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Objective 1: Train a motivated graduate student in the field of evolutionary genomics. The Lane lab currently houses a large resource of genome data that requires analysis, substantial expertise and ample computational resources. The lab is an excellent environment for a graduate student interested in using comparative genomics to answer evolutionary questions. In addition to available resources, PI Lane is a strong advocate for student mentoring. <P>Objective 2: Test the hypothesis that gene duplication is a critical feature of parasite evolution. Whereas overall genome reduction is the trend among parasites, novel genes are also required to carry out the specialized functions of a parasitic existence. We will utilize an "evolutionary gene networks" technique that allows for graphical visualization of gene family relationships to identify expanded gene families in the obligate and facultative parasites, relative to each other and free-living oomycetes. These data will implicate specific gene families as important factors in the evolution of a pathogenic lifestyle.
Non-Technical Summary:<br/>
Oomycete infections of crop plants and ornamentals cause blights, wilts, cankers, rusts, lesions and/or (root) rots whereas infestations in shellfish and finfish facilities can result in the loss of over 50% of high value brood stocks. As a lineage, oomycetes are a significant threat to U.S. National food security and cost agriculture and aquaculture industries billions in losses on an annual basis. This project will fund a graduate student to perform a comparative genomic analysis of related free living and pathogenic oomycetes to identify genomic changes related to becoming pathogenic. Understanding the evolution of pathogenicity factors is an important step in developing treatment strategies for oomycete infections.
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Approach:<br/>
This proposal will fund a graduate student to learn and perform cutting edge comparative genomic analyses. Using data already in hand, the student will analyze the genomes of two oomycetes, the free living Thraustotheca clavata and the facultative parasite Achlya hypogyna, using a combination of established and novel methods. Specifically, Evolutionary Gene Networks (EGNs) will be employed to form a genome-scale comparative framework to identify changes in gene content and number relative to lifestyle. Prior to the T. clavata and A. hypogyna data produced in the Lane lab, the only oomycete genomic information was from pathogenic members of the lineage. By adding two species that do not completely rely on attacking a host organism for sustenance, it is now possible to use to understand the genomic consequences of becoming a parasite. Together, this research will lay the groundwork for comprehensive molecular and cell biological studies on the evolution of parasitism and add significantly to the genomic data available from the ecologically and economically important oomycetes. All available oomycete data will be graphed in EGNs using a 60% percent protein sequence similarity value and an e-value of 1x10-10. Thousands of connected components are produced in a network, ranging from large components of rapidly evolving genes or domains (e.g. ABC transporter families), to components consisting of two nodes connected by a single "edge" (line indicating BLAST similarity). Custom program scripts written in the computer language, python, will sort the connected components. Based on the number of proteins from each species, the scripts will identify expanded gene families that are uniquely expanded in a particular species or lifestyle, highlighting cases of gene family expansion. Additionally, EGNs can rapidly identify instances of gene loss. Together, this approach will allow the quantification of gene loss, duplication and adaptation between related free living and pathogenic organisms of particular importance to the nations food supply. The student funded by this proposal will be recruited with the help of the Director of Graduate Diversity and Recruitment Initiatives in the URI Graduate School and will interface with the Northeastern Regional Aquaculture Consortium.