Project description:Reactive oxygen species (ROS) play a prominent role in signal transduction and cellular homeostasis in plants. However, imbalances between generation and elimination of ROS can give rise to oxidative stress in growing cells. Because ROS are important to cell growth, ROS modulation could be responsive to natural or human-mediated selection pressure in plants. To study the evolution of oxidative stress related genes in a single plant cell, we conducted comparative expression profiling analyses of the elongated seed trichomes (‘‘fibers’’) of cotton (Gossypium), using a phylogenetic approach. We measured expression changes during diploid progenitor species divergence, allopolyploid formation and parallel domestication of diploid and allopolyploid species, using a microarray platform that interrogates 42,429 unigenes. The distribution of differentially expressed genes in progenitor diploid species revealed significant up-regulation of ROS scavenging and potential signaling processes in domesticated G. arboreum. Similarly, in two independently domesticated allopolyploid species (G. barbadense and G. hirsutum) antioxidant genes were substantially up-regulated in comparison to antecedent wild forms. In contrast, analyses of three wild allopolyploid species indicate that genomic merger and ancient allopolyploid formation had no significant influences on regulation of ROS related genes. Remarkably, many of the ROS-related processes diagnosed as possible targets of selection were shared among diploid and allopolyploid cultigens, but involved different sets of antioxidant genes. Our data suggests that parallel human selection for enhanced fiber growth in several geographically widely dispersed species of domesticated cotton resulted in similar and overlapping metabolic transformations of the manner in which cellular redox levels have become modulated. We measured expression changes during diploid progenitor species divergence, allopolyploid formation and parallel domestication of diploid and allopolyploid species, using a microarray platform that interrogates 42,429 unigenes. The distribution of differentially expressed genes was studied for domesticated G. arboreum and two independently domesticated allopolyploid species (G. barbadense and G. hirsutum). These were compared to three wild allopolyploid species. Three biological replicates were performed.

Project description:Transcriptomic changes following recent natural hybridization and allopolyploidy in the salt marsh species Spartina x townsendii and Spartina anglica (Poaceae) Allopolyploidy results from two events: the merger of divergent genomes and genome duplication. Both events have important functional consequences for the evolution and adaption of newly formed allopolyploid species. In spite of significant progress made the last years, a few studies have decoupled the effects of hybridization from genome duplication in the observed patterns of expression changes accompanying allopolyploidy in natural conditions. We used Agilent Rice oligo-microarrays to explore gene expression changes following allopolyploidy in Spartina that includes a classical example of recent allopolyploid speciation, S. anglica formed during the 19th century following genome duplication of the hybrid S. x townsendii. Our data indicate important, thought different effects of hybridization and genome duplication in the expression patterns of the hybrid and allopolyploid. Deviation from parental additivity was most important following hybridization and was accompanied by maternal expression dominance, although transgressively expressed genes were also encountered. Maternal dominance is attenuated following genome duplication in S. anglica while this species exhibits an increased number of transgressively over expressed genes. These results reflect the decoupled effects of the “genomic shock” following hybridization and genome redundancy, on the genetic, epigenetic and regulatory mechanisms characterizing transcriptomic evolution in allopolyploids. We used Agilent Rice oligo-microarrays to explore gene expression changes among Spartina species, following interspesific hybridization and genome duplication (allopolyploidy). The analysed species included the parents S. maritima & S.alterniflora, the hybrid F1 S x. towensendii and the allopolyploid S.anglica. A total of 20 slides (five replicates per species) were hybridized on a 44 K Rice Agilent array using a one color desgin.

Project description:Background: Polyploidy has long been recognized as an important mechanism in eukaryotes evolution. Recent studies have documented dynamic changes in plant polyploid gene expression, which reflects genomic and functional plasticity of duplicate genes and genomes in plants. Genomewide approaches in a variety of allopolyploids, mostly synthetics, reveal a trend of non-additive gene expression. The aim of the study was to document expression divergence between a relatively recently formed natural allopolyploid (Coffea arabica) and its ancestral parents (Coffea canephora and Coffea eugenioides) and to verify if the divergence was ‘environment-dependent’.Results: Employing a microarray platform designed against 15,522 unigenes, we assayed gene expression levels in allopolyploid and its two parental diploids. For each gene, we determined expression variation levels between the three species grown under two sets of temperature conditions (26-22°C/30-26°C). More than 35% of genes were differentially expressed in each comparison at both temperatures, except for ‘allopolyploid versus Canephora’ at the ‘hottest’ temperature where an unexpected low gene expression divergence (<9%) were observed. Genes were binned in categories: ‘no change’, ‘additivity’, ‘transgressive’ and ‘dominance’ (‘Canephora-like’ and ‘Eugenioides-like’). The totally new phenomenon revealed by our study was a drastic modification of proportions between the allopolyploid and its parents when environmental conditions were modified. At the ‘hottest’ temperature, we found a virtual disappearance of gene categories classed as ‘transgressive’, ‘Eugenioides-like dominance’ or ‘additivity’ and a major increase in genes classed in the ‘Canephora-like dominance’ category. At this set of growing conditions, we therefore found very high bias that suggested a phenomenon of ‘dominance’ of C. canephora transcription profile. The Canephora genome parental expression state seems exhibited in strong preference to the Eugenioides genome parental state. Conclusion: Our data constitute evidence for a transcription profile divergence between allopolyploid and its parental species, massively affected by environmental conditions. The parental origin of the transcription profiles was not consistently biased towards one parental species, but appeared to be affected by environmental conditions. This phenomenon indicates the plasticity of allopolyploids and might ultimately explain better adaptation to environmental conditions.

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