A phylogenetic analysis of indel dynamics in the cotton genus.

@article{grover08mbe, abstract = {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 (A(T) and D(T)) 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/A(T) 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 D(T) and overall contraction in A(T) 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.}, address = {Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, Iowa 50011 USA.}, author = {Grover, Corrinne E. E. and Yu, Yeisoo and Wing, Rod A. A. and Paterson, Andrew H. H. and Wendel, Jonathan F. F. }, citeulike-article-id = {2662706}, issn = {1537-1719}, journal = {Molecular biology and evolution}, keywords = {evolution, genome\_size, genomics, indel, plant}, month = {April}, posted-at = {2008-04-13 03:44:11}, priority = {2}, title = {A phylogenetic analysis of indel dynamics in the cotton genus.}, url = {http://view.ncbi.nlm.nih.gov/pubmed/18400789}, year = {2008} }

TY - JOUR ID - grover08mbe L3 - citeulike-article-id:2662706 N2 - 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 (A(T) and D(T)) 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/A(T) 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 D(T) and overall contraction in A(T) 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. JF - Molecular biology and evolution SN - 1537-1719 AD - Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, Iowa 50011 USA. TI - A phylogenetic analysis of indel dynamics in the cotton genus. KW - evolution KW - genome_size KW - genomics KW - indel KW - plant AU - Grover, Corrinne AU - Yu, Yeisoo AU - Wing, Rod AU - Paterson, Andrew AU - Wendel, Jonathan PY - 2008/April/09/ UR - http://view.ncbi.nlm.nih.gov/pubmed/18400789 ER -