Genomics of Algae

Abstract

Algae are dominant contributors to primary production and have a major impact on biogeochemical cycles because of their unique metabolisms. Few algal genomes have so far been characterized, although whole genome sequences have now been generated from representatives of the green, red and brown algae. In addition, numerous projects are progressing to define algal transcriptomes using expressed sequence tags (ESTs) and microarrays. Multiple efforts based on comparative and functional genomics approaches have already generated an influx of exciting data about evolutionary origins and functional innovations of different algal species dispersed throughout the eukaryotic tree of life.

Key concepts:

  • Algal species have little common phylogeny and are widely dispersed throughout the eukaryotic tree of life.

  • Red and green algae lie within the Archaeplastida whereas brown algae lie within the Stramenopile and Alveolata lineages.

  • Brown algae have secondary plastids, thought to be derived from secondary endosymbiosis.

  • Chlamydomonas reinhardtii represents the bestā€studied experimental system for algae.

  • Diatom genomes are highly chimeric in nature, with genes derived from both partners of the secondary endosymbiosis, as well as large numbers of bacterial genes acquired by horizontal gene transfer.

  • The existence of C4 photosynthesis in algae has not yet been conclusively demonstrated.

  • Distinct algal species often comprise ecotypes optimized for growth in specific environmental conditions.

Keywords: algal genome; biofuel; chlamydomonas; diatom; prasinophyte; transcriptome

Figure 1.

Schematic representation of current views of plastid evolution in eukaryotic phytoplankton. (a) Engulfment of a cyanobacterial ancestor and subsequent reduction to a primary plastid by a eukaryotic host initially led to the formation of three lineages with primary plastids: the chlorophytes and land plants, rhodophytes and glaucophytes. (b) The subsequent uptake of a green or a red alga by independent hosts to form secondary endosymbioses resulted in euglenophytes, chlorarachniophytes and the monophyletic Chromalveolates. Chromalveolates, which represent the association of chromists (Stramenopiles, Haptophyta and Cryptophyta) and the Alveolata (Apicomplexa, Perkinsidae, Dinophyta and Ciliata), unite an extremely diverse array of protists. (c) Different Dinophyta have replaced their original secondary plastid with a green alga‐derived plastid either by serial secondary endosymbiosis (Lepidodinium) or even tertiary endosymbioses, for example, Karlodinium harbours a tertiary plastid of haptophyte origin. The heterokontophyte Rhopalodia gibba appears to have engulfed a cyanobacterial Cyanothece spp.

Figure 2.

Placement of the ongoing or completed (in bold) algal genome sequencing projects in the tree of eukaryotic life. Reproduced by the permission of the Editorial Office of Journal of Systematics and Evolution, Baldauf .

Figure 3.

Schematic representation of diatom evolution. The origin of the diatom ‘melting pot’ genome finds its origins in successive gene transfers after the primary and secondary endosymbioses that permitted gene transfer from prey nucleus to host nucleus as well as from organelles to nucleus. Diatoms also seem to have acquired genes through lateral gene transfer both before and after the diversification of pennates and centrics. Other driving forces of diversification have been proposed to be through the action of mobile transposable elements and by selective gene loss/expansions during niche adaptation (Bowler et al., ).

close

References

Allen AE, Vardi A and Bowler C (2006) An ecological and evolutionary context for integrated nitrogen metabolism and related signaling pathways in marine diatoms. Current Opinion in Plant Biology 9: 264–273.

Apt KE, KrothPancic PG and Grossman AR (1996) Stable nuclear transformation of the diatom Phaeodactylum tricornutum. Molecular & General Genetics 252: 572–579.

Armbrust EV, Berges JA, Bowler C et al. (2004) The genome of the diatom Thalassiosira pseudonana: ecology, evolution, and metabolism. Science 306: 79–86.

Baldauf SL (2008) An overview of the phylogeny and diversity of eukaryotes. Journal of Systematics and Evolution 46: 263–273.

Bowler C, Allen AE, Badger JH et al. (2008) The Phaeodactylum genome reveals the evolutionary history of diatom genomes. Nature 456: 239–244.

Chisti Y (2008) Biodiesel from microalgae beats bioethanol. Trends in Biotechnology 26: 126–131.

Connolly JA, Oliver MJ, Beaulieu JM et al. (2008) Correlated evolution of genome size and cell volume in diatoms (Bacillariophyceae). Journal of Phycology 44: 124–131.

Courties C, Vaquer A, Troussellier M et al. (1994) Smallest eukaryotic organism. Nature 370: 255.

Derelle E, Ferraz C, Rombauts S et al. (2006) Genome analysis of the smallest free‐living eukaryote Ostreococcus tauri unveils many unique features. Proceedings of the National Academy of Sciences of the USA 103: 11647–11652.

