototroph genomics ten years on

  • Regular Paper
  • Published:
Photosynthesis Research Aims and scope Submit manuscript

Abstract

The onset of the genome era means different things to different people, but it is clear that this new age brings with it paradigm shifts that will forever affect biological research. Less clear is just how these shifts are changing the scope and scale of research. Are gigabases of raw data more useful than a single well-understood gene? Do we really need a full genome to understand the physiology of a single organism? The photosynthetic field is poised at the periphery of the bulk of genome sequencing work—understandably skewed toward health-related disciplines—and, as such, is subject to different motivations, limitations, and primary focus for each new genome. To understand some of these differences, we focus here on various indicators of the impact that genomics has had on the photosynthetic community, now a full decade since the publication of the first photosynthetic genome. Many useful indicators are indexed in public databases, providing pre- and post-genome sequence snapshots of changes in factors such as publication rate, number of proteins characterized, and sequenced genome coverage versus known diversity. As more genomes are sequenced and metagenomic projects begin to pour out billions of bases, it becomes crucial to understand how to harness this data in order to accumulate possible benefits and avoid possible pitfalls, especially as resources become increasingly directed toward natural environments governed by photosynthetic activity, ranging from hot springs to tropical forest ecosystems to the open ocean.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6
Fig. 7
Fig. 8

Similar content being viewed by others

References

  • Arabidopsis Genome Initiative (AGI) (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408:796–815

    Article  Google Scholar 

  • Archibald JM (2005) Jumping genes and shrinking genomes-probing the evolution of eukaryotic photosynthesis with genomics. IUBMB Life 57:539–547

    Article  PubMed  CAS  Google Scholar 

  • Armbrust EV, Berges JA, Bowler C, Green BR, Martinez D, Putnam NH, Zhou S, Allen AE, Apt KE, Bechner M, Brzezinski MA, Chaal BK, Chiovitti A, Davis AK, Demarest MS, Detter JC, Glavina T, Goodstein D, Hadi MZ, Hellsten U, Hildebrand M, Jenkins BD, Jurka J, Kapitonov VV, Kroger N, Lau WW, Lane TW, Larimer FW, Lippmeier JC, Lucas S, Medina M, Montsant A, Obornik M, Parker MS, Palenik B, Pazour GJ, Richardson PM, Rynearson TA, Saito MA, Schwartz DC, Thamatrakoln K, Valentin K, Vardi A, Wilkerson FP, Rokhsar DS (2004) The genome of the diatom Thalassiosira pseudonana: ecology, evolution, and metabolism. Science 306:79–86

    Article  PubMed  CAS  Google Scholar 

  • Beja O, Suzuki MT, Heidelberg JF, Nelson WC, Preston CM, Hamada T, Eisen JA, Fraser CM, DeLong EF (2002) Unsuspected diversity among marine aerobic anoxygenic phototrophs. Nature 415:630–633

    Article  PubMed  CAS  Google Scholar 

  • Blankenship RE (1992) Origin and early evolution of photosynthesis. Photosynth Res 33:91–111

    Article  PubMed  CAS  Google Scholar 

  • Blattner FR, Plunkett G 3rd, Bloch CA, Perna NT, Burland V, Riley M, Collado-Vides J, Glasner JD, Rode CK, Mayhew GF, Gregor J, Davis NW, Kirkpatrick HA, Goeden MA, Rose DJ, Mau B, Shao Y (1997) The complete genome sequence of Escherichia coli K-12. Science 277:1453–1474

    Article  PubMed  CAS  Google Scholar 

  • Bouman HA, Ulloa O, Scanlan DJ, Zwirglmaier K, Li WK, Platt T, Stuart V, Barlow R, Leth O, Clementson L, Lutz V, Fukasawa M, Watanabe S, Sathyendranath S (2006) Oceanographic basis of the global surface distribution of Prochlorococcus ecotypes. Science 312:918–921

    Article  PubMed  CAS  Google Scholar 

  • Branscomb E, Predki P (2002) On the high value of low standards. J Bacteriol 184:6406–6409; discussion 6409

    Google Scholar 

  • Bryant DA, Frigaard NU (2006) Prokaryotic photosynthesis and phototrophy illuminated. Trends Microbiol 14:488–496

    PubMed  CAS  Google Scholar 

  • Bryant DA et al (2007) Candidatus Chloracidobacterium thermophilum: an aerobic phototrophic Acidobacterium. Science 317:523–526

