Useful algal genome sequencing
Whole-genome sequence analyses have become indispensable for algal research. Sequence analyses provide information on the evolution of different groups of algae and contribute to our understanding of the molecular mechanisms algae use to adapt to climate change as well as unlocking the potential to develop new and economically important products and technologies.
New sequencing methods such as “next generation sequencing” make it possible to sequence entire genomes in a relatively short time and a lot more cheaply than only a few years ago. Biological areas that frequently lack money and expensive instruments and that unlike “red”, “green” and “white” biotechnology are not part of the main focus of powerful industrial sectors such as the pharmaceutical, agricultural and chemical industries, are also likely to benefit from these developments.
The study of algae (phycology) is a field of biological research that has long been way outside the “mainstream” despite the fact that phycologists have repeatedly highlighted the huge ecological and increasing economic importance of algae that results from their role as suppliers of oxygen and primary members of the largest food chains in the world. This takes the form of animal feed and fertiliser and also of food for humans, particularly in Eastern Asia. Algae also produce raw materials such as carrageen, agar and agarose, algines and alginates, on which the modern food and cosmetic industries depend to a large degree and which are indispensable for cell culture laboratories.
Over the last few years, the technical progress and decreasing costs of sequencing methods has led to the deciphering of the genomes of representatives of important algal groups. Model algae have already been sequenced and a large number of other sequencing projects are in the pipeline. The results are providing us with new findings about the evolution of these organisms and their dominant functions in marine ecosystems. It is also envisaged that there will be an economic benefit to these findings.
While the Joint Genome Institute of the Department of Energy is the main coordinator of the majority of American algae projects, European algal research has received a considerable boost through the “Marine Genomics Europe” (MGE) excellence network that received funding under the 6th Research Framework of the EU between 2004 and 2008. The MGE involved 45 institutions from 14 European and two non-European countries, including a team led by Detlev Arendt and Jan Ellenberg at the European Molecular Biology Laboratory in Heidelberg. In addition, Dr. Klaus Valentin and his team at the Alfred Wegener Institute for Polar and Marine Research (AWI) have made important contributions to deciphering the genomes of algae.
Algal oil as a substitute for diesel?
The Alfred Wegener Institute (AWI) researchers were part of a large international consortium that focused on the complete decoding of the genome of the diatom Phaeodactylum tricornutum. Diatoms (Bacillariophyceae) are a large group of algae and one of the most common types of phytoplankton at the base of the marine food and metabolism chains, where they play an extraordinary role. It is estimated that diatoms account for 40 per cent of photosynthetic activity in the oceans, or in other words, one in five oxygen molecules that we breathe in is produced by these microscopically small, unicellular algae.
According to current knowledge amongst cell and evolutionary biologists, diatoms are so-called secondary endosymbionts. It has long been believed that diatoms inherited their chloroplasts and photosynthetic capabilities exclusively from unicellular eukaryotic red algae rather than as a result of engulfing prokaryotic cyanobacteria as is commonly assumed for green plants, green and red algae. However, the AWI researchers have been able to show that P. tricornutum possesses a broad range of photosynthesis genes that originate from different cell types, including green algae genes. The photosynthetic structures (plastids) of Phaeodactylum tricornutum therefore combine features from their green and red algae predecessors, which might also explain their enormous success in the oceans. The interpretation of the genome data benefitted from the previous publication of the DNA sequences of another diatom, Thalassiosira pseudonana, with which it was possible to compare the new diatom sequences.
Genes involved in the diatoms’ fat metabolism have attracted particular attention. This is due to the diatoms’ ability to synthesise omega-3 fatty acids. It is believed that this ability will play a major economic role in the future. The oils make marine fish an important source of human food and they originate mainly from these algae. Energy producers have recently identified diatoms as important producers of renewable biofuel.
In the USA, it goes without saying that the Department of Energy is highly interested in identifying new biofuel sources. The Joint Genome Institute, which is part of the US Department of Energy, has sequenced the genome of the freshwater alga Volvox carteri. Volvox is a chlorophyte green alga and an early ancestor of green land plants, amongst others. Up until now, biologists have used Volvox as a simple model for investigating multicellular organisms.
