Protist Workshop - Detailed Description

Why now?

The emergence of data on the scaffolding of the eukaryotic tree of life (e.g., Baldauf et al. 2000, Nozaki et al. 2003), coupled with continued advances in genome technologies (e.g., see http://www.tigr.org) and analytical approaches (e.g., Bininda-Emonds, Gittleman, and Steel 2002, Gatesy et al. 2002) create the opportunity for synthesis among researchers in these seemingly disparate areas. Such synthesis will identify challenges and potential solutions, while enhancing the ability of participating scientists to lead in the future data collection and analysis of protist genomes.

Identifying the challenges: The challenges in collecting and analyzing genomic data from protists are numerous and include the complex genetics of many of these lineages and the lack of basic biological information on others. As an example, many protist lineages have unstable karyotypes, with frequent chromosomal rearrangements occurring during cell division (e.g., Le Blancq and Adam 1998, Biderre et al. 1999). A further complication that has emerged from recent data is that lateral gene transfers have occurred among microbial eukaryotes (Katz 2002). Although the rate of such transfers is unknown, LGTs will provide challenges in interpreting genomic data and inferring aspects of the biology of related taxa. We are optimistic that the workshop will provide solutions and approaches for some of the challenges presented by protist genomes.


	Protists constitute the bulk of eukaryotic diversity yet protist genomes remain relatively unexplored. We are now moving out of the model organism stage of genomic sequencing and the power/importance of comparative genomics is becoming apparent. Much of the future of eukaryotic genomics lies in protist genomes. However, this work is hampered by a lack of understanding of protistology among genomicists and vice versa. This is at least partly due to the fact that protistologists and genome scientists do not often interact because of the great difference in their scientific approach and specialized terminology. We propose a workshop that will bridge these two groups by bringing together expertise in protist diversity, genomic data collection, and bioinformatics to spur protist genomic research and protist evolutionary biology from a genomic perspective. Specific objectives include: Introducing protist diversity, phylogeny and the role of genomics in the Tree of Life project. Identifying challenges in characterizing protist genomes, and proposing specific solutions to these challenges. Selecting the key protists for genomics approaches. Enabling meaningful dialogue among researches from diverse communities. This includes educating researchers studying protists about the latest technologies in genome sciences, informing leaders of genome centers about the diversity and biology of protists, and providing exposure to approaches to genome data analysis and large-scale systematic studies to the protist community. Disseminating findings of the workshop through peer-reviewed publications and online resources. A web site will be generated to include basic findings of the workshop. The workshop webpage will link to relevant web pages such as the microbial diversity web pages at www.mbl.edu/microscope and the Tree of Life at TOLweb.org. A description of appropriate mechanisms for training future scientists in the area of protist genomics will be provided. Providing a description of appropriate mechanisms for training future scientists in the area of protist genomics. We anticipate this workshop will be a critical step in focusing attention in the US (and worldwide) on protistan genomics and identifying the key areas that require immediate attention. The workshop will benefit both academic and applied sectors of our society. Furthering our understanding of the genomes of protists will provide insights into biological organization, and the origins and diversification of the many disease-causing protist lineages. Such information is needed to harness the potential of eukaryotic microbes in industrial processes and to comprehensively describe the biological diversity on Earth.
	Why now? The emergence of data on the scaffolding of the eukaryotic tree of life (e.g., Baldauf et al. 2000, Nozaki et al. 2003), coupled with continued advances in genome technologies (e.g., see http://www.tigr.org) and analytical approaches (e.g., Bininda-Emonds, Gittleman, and Steel 2002, Gatesy et al. 2002) create the opportunity for synthesis among researchers in these seemingly disparate areas. Such synthesis will identify challenges and potential solutions, while enhancing the ability of participating scientists to lead in the future data collection and analysis of protist genomes. Identifying the challenges: The challenges in collecting and analyzing genomic data from protists are numerous and include the complex genetics of many of these lineages and the lack of basic biological information on others. As an example, many protist lineages have unstable karyotypes, with frequent chromosomal rearrangements occurring during cell division (e.g., Le Blancq and Adam 1998, Biderre et al. 1999). A further complication that has emerged from recent data is that lateral gene transfers have occurred among microbial eukaryotes (Katz 2002). Although the rate of such transfers is unknown, LGTs will provide challenges in interpreting genomic data and inferring aspects of the biology of related taxa. We are optimistic that the workshop will provide solutions and approaches for some of the challenges presented by protist genomes.
	Protist Genomics workshop proposal Currently there are few opportunities for researchers with expertise in protists, genomics and bioinformatics to meet. Such interactions are necessary to successfully inform researchers about technologies and analytical approaches. To this end, we propose a mixture of interactions at the workshop. In addition to lectures that provide overviews of the participating fields, we will break the group into smaller sections ('breakout groups') to discuss specific topics. These smaller group interactions will enable efficient exchange of information among different researchers. Moreover, by keeping the size of the workshop relatively small (30 participants), we are optimistic that additional meaningful interactions will occur over meals and during breaks.