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Transcriptomic changes during senescence of leaves and fine roots of Populus trichocarpa

ABSTRACT: We studied the changes that occur in gene transcription during seasonal senescence in Populus trichocarpa pioneer leaves and fine roots. Plant senescence is a strictly regulated physiological process that allows relocating of valuable nutrients from senescent tissues before death. It might be induced by internal or external factors and among them, phytohormones play an undoubtedly significant role. Senescence was extensively studied in leaves, but the aging of other ephemeral organs, located underground, and its drivers are still poorly understood. We focused on collective results to fill in the knowledge gap about senescence of fine, absorptive roots and leaves in order to check if there are universal mechanisms involved during plant organ senescence. Transcriptional profiling was conducted with the use of microarrays to identify genes involved in developmental PCD. Samples were collected three times during a growth season. The first collection was considered as a control and was collected in early summer (July 7–15) when leaves and the root system were fully developed and functional. The second group of leaf and root samples were harvested in early autumn (October 1–7) when chlorophyll levels in leaves had decreased by approximately 40% and when fine roots had changed in color from white to brown. The third group of samples were harvested in the middle of autumn (November 2–9) when chlorophyll levels in leaves decreased by approximately 65% and fine roots were dark brown or black color. Our results reveal the important role of phytohormones in regulating the senescence of both studied organs. The transcriptomic analyses showed significant changes in gene expression that are associated with phytohormones, especially with ABA and jasmonates. We conclude that phytohormonal regulation of senescence in roots and leaves is organ-specific. In roots, phytohormones are involved indirectly in regulation of senescence by increasing tolerance for cold or resistance for pathogens, whereas such correlation was not observed in leaves.

ORGANISM(S): Populus sp. Populus trichocarpa

PROVIDER: GSE143559 | GEO | 2020/03/07

REPOSITORIES: GEO

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Project description:In the eastern United States the buckeye butterfly, Junonia coenia, shows a seasonal wing color polyphenism where adults emerging in the spring are pale brown, while those emerging in the autumn are dark red. This variation can be artificially induced in laboratory colonies, thus making J. coenia a useful model system to examine the developmental basis of phenotypic plasticity. We used RNA-seq to generate the first set of assembled transcripts for this species while simultaneously quantifying relative gene expression associated with development of alternative seasonal color morphs. The assembled consolidated wing transcriptome was 77.55 Mb. 16,251 contigs of over 1000bp in length were assembled, of which 3,145 were differentially expressed between stages and/or color morphs. Depending on the developmental stage, between 547 and 1420 transcripts were significantly differentially expressed between brown and red wing morphs. These extensive differences in gene expression stand in stark contrast to the much smaller numbers found in previous studies on genetic wing pattern variation, and suggest that environmentally induced phenotypic shifts may arise from very broad systemic processes. Overall gene ontology (GO) analyses revealed that genes associated with structural constituents of ribosomes and oxygen transport were significantly upregulated in the pale brown morph, while genes associated with peptidase activity were very significantly upregulated in the dark red morph. Focused analyses of candidate endocrine and pigmentation pathways revealed a number of notable genes upregulated in the red morph, including several ecdysone-related genes and cinnabar, an ommochrome pigment gene implicated in color pattern variation in other butterflies. Surprisingly, we found numerous melanin-related transcripts, including tan and yellow-family genes, strongly upregulated in the red morph, leading us to speculate that red pigmentation in autumn J. coenia may include red or brown melanins in addition to ommochromes. While we identified several endocrine and pigmentation genes as obvious candidates for color morph differentiation, we speculate that the majority of gene expression differences we observed were due to thermal stress response. The buckeye transcriptome provides a basis for further developmental studies of phenotypic plasticity.

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Transcriptomic changes during senescence of leaves and fine roots of Populus trichocarpa

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