Volvox forms spherical multicellular colonies; the body consists of a gelatine-like substance in which a small number of reproductive germ cells and hundreds of thousands of non-reproductive somatic cells are embedded. Volvox is closely related to Chlamydomonas, a unicellular, green alga which is frequently cultivated in the laboratory and the object of intensive investigation in terms of its potential as a biofuel producer. The Volvox genome was sequenced by the Joint Genome Institute back in 2007.
Brown and red algae
It seems surprising that brown algae (Phaeophyceae) which form huge algal forests along the rocky shores of polar and moderate oceans and can reach lengths of up to 160 m, are relatives of the tiny diatoms. This relationship was discovered many decades ago by comparative developmental biologists and biochemists and has now been confirmed by an international team of researchers, which includes researchers from AWI. The team is the first to determine the complete genome sequence of the brown alga Ectocarpus siliculosus genome. “We discovered a high proportion of genes in the brown alga that are characteristic of green algae, including the kinases and transporters typical of multicellular land plants,” explained Klaus Valentin, who was involved in the international cooperative project (quote: AWI 3rd June 2010). These results can be best explained by taking the theory that brown algae and diatoms arose from the fusion of a green alga with a red alga, rather than from the fusion of a unicellular red alga with photosynthetically inactive cells. The researchers have thus been able to refute a theory held to be true by many experts.
The genome of brown algae is also subject to intensive ecological research. Many brown algae species are characterised by extreme tolerance to stress, which enables them to live in tidal zones where they are alternately exposed to drought and intensive sunshine. The researchers are interested in the algae’s genetic adaptation to UV light and high temperatures, in particular in view of ongoing climatic change. The very versatile metabolism of this group of organisms that is very old in evolutionary terms is not yet known in great detail. It can be assumed that this type of research opens up new approaches for new products and technologies that go far beyond the algines and alginates that have so far been produced from brown algae.
The complete genome of a representative of another huge and economically important algal group, which has evolved into complex multicellular organisms (red algae, Rhodophyta), has also been sequenced. However, the data have not yet been published as researchers are still working on the analysis of the sequencing data. Japanese researchers deciphered the genome of another red alga species as long ago as 2004. However, this particular species, Cyanidioschyzon merolae, lives in an extreme habitat, i.e. hot, sulphur-containing springs, and is therefore not very representative of the group of red algae. It only has 16.5 million base pairs, which is the smallest genome of all photosynthetically active eukaryotes known to date.
The genomes of some species of lesser known algal groups have also been partially or completely sequenced, including the genome of Aureococcus anophagefferens (published on 21st February 2011 in the journal PNAS), which is a rather inconspicuous representative of offshore phytoplankton. Over the last few years, the frequency and intensity of Aureococcus algal blooms have increased across the globe. Such harmful algal blooms cause severe damage to the ecosystem of the area where they occur due to large-scale marine mortality which in turn severely impacts fishing and mussel harvests. Auoreococcus anophagefferens congregate in their billions per litre of seawater, thereby forming an extensive red layer on the sea’s surface. The researchers hope that knowledge of the genes will help them to understand why the alga blooms, when it blooms and how it is able to do so despite the fact that there are so many other competing plankton species in the water. Dr. Björn Rost from the AWI is focusing on the question as to how climate change (the warming and acidification of the oceans resulting from increasing atmospheric CO2 amounts) impacts the growth of phytoplankton and the occurrence of algal blooms . His “PhytoChange” project is funded with an Independent Investor Grant from the European Research Council.
Despite all the progress made in molecular biology studies of algae over the last decades, to date the majority of studies have only focused on a handful of the huge number of algal organisms. Researchers estimate that around 90 per cent of all phytoplankton species are still unknown. Only a few years ago, a group of international researchers, including Dr. Klaus Valentin and Dr. Linda Medlin from the AWI, detected a completely new group of algae based on the analysis of 18S ribosomal DNA sequences and fluorescence in situ hybridisation. The co-authors of the study, Dr. Klaus Valentin and Dr. Linda Medlin, explained that this newly discovered algal group does not fit into any known group of eukaryotes. The algae, known as picobiliphytes, are only a few micrometres in size, and are thus among the smallest representatives of known plant plankton and an excellent example of the broad range of new species still to be discovered in the oceans using molecular biology methods.