Integrative genomics: the biological impacts of DNA content diversity

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Protein coding genes in the human genome number only ~25,000 and constitute less than 2% of the total DNA sequence. Whereas classical genetics and comparative genomics have generated major insights into the roles of individual genes, the biological significance of the vast non-coding majority of the genome has remained enigmatic. Major initiatives involving sequence comparisons (e.g., ENCODE) are underway to determine whether and in what way portions of the non-genic majority of a typical mammalian genome may be functional in regulatory or other capacities. It is also possible that non-coding DNA plays important roles in a manner independent of nucleotide sequence, for example in maintaining or modifying the physical structure of chromosomes or the spatial arrangement of genes. These investigations are important, but it must be borne in mind that regulatory or other functions are very unlikely to account for the enormous diversity in DNA content observed across species - in animals, the smallest and larger genomes differ in size by a factor of 7,000. Of course, the DNA in a given genome need not have a specific function to exert important biological impacts. For example, there is strong evidence that DNA amount per nucleus is tightly linked to cell size and cell division rate, and that this may result in organism-level relationships with metabolic rate, developmental rate, body size, and other biological properties of fundamental significance. The research proposed here will focus on the patterns and biological significance of DNA content diversity from three perspectives. In the first project, my students and I will investigate the patterns and biological impacts of genome size diversity among several key groups of animals. This will be accomplished using both Feulgen image analysis densitometry and flow cytometry to estimate nuclear DNA content, and will be linked to morphological, developmental, and physiological parameters and analyzed within a phylogenetic context. The groups of animals to be analyzed have all been very poorly studied from the perspective of genome size to date, but are of particular interest for their theoretical and/or practical importance. These include i) the early-branching metazoan phyla (Porifera, Cnidaria, Ctenophora, and Placozoa), which are of particular phylogenetic interest in addition to providing opportunities to test possible links between genome size and devolpmental lifestyle, ii) crustaceans, which are very diverse both taxonomically and ecologically and provide an opportunity to investigate many aspects of genome evolution, and iii) parasitic helminths including flatworms and nematodes, which allows a test of the hypothesis that parasitism constrains body size/developmental rate and thus genome size. In the second project, we will investigate the prevalence and distributions of very large genomes (>5x human genome size) and use modern genomics tools to investigate the quantity and distribution of transposable elements in genomes that are currently far too large to be subject to complete genome sequencing. In the third project, we will investigate the biological significance of endopolyploidy, in which the genome is replicated up to thousands of times within individual cells. Endopolyploidy appears to be a very widespread phenomenon, and is particularly common in tissues involved in intensive protein excretion, and we intend to examine the degree and timing of endopolyploidization in tissues of particular interest such as insect ovaries with and without nutritive trophocytes ("nurse cells"), in the silk glands of domesticated silkworms, and in the venom and silk glands of spiders with varying feeding habits.