    Article  PubMed  CAS  Google Scholar 

  • Bult CJ, White O, Olsen GJ, Zhou L, Fleischmann RD, Sutton GG, Blake JA, FitzGerald LM, Clayton RA, Gocayne JD, Kerlavage AR, Dougherty BA, Tomb JF, Adams MD, Reich CI, Overbeek R, Kirkness EF, Weinstock KG, Merrick JM, Glodek A, Scott JL, Geoghagen NS, Venter JC (1996) Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii. Science 273:1058–1073

    Article  PubMed  CAS  Google Scholar 

  • Cho JC, Stapels MD, Morris RM, Vergin KL, Schwalbach MS, Givan SA, Barofsky DF, Giovannoni SJ (2007) Polyphyletic photosynthetic reaction centre genes in oligotrophic marine Gammaproteobacteria. Environ Microbiol 9:1456–1463

    Article  PubMed  CAS  Google Scholar 

  • Dufresne A, Salanoubat M, Partensky F, Artiguenave F, Axmann IM, Barbe V, Duprat S, Galperin MY, Koonin EV, Le Gall F, Makarova KS, Ostrowski M, Oztas S, Robert C, Rogozin IB, Scanlan DJ, Tandeau de Marsac N, Weissenbach J, Wincker P, Wolf YI, Hess WR (2003) Genome sequence of the cyanobacterium Prochlorococcus marinus SS120, a nearly minimal oxyphototrophic genome. Proc Natl Acad Sci USA 100:10020–10025

    Article  PubMed  CAS  Google Scholar 

  • Dufresne A, Garczarek L, Partensky F (2005) Accelerated evolution associated with genome reduction in a free-living prokaryote. Genome Biol 6:R14

    Article  PubMed  Google Scholar 

  • Eisen JA, Nelson KE, Paulsen IT, Heidelberg JF, Wu M, Dodson RJ, Deboy R, Gwinn ML, Nelson WC, Haft DH, Hickey EK, Peterson JD, Durkin AS, Kolonay JL, Yang F, Holt I, Umayam LA, Mason T, Brenner M, Shea TP, Parksey D, Nierman WC, Feldblyum TV, Hansen CL, Craven MB, Radune D, Vamathevan J, Khouri H, White O, Gruber TM, Ketchum KA, Venter JC, Tettelin H, Bryant DA, Fraser CM (2002) The complete genome sequence of Chlorobium tepidum TLS, a photosynthetic, anaerobic, green-sulfur bacterium. Proc Natl Acad Sci USA 99:9509–9514

    Article  PubMed  CAS  Google Scholar 

  • Fan Q, Lechno-Yossef S, Ehira S, Kaneko T, Ohmori M, Sato N, Tabata S, Wolk CP (2006) Signal transduction genes required for heterocyst maturation in Anabaena sp. strain PCC 7120. J Bacteriol 188:6688–6693

    Article  PubMed  CAS  Google Scholar 

  • Fleischmann RD, Adams MD, White O, Clayton RA, Kirkness EF, Kerlavage AR, Bult CJ, Tomb JF, Dougherty BA, Merrick JM et al (1995) Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 269:496–512

    Article  PubMed  CAS  Google Scholar 

  • Follows MJ, Dutkiewicz S, Grant S, Chisholm SW (2007) Emergent biogeography of microbial communities in a model ocean. Science 315:1843–1846

    Article  PubMed  CAS  Google Scholar 

  • Frigaard NU, Bryant DA (2004) Seeing green bacteria in a new light: genomics-enabled studies of the photosynthetic apparatus in green sulfur bacteria and filamentous anoxygenic phototrophic bacteria. Arch Microbiol 182:265–276

    Article  PubMed  CAS  Google Scholar 

  • Frigaard NU, Chew AG, Li H, Maresca JA, Bryant DA (2003) Chlorobium tepidum: insights into the structure, physiology, and metabolism of a green sulfur bacterium derived from the complete genome sequence. Photosynth Res 78:93–117

    Article  PubMed  CAS  Google Scholar 

  • Frigaard NU, Maresca JA, Yunker CE, Jones AD, Bryant DA (2004) Genetic manipulation of carotenoid biosynthesis in the green sulfur bacterium Chlorobium tepidum. J Bacteriol 186:5210–5220