Douglas S, Zauner S, Fraunholz M et al. (2001) The highly reduced genome of an enslaved algal nucleus. Nature 410: 1091–1096.

Dunahay T, Jarvis E and Roessler P (1995) Genetic transformation of the diatoms Cyclotella cryptica and Navicula saprophita. Journal of Phycology 31: 1004–1012.

Falciatore A, d'Alcala MR, Croot P and Bowler C (2000) Perception of environmental signals by a marine diatom. Science 288: 2363–2366.

Falciatore A, Casotti R, Leblanc C, Abrescia C and Bowler C (1999) Transformation of nonselectable reporter genes in marine diatoms. Marine Biotechnology 1: 239–251.

Fernandez E and Galvan A (2007) Inorganic nitrogen assimilation in Chlamydomonas. Journal of Experimental Botany 58: 2279–2287.

Fischer H, Robl I, Sumper M and Kröger N (1999) Targeting and covalent modification of cell wall and membrane proteins heterologously expressed in the diatom Cylindrotheca fusiformis (Bacillariophyceae). Journal of Phycology 35: 113–120.

Ghirardi ML, Posewitz MC, Maness PC et al. (2007) Hydrogenases and hydrogen photoproduction in oxygenic photosynthetic organisms. Annual Review of Plant Biology 58: 71–91.

Gollery M, Harper J, Cushman J et al. (2006) What makes species unique? The contribution of proteins with obscure features. Genome Biology 7: R57.

Govorunova EG, Jung K‐H, Sineshchekov OA and Spudich JL (2004) Chlamydomonas sensory rhodopsins A and B: cellular content and role in photophobic responses. Biophysical Journal 86: 2342–2349.

Grossman AR, Croft M, Gladyshev VN et al. (2007) Novel metabolism in Chlamydomonas through the lens of genomics. Current Opinion in Plant Biology 10: 190–198.

Gruber A, Vugrinec S, Hempel F et al. (2007) Protein targeting into complex diatom plastids: functional characterisation of a specific targeting motif. Plant Molecular Biology 64: 519–530.

Henderson GP, Gan L and Jensen GJ (2007) 3‐D ultrastructure of O. tauri: electron cryotomography of an entire eukaryotic cell. PLoS ONE 2: e749.

Hildebrand M (2005) Cloning and functional characterization of ammonium transporters from the marine diatom Cylindrotheca fusiformis. Journal of Phycology 41: 105–113.

Im C‐S, Zhang Z, Shrager J, Chang C‐W and Grossman A (2003) Analysis of light and CO2 regulation in Chlamydomonas reinhardtii using genome‐wide approaches. Photosynthesis Research 75: 111–125.

Keller LC, Romijn EP, Zamora I, Yates JR and Marshall WF (2005) Proteomic analysis of isolated Chlamydomonas centrioles reveals orthologs of ciliary‐disease genes. Current Biology 15: 1090–1098.

Kitao Y, Harada H and Matsuda Y (2008) Localization and targeting mechanisms of two chloroplastic β‐carbonic anhydrases in the marine diatom Phaeodactylum tricornutum. Physiologia Plantarum 133: 68–77.

Kroth PG, Chiovitti A, Gruber A et al. (2008) A model for carbohydrate metabolism in the diatom Phaeodactylum tricornutum deduced from comparative whole genome analysis. PLoS ONE 1: e1426.

Kuroiwa T (1998) The primitive red algae Cyanidium caldarium and Cyanidioschyzon merolae as model system for investigating the dividing apparatus of mitochondria and plastids. BioEssays 20: 344–354.

Leggat W, Hoegh‐Guldberg O, Dove S and Yellowlees D (2007) Analysis of an EST library from the dinoflagellate (Symbiodinium sp.) symbiont of reef‐building corals. Journal of Phycology 43: 1010–1021.

Maheswari U, Mock T, Armbrust EV and Bowler C (2009) Update of the diatom EST database: a new tool for digital transcriptomics. Nucleic Acids Research 37: D1001–D1005.

Matsuzaki M, Misumi O, Shin‐i T et al. (2004) Genome sequence of the ultrasmall unicellular red alga Cyanidioschyzon merolae 10D. Nature 428: 653–657.

Merchant SS, Prochnik SE, Vallon O et al. (2007) The Chlamydomonas genome reveals the evolution of key animal and plant functions. Science 318: 245–250.

Minoda A, Sakagami R, Yagisawa F, Kuroiwa T and Tanaka K (2004) Improvement of culture conditions and evidence for nuclear transformation by homologous recombination in a red alga, Cyanidioschyzon merolae 10D. Plant and Cell Physiology 45: 667–671.

