Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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RNA-seq experiment of tissue forming a lateral root after salt treatment in cyp79b2/b3 mutants containing multiple timepoints

ABSTRACT: We aimed to investigate the transcriptional changing in developing lateral roots in response to salt and cyp79b2/b3 mutation. Seedlings were turned (gravistimulation) to induce the formation of a lateral in the bending zone of the main root due to a local auxin maximum. These bending zones were dissected at 3 timepoints under salt and control conditions for cyp79b2/b3 and Col-0 wildtype and used for as an input RNA sequencing.

INSTRUMENT(S): Illumina NovaSeq 6000

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Christa Testerink

PROVIDER: E-MTAB-13311 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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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. mRNA profiling of hind wings from 4 developmental stages of two color morphs (Rosa and Linea) of the buckeye butterfly (J. coenia), generated by deep sequencing, in triplicate, using Illumina GAII or HiSeq 2000.

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RNA-seq experiment of tissue forming a lateral root after salt treatment in cyp79b2/b3 mutants containing multiple timepoints

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