Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcriptional signatures associated with species divergence in New Zealand Pachycladon (Brassicaceae)

ABSTRACT: 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

ORGANISM(S): Arabidopsis thaliana Pachycladon exile Pachycladon cheesemanii Pachycladon fastigiatum Pachycladon novaezelandiae Pachycladon enysii

PROVIDER: GSE19017 | GEO | 2009/11/17

SECONDARY ACCESSION(S): PRJNA121087

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Transcriptional signatures associated with species divergence in New Zealand Pachycladon (Brassicaceae)

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

Transcriptional signatures associated with species divergence in New Zealand Pachycladon (Brassicaceae)

Project description:Transcriptional signatures associated with species divergence in New Zealand Pachycladon (Brassicaceae)

| PRJNA121087 | ENA

Fungal collection photosensitizers set

Project description:The present study was designed to test the hypothesis of a widespread photochemical trait in fruiting body-forming fungal species. The biomaterial was selected based on Gill and Steglich's classification of fungal pigments, which focuses on their biosynthetic origin. With the aim to cover most described pigment types, 48 different species were selected. Second, dried and ground fruiting bodies were extracted and subjected to UPLC-HRMS/MS measurement.

2022-02-01 | MSV000088756 | MassIVE

New lepidium (brassicaceae) from new zealand.

Project description:A revision of the New Zealand endemic Lepidium oleraceum and allied species is presented. Sixteen species are recognised, 10 of these are new. The new species are segregated on the basis of morphological characters supported by molecular data obtained from three DNA markers (two rDNA and one cpDNA). One species, Lepidium castellanum sp. nov., is endemic to the Kermadec Islands where it is sympatric with Lepidium oleraceum. The North Island of New Zealand supports four species, with two of them, Lepidium amissum sp. nov. and Lepidium obtusatum, now extinct. The South Island supports six species, that, aside from Lepidium banksii, Lepidium flexicaule and Lepidium oleraceum, are all confined to the south-eastern half of the island (Lepidium aegrum sp. nov., Lepidium crassum sp. nov. and Lepidium juvencum sp. nov.). One of these, Lepidium juvencum sp. nov., extends to Stewart Island. The Chatham Islands support six species (Lepidium flexicaule, Lepidium oblitum sp. nov., Lepidium oleraceum, Lepidium oligodontum sp. nov., Lepidium panniforme sp. nov., and Lepidium rekohuense sp. nov.), one of which, Lepidium oligodontum sp. nov., extends to the Antipodes Islands group. The remote, subantarctic Bounty Islands group supports one endemic, Lepidium seditiosum sp. nov., which is the only vascular plant to be recorded from there. Lepidium limenophylax sp. nov. is known from islands off the south-western side of Stewart Island/Rakiura, The Snares and Auckland islands. Lepidium naufragorum, although not related to Lepidium oleraceum and its allies, is also treated because populations with entire leaves are now known. Typification is undertaken for Lepidium banksii, Lepidium oleraceum, Lepidium oleraceum var. acutidentatum, var. frondosum and var. serrulatum.

| S-EPMC3689132 | biostudies-literature

Brassicaceae

Project description:Brassicaceae species transcriptome analysis

| PRJNA242124 | ENA

Divergence of regulatory networks governed by the orthologous transcription factors FLC and PEP1 in Brassicaceae species.

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

Divergence of regulatory networks governed by the orthologous transcription factors FLC and PEP1 in Brassicaceae species

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

Brassicaceae

Project description:Various representative species from the mustard family (Brassicaceae). Raw sequence reads

| PRJNA806513 | ENA

Project description:Chrysanthemum nankingense above-ground transcriptome

| PRJNA810751 | ENA

Corn co-culture with Metarhizium

Project description:Metarhizium species were grown in plate (M-100 agar) co-culture with corn, for 4 and 7 days. Plate contents (plant material above hypocotyl removed) were ground under liquid nitrogen and extracted with methanol.

2020-05-10 | MSV000085395 | MassIVE

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data