MBE Advance Access published online on April 9, 2008
Molecular Biology and Evolution, doi:10.1093/molbev/msn085
Research Article |
A phylogenetic analysis of indel dynamics in the cotton genus
1 Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, Iowa 50011 USA
2 Arizona Genomics Institute, University of Arizona, Tucson, Arizona 85721
3 Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30602
4 Corresponding author: Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, Iowa 50011; email: jfw{at}iastate.edu; phone: 515-294-7172; fax: 515-294-1337
Received for publication November 27, 2007. Revision received February 21, 2008. Accepted for publication April 2, 2008.
Genome size evolution is a dynamic process involving counterbalancing mechanisms whose actions vary across lineages and over time. While the primary mechanism of expansion, transposable element (TE) amplification, has been widely documented, the evolutionary dynamics of genome contraction have been less thoroughly explored. To evaluate the relative impact and evolutionary stability of the mechanisms that affect genome size, we conducted a phylogenetic analysis of indel rates for two genomic regions in four Gossypium genomes: the two co-resident genomes (AT and DT) of tetraploid cotton and its model diploid progenitors, Gossypium arboreum (A) and Gossypium raimondii (D). We determined the rates of sequence gain or loss along each branch, partitioned by mechanism, and how these changed during species divergence. In general, there has been a propensity toward growth of the diploid genomes and contraction in the polyploid. Most of the size difference between the diploid species occurred prior to polyploid divergence, and was largely attributable to TE amplification in the A/AT genome. After separating from the true parents of the polyploid genomes, both diploid genomes experienced slower sequence gain than in the ancestor, due to fewer TE insertions in the A genome and a combination of increased deletions and decreased TE insertions in the D genome. Both genomes of the polyploid displayed increased rates of deletion and decreased rates of insertion, leading to a rate of near stasis in DT and overall contraction in AT resulting in polyploid genome contraction. As expected, TE insertions contributed significantly to the genome size differences; however, intra-strand homologous recombination, although rare, had the most significant impact on the rate of deletion. Small indel data for the diploids suggest the possibility of a bias, as the smaller genomes add less or delete more sequence through small indels than do the larger genomes, whereas data for the polyploid suggests increased sequence turnover in general (both as small deletions and small insertions). Illegitimate recombination, although not demonstrated to be a dominant mechanism of genome size change, was biased in the polyploid toward deletions, which may provide a partial explanation of polyploid genomic downsizing.
Key Words: genome size evolution • genome evolution • cotton • illegitimate recombination • rates of genome size change