    Article  PubMed  CAS  Google Scholar 

  • Garrity GM, Holt JG (2001) Phylum BXI. Chlorobi phy. nov. In: Boone DR, Castenholz RW (eds) Bergey’s manual of systematic bacteriology. Springer, New York

    Google Scholar 

  • Gerdes SY, Kurnasov OV, Shatalin K, Polanuyer B, Sloutsky R, Vonstein V, Overbeek R, Osterman AL (2006) Comparative genomics of NAD biosynthesis in cyanobacteria. J Bacteriol 188:3012–3023

    Article  PubMed  CAS  Google Scholar 

  • Giraud E, Moulin L, Vallenet D, Barbe V, Cytryn E, Avarre JC, Jaubert M, Simon D, Cartieaux F, Prin Y, Bena G, Hannibal L, Fardoux J, Kojadinovic M, Vuillet L, Lajus A, Cruveiller S, Rouy Z, Mangenot S, Segurens B, Dossat C, Franck WL, Chang WS, Saunders E, Bruce D, Richardson P, Normand P, Dreyfus B, Pignol D, Stacey G, Emerich D, Vermeglio A, Medigue C, Sadowsky M (2007) Legumes symbioses: absence of Nod genes in photosynthetic Bradyrhizobia. Science 316:1307–1312

    Article  PubMed  Google Scholar 

  • Heinnickel M, Agalarov R, Svensen N, Krebs C, Golbeck JH (2006) Identification of FX in the heliobacterial reaction center as a [4Fe-4S] cluster with an S = 3/2 ground spin state. Biochemistry 45:6756–6764

    Article  PubMed  CAS  Google Scholar 

  • Heinnickel M, Shen G, Golbeck JH (2007) Identification and characterization of PshB, the dicluster ferredoxin that harbors the terminal electron acceptors F(A) and F(B) in Heliobacterium modesticaldum. Biochemistry 46:2530–2536

    Article  PubMed  CAS  Google Scholar 

  • Herter S, Fuchs G, Bacher A, Eisenreich W (2002) A bicyclic autotrophic CO2 fixation pathway in Chloroflexus aurantiacus. J Biol Chem 277:20277–20283

    Article  PubMed  CAS  Google Scholar 

  • Hess WR (2004) Genome analysis of marine photosynthetic microbes and their global role. Curr Opin Biotechnol 15:191–198

    Article  PubMed  CAS  Google Scholar 

  • Hess WR, Rocap G, Ting CS, Larimer F, Stilwagen S, Lamerdin J, Chisholm SW (2001) The photosynthetic apparatus of Prochlorococcus: insights through comparative genomics. Photosynth Res 70:53–71

    Article  PubMed  CAS  Google Scholar 

  • Howe CJ, Barbrook AC, Koumandou VL, Nisbet RE, Symington HA, Wightman TF (2003) Evolution of the chloroplast genome. Philos Trans R Soc Lond B Biol Sci 358:99–106; discussion 106–107

    Article  PubMed  CAS  Google Scholar 

  • Jackson CR, Dugas SL (2003) Phylogenetic analysis of bacterial and archaeal arsC gene sequences suggests an ancient, common origin for arsenate reductase. BMC Evol Biol 3:18

    Article  PubMed  Google Scholar 

  • Kaneko T, Sato S, Kotani H, Tanaka A, Asamizu E, Nakamura Y, Miyajima N, Hirosawa M, Sugiura M, Sasamoto S, Kimura T, Hosouchi T, Matsuno A, Muraki A, Nakazaki N, Naruo K, Okumura S, Shimpo S, Takeuchi C, Wada T, Watanabe A, Yamada M, Yasuda M, Tabata S (1996) Sequence analysis of the genome of the unicellular cyanobacterium Synechocystis sp. strain PCC6803. II. Sequence determination of the entire genome and assignment of potential protein-coding regions. DNA Res 3:109–136

    Article  PubMed  CAS  Google Scholar 

  • Kaneko T, Nakamura Y, Wolk CP, Kuritz T, Sasamoto S, Watanabe A, Iriguchi M, Ishikawa A, Kawashima K, Kimura T, Kishida Y, Kohara M, Matsumoto M, Matsuno A, Muraki A, Nakazaki N, Shimpo S, Sugimoto M, Takazawa M, Yamada M, Yasuda M, and Tabata S (2001) Complete genomic sequence of the filamentous nitrogen-fixing cyanobacterium Anabaena sp. strain PCC 7120. DNA Res 8:205–213; 227–253