Mitra M, Mason CB, Xiao Y et al. (2005) The carbonic anhydrase gene families of Chlamydomonas reinhardtii. Canadian Journal of Botany‐Revue Canadienne De Botanique 83: 780–795.

Montsant A, Allen AE, Coesel S et al. (2007) Identification and comparative genomic analysis of signaling and regulatory components in the diatom Thalassiosira pseudonana. Journal of Phycology 43: 585–603.

Montsant A, Jabbari K, Maheswari U and Bowler C (2005) Comparative genomics of the pennate diatom Phaeodactylum tricornutum. Plant Physiology 137: 500–513.

Moulager M, Monnier A, Jesson B et al. (2007) Light‐dependent regulation of cell division in Ostreococcus: evidence for a major transcriptional input. Plant Physiology 144: 1360–1369.

Nelson DM, Treguer P, Brzezinski MA, Leynaert A and Queguiner B (1995) Production and dissolution of biogenic silica in the ocean: revised global estimates, comparison with regional data and relationship to biogenic sedimentation. Global Biogeochemical Cycles 9: 359–372.

Palenik B, Grimwood J, Aerts A et al. (2007) The tiny eukaryote Ostreococcus provides genomic insights into the paradox of plankton speciation. Proceedings of the National Academy of Sciences of the USA 104: 7705–7710.

Peters AF, Scornet D, Ratin M et al. (2008) Life‐cycle‐generation‐specific developmental processes are modified in the immediate upright mutant of the brown alga Ectocarpus siliculosus. Development 135: 1503–1512.

Poulsen N, Chesley PM and Kroger N (2006) Molecular genetic manipulation of the diatom Thalassiosira pseudonana (Bacillariophyceae). Journal of Phycology 42: 1059–1065.

Proschold T, Harris EH and Coleman AW (2005) Portrait of a species: Chlamydomonas reinhardtii. Genetics 170: 1601–1610.

Reisdorph NA and Small GD (2004) The CPH1 gene of Chlamydomonas reinhardtii encodes two forms of cryptochrome whose levels are controlled by light‐induced proteolysis. Plant Physiology 134: 1546–1554.

Reyes‐Prieto A, Weber APM and Bhattacharya D (2007) The origin and establishment of the plastid in algae and plants. Annual Review of Genetics 41: 147–168.

Siaut M, Heijde M, Mangogna M et al. (2007) Molecular toolbox for studying diatom biology in Phaeodactylum tricornutum. Gene 406: 23–35.

Steinke M, Malin G and Liss PS (2002) Trophic interactions in the sea: an ecological role for climate relevant volatiles? Journal of Phycology 38: 630–638.

Swartz TE, Tseng TS, Frederickson MA et al. (2007) Blue‐light‐activated histidine kinases: two‐component sensors in bacteria. Science 317: 1090–1093.

Takahashi F, Yamagata D, Ishikawa M et al. (2007) AUREOCHROME, a photoreceptor required for photomorphogenesis in stramenopiles. Proceedings of the National Academy of Sciences of the USA 104: 19625–19630.

Waaland JR, Stiller JW and Cheney DP (2004) Macroalgal candidates for genomics. Journal of Phycology 40: 26–33.

Worden AZ, Nolan JK and Palenik B (2004) Assessing the dynamics and ecology of marine picophytoplankton: the importance of the eukaryotic component. Limnology and Oceanography 49: 168–179.

Xu Y, Feng L, Jeffrey PD, Shi YG and Morel FMM (2008) Structure and metal exchange in the cadmium carbonic anhydrase of marine diatoms. Nature 452: 56–61.

Yoon HS, Hackett JD, Ciniglia C, Pinto G and Bhattacharya D (2004) A molecular timeline for the origin of photosynthetic eukaryotes. Molecular Biology and Evolution 21: 809–818.

Zhang Z, Shrager J, Jain M et al. (2004) Insights into the survival of Chlamydomonas reinhardtii during sulfur starvation based on microarray analysis of gene expression. Eukaryotic Cell 3: 1331–1348.

Zipfel C (2008) Pattern‐recognition receptors in plant innate immunity. Current Opinion in Immunology 20: 10–16.

Further Reading

Edwards GE, Franceschi VR and Voznesenskaya EV (2004) Single‐cell C‐4 photosynthesis versus the dual‐cell (Kranz) paradigm. Annual Review of Plant Biology 55: 173–196.

Falciatore A and Bowler C (2005) The evolution and function of blue and red light photoreceptors. Current Topics in Developmental Biology 68: 317–350.

Contact Editor close
Submit a note to the editor about this article by filling in the form below.

* Required Field

How to Cite close
Heijde, Marc, and Bowler, Chris(Sep 2009) Genomics of Algae. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0021254]