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Given the prevalence of polyploidy in plants and its significance to plant evolution, developing an enhanced understanding of genomic interactions and processes of genomic change in the polyploid nucleus has fundamental importance to many areas of biology and crop productivity. Here we have sought to partially redress this gap in our knowledge, by undertaking studies that have addressed the tempo (e.g., stochastically regular vs. episodic bursts), directionality (both phylogenetically and with respect to genomic contraction or expansion), and absolute scale of genome size change in diploid and polyploid plants. The cotton genus (Gossypium) is particularly well suited to addressing these questions, with direct relevance to the productivity and quality of one of the world's leading crops.

We are comparing divergent diploid (A-genome and D-genome) and allopolyploid (AD-genome) members of the cotton genus (Gossypium), noting that these diploids have genomes that vary twofold in size. Our analyses are phylogenetically informed through the inclusion of the outgroup species Gossypioides kirkii, an approach we argue is essential for maximizing inference of scope and scale of genome evolution, and for evaluating the relative roles of the various responsible genetic mechanisms. With the D genome well-characterized and entered into the sequencing queue, a genome-wide genetically anchored scaffold of A-genome BACs is the next logical step toward the long-term goal of characterizing genomic diversity in the genus, thereby enabling a host of future studies.

We are building the conceptual framework needed to understand the architecture of the highly repetitive A-genome, an essential prelude to unraveling the unique features that distinguish cultivated allopolyploid cottons from their diploid progenitors, by identification and sequencing of a set of approximately 100 BACs, systematically sampling diverse genomic contexts to gain insight into the structure and evolution of DNA elements that account for the twofold difference in the size of the A- and D-genomes since their divergence from a common ancestor, and to clarify the types and levels of intergenomic evolution that have occurred since the joining of two widely divergent diploid genomes in a common polyploid nucleus. These data will be supplemented by comparative FISH and phylogenetic analyses that, in conjunction with the BAC sequence data, provide unparalleled insight into the evolutionary processes responsible for genome evolution during diploid divergence and following polyploid formation.

Current progress: Thus far, all twenty G. raimondii BACs have been sequenced and the remaining eighty (G. arboreum [20], G. hirsutum [20 AT, 20DT], G. kirkii [20]) are in various stages of sequencing. Once sequencing is completed, comparative analysis of these twenty loci can begin.

Loci selected from chromosomes 2 and 8 in G. raimondii.

We welcome your comments and suggestions.