Alumni & Development
Biology Alumni Newsletter: Summer 2011
Daphnia and cacao tree genomes sequenced
Commonly known as the water flea, Daphnia pulex is the first crustacean to have its genome sequenced. Although it is the size of a grain of rice, this freshwater organism has the most genes, about 31,000, of any animal studied to date, including humans, who have only 23,000 genes. Scientists from the Daphnia Genomics Consortium (DGC) reported their findings in the Feb. 4 issue of Science.
The consortium, a network of over 475 researchers throughout the world, is led by the IU Bloomington Center for Genomics and Bioinformatics (CGB), and the genome sequence was supported by the U.S. Department of Energy’s Joint Genome Institute.
Daphnia has been studied for over a century, but this microcrustacean still has the ability to surprise. Ten important new findings on Daphnia were reported in the article, “The Ecoresponsive Genome of Daphnia pulex,” written by project leader John K. Colbourne, et al. In addition, nearly 40 companion papers were published based on data found in the study. Findings include the fact that 35% of its genes are new to science, literally undocumented in any other organism, and of all sequenced arthropod genomes (insects, crustaceans, and their relatives) studied so far, Daphnia share the most genes with humans.
“Maturing genomic tools for research, applied to questions that are built on the animal’s ecology and population structures, transform Daphnia into a versatile model species for understanding (1) mechanisms of inheritance and development, (2) the process of physiological acclimation and genetic adaptation to changing environments and (3) the genetic plus environmental basis of complex phenotypic traits,” states the consortium’s website. “A rich literature documents how Daphnia copes with environmental hardship; it is known to be a sensitive sentinel species in freshwater ecosystems and is widely used in ecotoxicological studies. Increasingly, Daphnia is being used as a surrogate species to understand genomic responses to environmental stressors that are important factors in human health and well being.”
Biology Professor Peter Cherbas, director of CGB, praises the project’s efforts, saying “Assembling so many experts around a shared research goal is no small feat. We’re obviously proud of the CGB’s catalytic role. The genome project signals the coming-of-age of Daphnia as a research tool for investigating the molecular underpinnings of key ecological and environmental problems.”
The flagship paper describing Daphnia’s genome sequence is authored by 20 IU scientists including professors, postdoctoral fellows and graduate students from the schools of Arts and Science, Public and Environmental Affairs, Informatics and Computing, and was supported in part by the METACyt Initiative of Indiana University, funded in part through a major grant from the Lilly Endowment, Inc. Principal investigators and lab personnel from the biology labs of Mike Lynch, Matt Hahn and Justen Andrews also contributed.
Another large genomics project to which the CGB has substantially contributed is the sequencing and analysis of Theobroma cacao, the tree that produces cocoa beans that are processed into chocolate. In September of last year, candy company Mars Inc., the project’s sponsor, and CGB project leader, Keithanne Mockaitis, announced that the cacao genome had been sequenced. This is the largest genome the CGB has sequenced thus far, with an estimate of roughly 400 million base pairs and 35,000 genes.
The importance of this project is great as farmers and breeders in Asia, South America and West Africa use such genetic findings to improve their planting stocks. With the September announcement, data were released to the public as the Cacao Genome Database. Keithanne Mockaitis, sequencing director of the CGB stated, “When you need to wait three or more years for a tree you plant to bear the beans you sell, you want as much information as possible about the seedlings you’re planting. Making the genome data public further enables breeders, farmers and researchers around the world to use a common set of tools, and to share information that will help them fight the spread of disease in their crops.” The findings could also help reduce poverty in these countries as having more reliable genome data can lead to more sustainable crops.
The Cacao Genome project is a consortium of academic, government and industry partners led by Mars Inc. and the U.S. Department of Agriculture, and including Indiana University, Clemson University, Washington State University, the National Center for Genome Resources, nonprofit organization Public Intellectual Property Resources for Agriculture (PIPRA), the HudsonAlpha Institute, and IBM.
Other IU contributors to the project include CGB research associates James Ford and Zach Smith, data analyst Ram Podicheti, and Don Gilbert, bioinformaticist in the Department of Biology.
More information regarding both projects can be found at the following links: