A Tale of Two 'omes: Comparative Genomics and Important Genes in Specialized Tissues

Abstract

Analysis of complex traits like plant specialized metabolism is a difficult task in non-model systems as plant specialized metabolism is controlled by a number of factors such as environment, genotype, age, and tissue. To help address this problem, we have taken a bioinformatic approach that involves sequencing select tissues that are enrichedfor the biosynthesis of specialized metabolites. Using this approach, we have sequenced multiple tissues from a variety of species and compared them against one another. This comparative approach has allowed us to identify some of the genes responsible for the biochemical differences in and between species as well as genes that may be involved in control of specialized tissue development or metabolism. This dissertation begins with a brief introduction of plant metabolism, and pays special attention to historical and present views of plant metabolism, the importance of specialized metabolism, its evolution, and why it is advantageous to study specialized metabolism from specialized tissues like glandular trichomes and rhizomes. To this end, I detail our production and comparisons of glandular trichomes of several Solanum species using next-generation 454 sequencing. I also extensively review the underground stems, or rhizomes, of Viridiplantae. Discussions of our production and comparison of rhizome EST libraries from Zingiber officinale, Curcuma longa, and several Sorghum species are also made. My efforts to lay the groundwork that will hopefully permit functional analysis of interesting genes identified through our sequence comparisons of glandular trichome or rhizome EST libraries, in non-model systems are also discussed.