J F Wendel

..Using these assemblies as templates, we describe the design and creation and of a publicly available oligonucleotide array for cotton, useful for all four of the cultivated species...

..Toward the long-term goal of characterizing the spectrum of diversity among cotton genomes, the worldwide cotton community has prioritized the D genome progenitor Gossypium raimondii for complete sequencing...

....

..Here we describe global patterns of gene expression accompanying genomic merger and doubling in inter-specific crosses in the cotton genus (Gossypium L.)...

..Owing to this redundancy, these genomes can play host to an array of evolutionary processes that act on duplicate genes...

....

..Moreover, the research sets the stage for fine-scale analysis of the evolutionary dynamics and directionality of change for the full spectrum of genomic constituents...

....

..We suggest that dynamic fluctuation in copy number will prove common for nuclear genes, and we discuss the implications of this perspective for inferences of orthology and functional evolution...

..Potential explanations for this latter phenomenon, including gene duplication, gene flow, and lineage sorting, are discussed...

..These contrasts indicate polyploid speciation in plants is accompanied by a diverse array of molecular evolutionary phenomena, which will vary among both genomic constituents and taxa...

..In addition, some genomic regions show multiple patterns of homoeologous recombination among species...

....

..It is suggested that more robust insights are likely to emerge from the use of single-copy or low-copy nuclear genes...

..However, the duplicated copies of MYB1 in the tetraploid are not expressed at equal levels or equivalently in all organs, suggesting possible functional differentiation...

..These observations indicate that for these two pairs of Adh loci, the null hypothesis of equivalent evolutionary dynamics for duplicated genes in allotetraploid cotton is rejected...

..hirsutum and G. barbadense, leading to convergent rather than parallel genetic alterations and resulting morphology...

..Genes implicated in vesicle coating and trafficking were found to be overexpressed throughout all stages of fiber development studied, indicating their important role in maintaining rapid growth of this unique plant cell...

..These results demonstrate that relative expression levels of homeologous genes may be measured by microarrays and that deviation from equal expression levels of homeologous loci may be common in the allotetraploid nucleus of Gossypium...

..Evidence suggests, however, that domestication may increase expression bias in fibers toward the D genome, potentially implicating D-genome recruitment under human selection during domestication...

..Furthermore, these results suggest that both large- and small-scale regulatory mechanisms may control homoeolog expression patterns...

..Both long-term and immediate responses to polyploidization were implicated. Data suggest that some silencing events are epigenetically induced during the allopolyploidization process...

..Using the mean synonymous substitution rate calculated across the 48 genes, allopolyploid cotton is estimated to have formed circa 1.5 million years ago (MYA), after divergence of the diploid progenitors about 6.7 MYA...

..In conjunction with previous work, the data here confirm the conclusion that genome size evolution reflects many forces that collectively operate heterogeneously among genomic regions...

..The assembly and associated information provide a framework for future investigation of cotton functional and evolutionary genomics...

....

..Further, we provide evidence for present-day transcription of LINEs, a relatively minor component of Gossypium genomes, whereas the more abundant LTR retrotransposons display limited expression and only under stressed conditions...

....

..Interestingly, the magnitude of transpositional bursts in each lineage corresponds directly with extant estimated copy number...

..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...

..These data indicate that rates of DNA loss can be highly variable even within a single plant genus, and that the known mechanisms of DNA loss can indeed reverse the march toward genomic obesity...

..Like maize, Gossypium has undergone a threefold increase in genome size due to the accumulation of LTR retrotransposons over the 5-10 Myr since its origin...

..These results provide a detailed portrayal of gene silencing events that can occur following allopolyploidization and suggest epigenetic causal factors...

....

..We also highlight several recent and pertinent examples from the literature. These examples demonstrate the importance of the functional characteristics of genes and the source of duplication in influencing evolutionary outcome...

....

..Polyploidy has extensive effects on gene expression, with gene silencing accompanying polyploid formation and continuing over evolutionary time...

..Meta-analysis linked to synteny-based and expression-based information provides clues about specific genes and families involved in QTL networks...

..These data provide new insights into polyploid evolution and represent a foundation for assembly of a finished sequence of the cotton genome...

..Three recent reports have provided intriguing new insights into the patterns, timing and mechanisms of gene expression changes that accompany polyploidy in plants...

..These results show that developmental regulation of gene expression is changed immediately upon hybridization between diploid species, possibly due to epigenetic factors or regulatory mismatch...

..Our data suggest a model for the evolutionary origin of a novel morphology through differential gene regulation causing prolongation of an ancestral developmental program...

..Gossypium gossypioides provides a striking example of the previously unsuspected chimeric nature of some plant genomes and the resulting phylogenetic complexity produced by multiple historical reticulation events...

..It is likely that the evolutionary success of allopolyploidy is in part attributable to epigenetic phenomena that we are only just beginning to understand...

..Increasing knowledge of the correspondence of the cotton and Arabidopsis genomes provides several avenues by which genetic dissection of cotton fiber development may be accelerated...

..Hybridization rather than genome doubling seems to have triggered most of the methylation changes observed in Spartina anglica...

..We speculate that biased correlation of methylation-polymorphic sites and genes in cotton may be a consequence of polyploidy and the attendant doubling of all genes...

..We suggest that cryptic and seemingly improbable interspecific introgression and molecular differentiation may be more common than appreciated in angiosperm evolution...

....