    Google Scholar 

  • Kaneko T, Nakamura Y, Sato S, Minamisawa K, Uchiumi T, Sasamoto S, Watanabe A, Idesawa K, Iriguchi M, Kawashima K, Kohara M, Matsumoto M, Shimpo S, Tsuruoka H, Wada T, Yamada M, Tabata S (2002) Complete genomic sequence of nitrogen-fixing symbiotic bacterium Bradyrhizobium japonicum USDA110. DNA Res 9:189–197

    Article  PubMed  Google Scholar 

  • Kanzler BE, Pfannes KR, Vogl K, Overmann J (2005) Molecular characterization of the nonphotosynthetic partner bacterium in the consortium “Chlorochromatium aggregatum”. Appl Environ Microbiol 71:7434–7441

    Article  PubMed  CAS  Google Scholar 

  • Kawarabayasi Y, Hino Y, Horikawa H, Jin-no K, Takahashi M, Sekine M, Baba S, Ankai A, Kosugi H, Hosoyama A, Fukui S, Nagai Y, Nishijima K, Otsuka R, Nakazawa H, Takamiya M, Kato Y, Yoshizawa T, Tanaka T, Kudoh Y, Yamazaki J, Kushida N, Oguchi A, Aoki K, Masuda S, Yanagii M, Nishimura M, Yamagishi A, Oshima T, Kikuchi H (2001) Complete genome sequence of an aerobic thermoacidophilic crenarchaeon, Sulfolobus tokodaii strain7. DNA Res 8:123–140

    Article  PubMed  CAS  Google Scholar 

  • Keeling PJ (2004) Diversity and evolutionary history of plastids and their hosts. Am J Bot 91:1481–1493

    Article  Google Scholar 

  • Kroth PG (2002) Protein transport into secondary plastids and the evolution of primary and secondary plastids. Int Rev Cytol 221:191–255

    Article  PubMed  CAS  Google Scholar 

  • Kunst F, Ogasawara N, Moszer I, Albertini AM, Alloni G, Azevedo V, Bertero MG, Bessieres P, Bolotin A, Borchert S, Borriss R, Boursier L, Brans A, Braun M, Brignell SC, Bron S, Brouillet S, Bruschi CV, Caldwell B, Capuano V, Carter NM, Choi SK, Codani JJ, Connerton IF, Danchin A et al (1997) The complete genome sequence of the gram-positive bacterium Bacillus subtilis. Nature 390:249–256

    Article  PubMed  CAS  Google Scholar 

  • Larimer FW, Chain P, Hauser L, Lamerdin J, Malfatti S, Do L, Land ML, Pelletier DA, Beatty JT, Lang AS, Tabita FR, Gibson JL, Hanson TE, Bobst C, Torres JL, Peres C, Harrison FH, Gibson J, Harwood CS (2004) Complete genome sequence of the metabolically versatile photosynthetic bacterium Rhodopseudomonas palustris. Nat Biotechnol 22:55–61

    Article  PubMed  CAS  Google Scholar 

  • Larkum AW, Lockhart PJ, Howe CJ (2007) Shopping for plastids. Trends Plant Sci 12:189–195

    Article  PubMed  CAS  Google Scholar 

  • Leister D (2003) Chloroplast research in the genomic age. Trends Genet 19:47–56

    Article  PubMed  CAS  Google Scholar 

  • Martin W, Rujan T, Richly E, Hansen A, Cornelsen S, Lins T, Leister D, Stoebe B, Hasegawa M, Penny D (2002) Evolutionary analysis of Arabidopsis, cyanobacterial, and chloroplast genomes reveals plastid phylogeny and thousands of cyanobacterial genes in the nucleus. Proc Natl Acad Sci USA 99:12246–12251

    Article  PubMed  CAS  Google Scholar 

  • Martiny AC, Coleman ML, Chisholm SW (2006) Phosphate acquisition genes in Prochlorococcus ecotypes: evidence for genome-wide adaptation. Proc Natl Acad Sci USA 103:12552–12557

