Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| ERR14224626_1.fastq.gz | Fastqsanger.gz | |||
| ERR14224626_2.fastq.gz | Fastqsanger.gz | |||
| ERR14209146.fastq.gz | Fastqsanger.gz | |||
| ERR14209147.fastq.gz | Fastqsanger.gz |
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Project description:Chromatin, DNA and RNA were extracted from young A. alpina Pajares primary stem leaves. Chromatin and DNA methylation immunoprecipitation experiments were performed using commercially available antibodies and analyzed by Illumina sequencing (ChIP-seq and MeDIP-seq). Transcriptome data were generated by RNA-seq. ChIP-seq analysis of H3K4me3, H3K27me3 and H3K27me1 enrichment profiles and MeDIP-seq analysis of 5mC enrichment profiles in 2 biological replicates. RNA-seq analysis of mRNA levels in 1 biological replicate.
2015-02-03 | E-GEOD-54560 | biostudies-arrayexpress
Project description:Polycarpic perennials maintain vegetative growth after flowering. PERPETUAL FLOWERING 1 (PEP1), the orthologue of FLOWERING LOCUS C (FLC) inArabis alpina regulates flowering and contributes to polycarpy in a vernalisation-dependent pathway. pep1 mutants do not require vernalisation to flower and have reduced return to vegetative growth as all of their axillary branches become reproductive. To identify additional genes that regulate flowering and contribute to perennial traits we performed an enhancer screen of pep1. Using mapping-by-sequencing, we cloned a mutant (enhancer of pep1-055, eop055), performed transcriptome analysis and physiologically characterised the role it plays on perennial traits in an introgression line carrying the eop055 mutation and a functional PEP1 wild-type allele. eop055 flowers earlier than pep1 and carries a lesion in the A. alpina orthologue of the APETALA2 (AP2)-like gene, TARGET OF EAT2 (AaTOE2). AaTOE2 is a floral repressor and acts upstream of SQUAMOSA PROMOTER-BINDING PROTEIN-LIKE 5 (AaSPL5). In the wild-type background, which requires cold treatment to flower, AaTOE2 regulates the age-dependent response to vernalisation. In addition, AaTOE2 ensures the maintenance of vegetative growth by delaying axillary meristem initiation and repressing flowering of axillary buds before and during cold exposure. We conclude that AaTOE2 is instrumental in fine tuning different developmental traits in the perennial life cycle of A. alpina.
2021-01-26 | GSE145716 | GEO
Project description:Perennial plants maintain their life span through several growth seasons. Arabis alpina serves as model Brassicaceae species to study perennial traits. A. alpina lateral stems have a proximal vegetative zone with a dormant bud zone, and a distal senescing seed-producing inflorescence zone. We addressed the questions of how this zonation is distinguished at the anatomical level, whether it is related to nutrient storage, and which signals affect the zonation. We found that the vegetative zone ehxibits secondary growth, which we termed the perennial growth zone (PZ). High-molecular weight carbon compounds accumulate there in cambium and cambium derivatives. Neither vernalization nor flowering were requirements for secondary growth and sequestration of storage compounds. The inflorescence zone with only primary growth, termed annual growth zone (AZ), or roots exhibited different storage characteristics. Following cytokinin application, cambium activity was enhanced and secondary phloem parenchyma was formed in the PZ and also in the AZ. In transcriptome analysis cytokinin-related genes represented enriched gene ontology terms and were expressed at higher level in PZ than AZ. Thus, A. alpina uses primarily the vegetative PZ for nutrient storage, coupled to cytokinin-promoted secondary growth. This finding lays a foundation for future studies addressing signals for perennial growth.
2020-06-14 | GSE152417 | GEO
Project description:Chromatin, DNA and RNA were extracted from young A. alpina Pajares primary stem leaves. Chromatin and DNA methylation immunoprecipitation experiments were performed using commercially available antibodies and analyzed by Illumina sequencing (ChIP-seq and MeDIP-seq). Transcriptome data were generated by RNA-seq.
2015-02-03 | GSE54727 | GEO
Project description:Chromatin, DNA and RNA were extracted from young A. alpina Pajares primary stem leaves. Chromatin and DNA methylation immunoprecipitation experiments were performed using commercially available antibodies and analyzed by Illumina sequencing (ChIP-seq and MeDIP-seq). Transcriptome data were generated by RNA-seq.
2015-02-03 | GSE54560 | GEO
Project description:Polycarpic perennials maintain vegetative growth after flowering. PERPETUAL FLOWERING 1 (PEP1), the orthologue of FLOWERING LOCUS C (FLC) inArabis alpina regulates flowering and contributes to polycarpy in a vernalisation-dependent pathway. pep1 mutants do not require vernalisation to flower and have reduced return to vegetative growth as all of their axillary branches become reproductive. To identify additional genes that regulate flowering and contribute to perennial traits we performed an enhancer screen of pep1. Using mapping-by-sequencing, we cloned a mutant (enhancer of pep1-055, eop055), performed transcriptome analysis and physiologically characterised the role it plays on perennial traits in an introgression line carrying the eop055 mutation and a functional PEP1 wild-type allele. eop055 flowers earlier than pep1 and carries a lesion in the A. alpina orthologue of the APETALA2 (AP2)-like gene, TARGET OF EAT2 (AaTOE2). AaTOE2 is a floral repressor and acts upstream of SQUAMOSA PROMOTER-BINDING PROTEIN-LIKE 5 (AaSPL5). In the wild-type background, which requires cold treatment to flower, AaTOE2 regulates the age-dependent response to vernalisation. In addition, AaTOE2 ensures the maintenance of vegetative growth by delaying axillary meristem initiation and repressing flowering of axillary buds before and during cold exposure. We conclude that AaTOE2 is instrumental in fine tuning different developmental traits in the perennial life cycle of A. alpina.
2021-01-26 | GSE145718 | GEO
Project description:Flowering of perennial Arabis alpina, is differentially regulated on primary and axillary shoots. Although contributions of vernalization and aging pathways have been analyzed, those of photoperiodic flowering genes CONSTANS (CO), FLOWERING LOCUS T (FT), and TWIN-SISTER OF FT (TSF) remain unexplored. CRISPR-Cas9 mutations in AaCO and AaFT/TWIN SISTER OF FT-LIKE (TSFL) were recovered. Aaco and Aaft/tsfl mutants in pep1 background were scored for flowering time, inflorescence branching and floral phenotypes under long (LD) or short days (SD) and after vernalization. RNAseq data on primary and axillary branches were compared. AaCO activates AaFT/TSFL transcription in leaves, and Aaco and Aaft tsfl mutations delay flowering under LDs. Axillary branches flowered in Aaco mutants but not in Aaft tsfl mutants. Both lacked inflorescence branches and flowers on the primary shoot under LDs. However, Aaft tsfl mutants produced some flowers after vernalization, and Aaco a few in SDs. RNAseq identified genes responsive to AaFT, TSFL and AaCO on the primary shoot and in axillary branches. Therefore, AaCO-AaFT promote flowering of A. alpina under LDs, but with distinct roles in axillary branch flowering. Both genes are required for inflorescence branching and flower formation on the primary shoot. The complex role of the CO-FT module in inflorescence architecture may underlie the polycarpic, perennial life history of A. alpina.
2026-01-31 | GSE317358 | GEO