Friday, February 4, 2011

Little water flea has big genome

Credit: Paul Hebert, University of Guelph
The little water flea used to have pride of place on the front cover of the Leaving Certificate Biology textbook when I was going to school. Little did we realise then that Daphnia would turn out to be so impressive!

Research just published in Science shows that the near-microscopic freshwater crustacean Daphnia pulex (the water flea) is the animal with most genes (about 31,000 in total).

"Daphnia's high gene number is largely because its genes are multiplying, creating copies at a higher rate than other species," said project leader and CGB (Centre for Genomics and Bioinformatics, Indiana University) genomics director John Colbourne.

"We estimate a rate that is three times greater than those of other invertebrates and 30 percent greater than that of humans."

Colbourne postulates that "since the majority of duplicated and unknown genes are sensitive to environmental conditions, their accumulation in the genome could account for Daphnia's flexible responses to environmental change."

Much of the media coverage has centred around the fact that the water flea outstrips humans in terms of gene number (humans have around 23,000 genes). This "paradox" known as the C-value enigma or C-value paradox is based on the fact that the genome size of an organism does not correlate with the complexity of the organism.

'Daphnia is an exquisite aquatic sensor, a modern version of the mineshaft canary' - James KlaunigIt's not a new idea - the term was first used in 1971 and the solution lies in the fact that lots of DNA in eukaryotes (i.e. non-bacteria) does not code for genes. For example, only about 1.5% of the human genome codes for genes. The wheat genome, for example, is five times larger than the human genome.

Daphnia have long been studied because they can be an indicator of environmental health in freshwater bodies. "Daphnia is an exquisite aquatic sensor, a potential high-tech and modern version of the mineshaft canary", says James Klaunig of Indiana University.

"With knowledge of its genome, and using both field sampling and laboratory studies, the possible effects of environmental agents on cellular and molecular processes can be resolved and linked to similar processes in humans."

[For our Irish Readers: Does anyone have an image of the front cover of the Leaving Certificate Biology Textbook with Daphnia ? If so, let me know and I'll add it to the post]

Colbourne, J., Pfrender, M., Gilbert, D., Thomas, W., Tucker, A., Oakley, T., Tokishita, S., Aerts, A., Arnold, G., Basu, M., Bauer, D., Caceres, C., Carmel, L., Casola, C., Choi, J., Detter, J., Dong, Q., Dusheyko, S., Eads, B., Frohlich, T., Geiler-Samerotte, K., Gerlach, D., Hatcher, P., Jogdeo, S., Krijgsveld, J., Kriventseva, E., Kultz, D., Laforsch, C., Lindquist, E., Lopez, J., Manak, J., Muller, J., Pangilinan, J., Patwardhan, R., Pitluck, S., Pritham, E., Rechtsteiner, A., Rho, M., Rogozin, I., Sakarya, O., Salamov, A., Schaack, S., Shapiro, H., Shiga, Y., Skalitzky, C., Smith, Z., Souvorov, A., Sung, W., Tang, Z., Tsuchiya, D., Tu, H., Vos, H., Wang, M., Wolf, Y., Yamagata, H., Yamada, T., Ye, Y., Shaw, J., Andrews, J., Crease, T., Tang, H., Lucas, S., Robertson, H., Bork, P., Koonin, E., Zdobnov, E., Grigoriev, I., Lynch, M., & Boore, J. (2011). The Ecoresponsive Genome of Daphnia pulex Science, 331 (6017), 555-561 DOI: 10.1126/science.1197761


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