    Article  PubMed  CAS  Google Scholar 

  • Matsuzaki M, Misumi O, Shin IT, Maruyama S, Takahara M, Miyagishima SY, Mori T, Nishida K, Yagisawa F, Yoshida Y, Nishimura Y, Nakao S, Kobayashi T, Momoyama Y, Higashiyama T, Minoda A, Sano M, Nomoto H, Oishi K, Hayashi H, Ohta F, Nishizaka S, Haga S, Miura S, Morishita T, Kabeya Y, Terasawa K, Suzuki Y, Ishii Y, Asakawa S, Takano H, Ohta N, Kuroiwa H, Tanaka K, Shimizu N, Sugano S, Sato N, Nozaki H, Ogasawara N, Kohara Y, Kuroiwa T (2004) Genome sequence of the ultrasmall unicellular red alga Cyanidioschyzon merolae 10D. Nature 428:653–657

    Article  PubMed  CAS  Google Scholar 

  • McFadden GI (1999) Endosymbiosis and evolution of the plant cell. Curr Opin Plant Biol 2:513–519

    Article  PubMed  CAS  Google Scholar 

  • Meeks JC, Elhai J, Thiel T, Potts M, Larimer F, Lamerdin J, Predki P, Atlas R (2001) An overview of the genome of Nostoc punctiforme, a multicellular, symbiotic cyanobacterium. Photosynth Res 70:85–106

    Article  PubMed  CAS  Google Scholar 

  • Meeks JC, Campbell EL, Summers ML, Wong FC (2002) Cellular differentiation in the cyanobacterium Nostoc punctiforme. Arch Microbiol 178:395–403

    Article  PubMed  CAS  Google Scholar 

  • Moran MA, Buchan A, Gonzalez JM, Heidelberg JF, Whitman WB, Kiene RP, Henriksen JR, King GM, Belas R, Fuqua C, Brinkac L, Lewis M, Johri S, Weaver B, Pai G, Eisen JA, Rahe E, Sheldon WM, Ye W, Miller TR, Carlton J, Rasko DA, Paulsen IT, Ren Q, Daugherty SC, Deboy RT, Dodson RJ, Durkin AS, Madupu R, Nelson WC, Sullivan SA, Rosovitz MJ, Haft DH, Selengut J, Ward N (2004) Genome sequence of Silicibacter pomeroyi reveals adaptations to the marine environment. Nature 432:910–913

    Article  PubMed  CAS  Google Scholar 

  • Nakamura Y, Kaneko T, Sato S, Ikeuchi M, Katoh H, Sasamoto S, Watanabe A, Iriguchi M, Kawashima K, Kimura T, Kishida Y, Kiyokawa C, Kohara M, Matsumoto M, Matsuno A, Nakazaki N, Shimpo S, Sugimoto M, Takeuchi C, Yamada M, Tabata S (2002) Complete genome structure of the thermophilic cyanobacterium Thermosynechococcus elongatus BP-1. DNA Res 9:123–130

    Article  PubMed  CAS  Google Scholar 

  • Nakamura Y, Kaneko T, Sato S, Mimuro M, Miyashita H, Tsuchiya T, Sasamoto S, Watanabe A, Kawashima K, Kishida Y, Kiyokawa C, Kohara M, Matsumoto M, Matsuno A, Nakazaki N, Shimpo S, Takeuchi C, Yamada M, Tabata S (2003) Complete genome structure of Gloeobacter violaceus PCC 7421, a cyanobacterium that lacks thylakoids. DNA Res 10:137–145

    Article  PubMed  CAS  Google Scholar 

  • Olson JM, Blankenship RE (2004) Thinking about the evolution of photosynthesis. Photosynth Res 80:373–386

    Article  PubMed  CAS  Google Scholar 

  • Overmann J (1999) Green sulfur bacteria. Encyclopedia of life sciences. Wiley, Chichester

    Google Scholar 

  • Overmann J (2006) Symbiosis between non-related bacteria in phototrophic consortia. Prog Mol Subcell Biol 41:21–37

    Article  PubMed  CAS  Google Scholar 

  • Oyaizu H, Debrunner-Vossbrinck B, Mandelco L, Studier JA, Woese CR (1987) The green non-sulfur bacteria: a deep branching in the eubacterial line of descent. Syst Appl Microbiol 9:47–53

