Genome Evolution

Eukaryotic genomes vary remarkably in size, even between closely related species, primarily due to differences in the fraction of non-coding DNA. The existence of this variation reflects the net effects of mechanisms that expand and contract genomes, mechanisms whose balance (thus overall effects) can vary in magnitude and direction throughout evolution. Several different mechanisms have been implicated in genome size change (polyploidy, transposable element proliferation, intra-strand homologous recombination, illegitimate recombination); however, the relative importance of these mechanisms to genome size change in different lineages remains uncertain. Our research focuses on the mechanisms that influence genome size in Gossypium and the rates at which these genomes have expanded and contracted over time. Although Gossypium is a relatively young genus (~5 - 10 my) and all diploid species have the same basic chromosome number (n=13; polyploid species, n=26), the range in genome size is nearly 3-fold, from 885 Mbp to 2570 Mbp per 1C nucleus. This range in genome size, set in a phylogenetic background, has provided ample opportunity to use a variety of approaches to further our understanding of genome size evolution in Gossypium, as well as plants in general.

In order to better understand genome size evolution in Gossypium, our lab has taken two general approaches toward revealing the mechanisms and direction of change, as well as the pace and pattern. Since it is widely accepted that transposable elements are primary contributors to genome size evolution, as well as genome evolution in general, we have focused part of our efforts at understand the populations of transposable elements that occupy the genomes of Gossypium. Specifically, our experiments have allowed us to characterize the TE content from 4 species that differ nearly 3-fold in size, and, by dating these TEs, we begin to paint a picture of transposable element gains and losses in these genome which is marked by the punctuated bursts of activity that have been demonstrated in other systems. More detailed information concerning these experiments and analyses can be found on our transposable element dynamics and genome size in Gossypium project page .

The second approach aimed at understanding genome size evolution in Gossypium involves comparative sequencing of orthologous BAC-sized regions (100-200kb) from 4 species representing 5 genomes (3 diploid species and 1 allotetraploid species). Specifically, BAC-sized orthologous tracts from three diploid genomes (A, D, and the outgroup, Gossypioides kirkii) are being comparing to each other and to the two homoeologous regions from polyploid cotton (A T and D T from Gossypium hirsutum). From this quintet of genomes, we are able to polarize gaps as insertions or deletions that occurred pre- or post- polyploid genome divergence, which provides insight into the pace and influences of genome size evolution that have influenced Gossypium size evolution, both in the shared ancestor of the A/A T and D/D T genomes, as well as for the extant lineages themselves. More detailed information concerning this project can be found on our indel mechanisms and dynamics, and their influences on genome size in Gossypium project page.