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A phylogenetic analysis of indel dynamics in the cotton genus.
Mol Biol Evol 2008; 25(7):1415-28MB

Abstract

Genome size evolution is a dynamic process involving counterbalancing mechanisms whose actions vary across lineages and over time. Whereas 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 2 genomic regions in 4 Gossypium genomes: the 2 coresident 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, intrastrand 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 suggest 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.

Authors+Show Affiliations

Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Iowa, USA.No affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info available

Pub Type(s)

Journal Article
Research Support, U.S. Gov't, Non-P.H.S.

Language

eng

PubMed ID

18400789

Citation

Grover, Corrinne E., et al. "A Phylogenetic Analysis of Indel Dynamics in the Cotton Genus." Molecular Biology and Evolution, vol. 25, no. 7, 2008, pp. 1415-28.
Grover CE, Yu Y, Wing RA, et al. A phylogenetic analysis of indel dynamics in the cotton genus. Mol Biol Evol. 2008;25(7):1415-28.
Grover, C. E., Yu, Y., Wing, R. A., Paterson, A. H., & Wendel, J. F. (2008). A phylogenetic analysis of indel dynamics in the cotton genus. Molecular Biology and Evolution, 25(7), pp. 1415-28. doi:10.1093/molbev/msn085.
Grover CE, et al. A Phylogenetic Analysis of Indel Dynamics in the Cotton Genus. Mol Biol Evol. 2008;25(7):1415-28. PubMed PMID: 18400789.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - A phylogenetic analysis of indel dynamics in the cotton genus. AU - Grover,Corrinne E, AU - Yu,Yeisoo, AU - Wing,Rod A, AU - Paterson,Andrew H, AU - Wendel,Jonathan F, Y1 - 2008/04/09/ PY - 2008/4/11/pubmed PY - 2008/9/23/medline PY - 2008/4/11/entrez SP - 1415 EP - 28 JF - Molecular biology and evolution JO - Mol. Biol. Evol. VL - 25 IS - 7 N2 - Genome size evolution is a dynamic process involving counterbalancing mechanisms whose actions vary across lineages and over time. Whereas 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 2 genomic regions in 4 Gossypium genomes: the 2 coresident 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, intrastrand 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 suggest 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. SN - 1537-1719 UR - https://www.unboundmedicine.com/medline/citation/18400789/A_phylogenetic_analysis_of_indel_dynamics_in_the_cotton_genus_ L2 - https://academic.oup.com/mbe/article-lookup/doi/10.1093/molbev/msn085 DB - PRIME DP - Unbound Medicine ER -