    PubMed  CAS  Google Scholar 

  • Palenik B, Grimwood J, Aerts A, Rouze P, Salamov A, Putnam N, Dupont C, Jorgensen R, Derelle E, Rombauts S, Zhou K, Otillar R, Merchant SS, Podell S, Gaasterland T, Napoli C, Gendler K, Manuell A, Tai V, Vallon O, Piganeau G, Jancek S, Heijde M, Jabbari K, Bowler C, Lohr M, Robbens S, Werner G, Dubchak I, Pazour GJ, Ren Q, Paulsen I, Delwiche C, Schmutz J, Rokhsar D, Van de Peer Y, Moreau H, Grigoriev IV (2007) The tiny eukaryote Ostreococcus provides genomic insights into the paradox of plankton speciation. Proc Natl Acad Sci USA 104:7705–7710

    Article  PubMed  CAS  Google Scholar 

  • Pradella S, Allgaier M, Hoch C, Pauker O, Stackebrandt E, Wagner-Dobler I (2004) Genome organization and localization of the pufLM genes of the photosynthesis reaction center in phylogenetically diverse marine Alphaproteobacteria. Appl Environ Microbiol 70:3360–3369

    Article  PubMed  CAS  Google Scholar 

  • Raymond J, Zhaxybayeva O, Gogarten JP, Gerdes SY, Blankenship RE (2002) Whole-genome analysis of photosynthetic prokaryotes. Science 298:1616–1620

    Article  PubMed  CAS  Google Scholar 

  • Raymond J, Zhaxybayeva O, Gogarten JP, Blankenship RE (2003) Evolution of photosynthetic prokaryotes: a maximum-likelihood mapping approach. Philos Trans R Soc Lond B Biol Sci 358:223–230

    Article  PubMed  Google Scholar 

  • Rocap G, Larimer FW, Lamerdin J, Malfatti S, Chain P, Ahlgren NA, Arellano A, Coleman M, Hauser L, Hess WR, Johnson ZI, Land M, Lindell D, Post AF, Regala W, Shah M, Shaw SL, Steglich C, Sullivan MB, Ting CS, Tolonen A, Webb EA, Zinser ER, Chisholm SW (2003) Genome divergence in two Prochlorococcus ecotypes reflects oceanic niche differentiation. Nature 424:1042–1047

    Article  PubMed  CAS  Google Scholar 

  • Rusch DB, Halpern AL, Sutton G, Heidelberg KB, Williamson S, Yooseph S, Wu D, Eisen JA, Hoffman JM, Remington K, Beeson K, Tran B, Smith H, Baden-Tillson H, Stewart C, Thorpe J, Freeman J, Andrews-Pfannkoch C, Venter JE, Li K, Kravitz S, Heidelberg JF, Utterback T, Rogers YH, Falcon LI, Souza V, Bonilla-Rosso G, Eguiarte LE, Karl DM, Sathyendranath S, Platt T, Bermingham E, Gallardo V, Tamayo-Castillo G, Ferrari MR, Strausberg RL, Nealson K, Friedman R, Frazier M, Venter JC (2007) The Sorcerer II global ocean sampling expedition: Northwest Atlantic through Eastern Tropical Pacific. PLoS Biol 5:e77

    Article  PubMed  CAS  Google Scholar 

  • Schomburg I, Chang A, Ebeling C, Gremse M, Heldt C, Huhn G, Schomburg D (2004) BRENDA, the enzyme database: updates and major new developments. Nucleic Acids Res 32:D431–D433

    Article  PubMed  CAS  Google Scholar 

  • Sullivan MB, Lindell D, Lee JA, Thompson LR, Bielawski JP, Chisholm SW (2006) Prevalence and evolution of core photosystem II genes in marine cyanobacterial viruses and their hosts. PLoS Biol 4:e234

    Article  PubMed  CAS  Google Scholar 

  • Swingley WD, Blankenship RE, Raymond J (2007a) Insights into cyanobacterial evolution from comparative genomics. In: Herrero A, Flores E (eds) The cyanobacteria: molecular biology, genomics and evolution. Caister Academic Press

  • Swingley WD, Sadekar S, Mastrian SD, Matthies HJ, Hao J, Ramos H, Acharya CR, Conrad AL, Taylor HL, Dejesa LC, Shah MK, O’Huallachain M E, Lince MT, Blankenship RE, Beatty JT, Touchman JW (2007b) The complete genome sequence of Roseobacter denitrificans reveals a mixotrophic rather than photosynthetic metabolism. J Bacteriol 189:683–690

