Transcriptional signatures associated with species divergence in New Zealand Pachycladon (Brassicaceae)
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ABSTRACT:
PROVIDER: PRJNA121087 | ENA |
REPOSITORIES: ENA
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Project description:Comparative gene expression profiling of a) above-ground tissues of three fruiting species (P. cheesemanii, ch, P. exile, ex, P. novae-zelandiae, nz), b) above-ground tissues of two rosette stage species (P. fastigiatum, fa, P. enysii, en) and c) roots of all five species using heterologous A. thaliana microarrays 8-12 specimens per species grown in common garden, RNA from roots and aboveground tissues extracted separately from each specimen, individual samples pooled in equal amounts resulting in five above ground samples (ch_l, ex_l, nz_l, fa_l, en_l) and five root samples (ch_r, ex_r, nz_r, fa_r, en_r), 36 two channel microarrays used in total: five above-ground samples hybridized in a loop-like fashion using 14 arrays, five root samples hybridized in a loop-wise fashion using 10 arrays; five root and three leaf samples hybridized in a loop-like fashion using 12 arrays, thus each sample hybridized multiple times (4-12) while being labelled either with cy3 or cy5
2009-11-16 | E-GEOD-19017 | biostudies-arrayexpress
Project description:Comparative gene expression profiling of a) above-ground tissues of three fruiting species (P. cheesemanii, ch, P. exile, ex, P. novae-zelandiae, nz), b) above-ground tissues of two rosette stage species (P. fastigiatum, fa, P. enysii, en) and c) roots of all five species using heterologous A. thaliana microarrays
2009-11-17 | GSE19017 | GEO
Project description:Tag profiling and expression analysis of genes from Pachycladon enysii and Pachycladon fastigiatum
2011-06-01 | E-MTAB-610 | biostudies-arrayexpress
Project description:Genome-wide landscapes of transcription factor (TF) binding sites (BSs) diverge during evolution, conferring species-specific transcriptional patterns. The rate of divergence varies in different metazoan lineages but has not been widely studied in plants. We identified the BSs and assessed the effects on transcription of FLOWERING LOCUS C (FLC) and PERPETUAL FLOWERING 1 (PEP1), two orthologous MADS-box TFs that repress flowering and confer vernalization requirement in the Brassicaceae species Arabidopsis thaliana and Arabis alpina, respectively. We found the BSs that were conserved in both species, and that these contained a CArG-box that is recognised by MADS-box TFs. The CArG-box consensus at conserved BSs was extended compared to the core motif. By contrast, species-specific BSs usually lacked the CArG-box in the other species. Flowering-time genes were highly overrepresented among conserved targets and their CArG-boxes were widely conserved among Brassicaceae species. Cold-regulated genes (COR) were also overrepresented among targets, but the cognate BSs and the identity of the regulated genes were different in each species. In cold, COR gene transcript levels were increased in flc and pep1-1 mutants compared to wild-type and this correlated with reduced growth in pep1-1. Therefore FLC orthologs regulate a set of conserved target genes mainly involved in reproductive development and were later independently recruited to modulate stress responses in different Brassicaceae lineages. Analysis of TF BSs in these lineages thus distinguishes widely conserved targets representing the core function of the TF from those that were recruited later in evolution.
2018-01-01 | GSE89889 | GEO
Project description:Genome-wide landscapes of transcription factor (TF) binding sites (BSs) diverge during evolution, conferring species-specific transcriptional patterns. The rate of divergence varies in different metazoan lineages but has not been widely studied in plants. We identified the BSs and assessed the effects on transcription of FLOWERING LOCUS C (FLC) and PERPETUAL FLOWERING 1 (PEP1), two orthologous MADS-box TFs that repress flowering and confer vernalization requirement in the Brassicaceae species Arabidopsis thaliana and Arabis alpina, respectively. We found that only 17% of their BSs were conserved in both species and that these contained a CArG-box that is recognised by MADS-box TFs. The CArG-box consensus at conserved BSs was extended compared to the core motif. By contrast, species-specific BSs usually lacked the CArG-box in the other species. Flowering-time genes were highly overrepresented among conserved targets and their CArG-boxes were widely conserved among Brassicaceae species. Cold-regulated genes (COR) were also overrepresented among targets, but the cognate BSs and the identity of the regulated genes were different in each species. In cold, COR gene transcript levels were increased in flc and pep1-1 mutants compared to wild-type and this correlated with reduced growth in pep1-1. Therefore FLC orthologs regulate a set of conserved target genes mainly involved in reproductive development and were later independently recruited to modulate stress responses in different Brassicaceae lineages. Analysis of TF BSs in these lineages thus distinguishes widely conserved targets representing the core function of the TF from those that were recruited later in evolution.
2018-01-01 | GSE89638 | GEO
Project description:Tag profiling and expression analysis of genes from Pachycladon enysii and Pachycladon fastigiatum. ArrayExpress Release Date: 2011-06-01 Publication Title: Short read expression profiling in a non-model allopolyploid plant Publication Author List: Voelckel, C, Gruenheit, N, Biggs, P, Deusch, O, Lockhart, PJ Person Roles: submitter Person Last Name: Voelckel Person First Name: Claudia Person Mid Initials: Person Email: c.voelckel@massey.ac.nz Person Phone: Person Address: Institute of Molecular Biosciences, Private Bag 11 222, Palmerston North 4442 Person Affiliation: Institute of Molecular Biosciences, Allan Wilson Centre for Molecular Ecology and Evolution
2011-07-14 | GSE30618 | GEO
Project description:Pachycladon cheesemanii Organism overview
| PRJNA83889 | ENA