NEW YORK (GenomeWeb) – The Fragilariopsis cylindrus polar alga genome harbors a number of divergent alleles that may enable it to cope with the extremes of life in the Southern Ocean, a team of international researchers has reported.
During the winter, which is marked by periods of extensive darkness, F. cylindrus becomes part of sea ice. The ice can reach sub-zero temperatures Celsius, can have high salinity, and can have low diffusion and exchange of dissolved gasses and nutrients. In the summer, the alga is released when the ice melts.
As they reported this week in Nature, researchers at the Joint Genome Institute, the Earlham Institute, and elsewhere sequenced F. cylindrus and compared its genome to related temperate water-dwelling diatoms. The researchers found that nearly a quarter of the F. cylindrus genome is made up highly divergent alleles, and suggested that these allelic differences may be enabling it to endure life in polar waters.
"These alleles were differentially expressed across important environmental conditions, and we found evidence that those conditions were causing the allelic differentiation," first author Thomas Mock from the University of East Anglia said in a statement. "As the effective population size of this polar diatom is huge, there is an allele for every occasion, which seems to make this organism extremely adaptable to changing environmental conditions."
He and his colleagues sequenced the F. cylindrus genome on both Sanger and Pacific Biosciences platforms to yield a 61.1 megabase assembly. About 24.7 percent, 15.1 Mb, were loci with divergent alleles. The researchers noted that using both sequencing approaches enabled them to resolve divergent alleles from paralogous genes.
By comparing the F. cylindrus genome to the genomes of the Thalassiosira pseudonana and Phaedactylum tricornutum diatoms, Mock and his colleagues found that it was enriched for metal-binding protein families, particularly copper- and zinc-binding proteins. Zinc levels are fairly high in the surface waters of the Southern Ocean, they noted, and that could have sparked the expansion of the zinc-binding MYND domains in the F. cylindrus genome, which contains 121 such domains, compared to seven in T. pseudonana and 12 in P. tricornutum.
The researchers also profiled the F. cylindrus transcriptome under various growth conditions, such as darkness, low iron, and high and low temperatures. When they mimicked polar winter conditions by growing F. cylindrus in darkness for seven days, for instance, genes involved in photosynthesis were downregulated as ones involved in starch, sucrose, and lipid metabolism were upregulated.
Some two thirds of the diverged alleles exhibited more than four-fold change in differential expression under one of the different growth conditions as compared to optimal conditions. This suggested to the researchers that the individual alleles might be under different regulatory controls. Indeed, they noted lower sequence identity among promoter regions of diverged allele pairs, indicating functional diversity. In addition, alleles with higher ratios of non-synonymous to synonymous nucleotide substitution exhibited increased condition-dependent differences in expression, suggesting a link between diversifying selection and allelic differentiation.
This allelic divergence appears to be the result of both selection and a high mutation drift parameter, Mock and his colleagues said. They estimated F. cylindrus to have an effective population size of 165 million and a recombination rate that's five times that of the mutation rate. They further noted that the F. cylindrus alleles coalesced only recently at the onset of the last glacial period, which started 110,000 years ago.
"Our studies suggest that the diversification of alleles took place only recently and is maintained in the vast gene pool of the diatom, which allows it to thrive under the highly variable environmental conditions of the Southern Ocean," the researchers wrote.