    Article  PubMed  CAS  Google Scholar 

  • Trost JT, Blankenship RE (1989) Isolation of a photoactive Photosynthetic Reaction Center-Core Antenna Complex from Heliobacillus mobilis. Biochemistry 28:9898–9904

    Article  PubMed  CAS  Google Scholar 

  • Valladares A, Maldener I, Muro-Pastor AM, Flores E, Herrero A (2007) Heterocyst development and diazotrophic metabolism in terminal respiratory oxidase mutants of the cyanobacterium Anabaena sp. Strain PCC 7120. J Bacteriol 189:4425–4430

    Article  PubMed  CAS  Google Scholar 

  • Xiong J, Inoue K, Bauer CE (1998) Tracking molecular evolution of photosynthesis by characterization of a major photosynthesis gene cluster from Heliobacillus mobilis. Proc Natl Acad Sci USA 95:14851–14856

    Article  PubMed  CAS  Google Scholar 

  • Yanyushin MF, del Rosario MC, Brune DC, Blankenship RE (2005) New class of bacterial membrane oxidoreductases. Biochemistry 44:10037–10045

    Article  PubMed  CAS  Google Scholar 

  • Yooseph S, Sutton G, Rusch DB, Halpern AL, Williamson SJ, Remington K, Eisen JA, Heidelberg KB, Manning G, Li W, Jaroszewski L, Cieplak P, Miller CS, Li H, Mashiyama ST, Joachimiak MP, van Belle C, Chandonia JM, Soergel DA, Zhai Y, Natarajan K, Lee S, Raphael BJ, Bafna V, Friedman R, Brenner SE, Godzik A, Eisenberg D, Dixon JE, Taylor SS, Strausberg RL, Frazier M, Venter JC (2007) The Sorcerer II Global Ocean Sampling Expedition: Expanding the Universe of Protein Families. PLoS Biol 5:e16

    Article  PubMed  CAS  Google Scholar 

  • Yutin N, Suzuki MT, Teeling H, Weber M, Venter JC, Rusch DB, Beja O (2007) Assessing diversity and biogeography of aerobic anoxygenic phototrophic bacteria in surface waters of the Atlantic and Pacific Oceans using the Global Ocean Sampling expedition metagenomes. Environ Microbiol 9:1464–1475

    Article  PubMed  CAS  Google Scholar 

  • Zhang CC, Laurent S, Sakr S, Peng L, Bedu S (2006) Heterocyst differentiation and pattern formation in cyanobacteria: a chorus of signals. Mol Microbiol 59:367–375

    Article  PubMed  CAS  Google Scholar 

  • Zhao Y, Shi Y, Zhao W, Huang X, Wang D, Brown N, Brand J, Zhao J (2005) CcbP, a calcium-binding protein from Anabaena sp. PCC 7120, provides evidence that calcium ions regulate heterocyst differentiation. Proc Natl Acad Sci USA 102:5744–5748

    Article  PubMed  CAS  Google Scholar 

  • Zhaxybayeva O, Gogarten JP, Charlebois RL, Doolittle WF, Papke RT (2006) Phylogenetic analyses of cyanobacterial genomes: quantification of horizontal gene transfer events. Genome Res 16:1099–1108

    Article  PubMed  CAS  Google Scholar 

Download references

Acknowledgments

The authors wish to thank Robert Blankenship for his comments and suggestions, Marilyn Gunner for the invitation to contribute to this special issue, and the host of researchers—most of whom are unnamed and uncited here due to necessary brevity—for their tireless efforts to bring genomics to the photosynthesis community and vice versa. WS acknowledges support through a JSPS Fellowship. JR acknowledges support through an E.O. Lawrence Postdoctoral Fellowship while at Lawrence Livermore Lab.

Author information

Authors and Affiliations

  1. School of Natural Sciences, University of California, Merced, Merced, CA, USA

    Jason Raymond

  2. Institute of Low Temperature Science, Hokkaido University, Sapporo, Japan

    Wesley D. Swingley

Authors
  1. Jason Raymond
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Wesley D. Swingley
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Jason Raymond.

Electronic supplementary material

Below is the link to the electronic supplementary material.

(XLS 420 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Raymond, J., Swingley, W.D. Phototroph genomics ten years on. Photosynth Res 97, 5–19 (2008). https://doi.org/10.1007/s11120-008-9308-z

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11120-008-9308-z

Keywords

Search

Navigation