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Fragaria x ananassa

ABSTRACT: Comprehensive transcriptome analysis of phytohormone pathway genes and miRNAs in ABA initiated strawberry receptacle ripening

PROVIDER: PRJNA267010 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR1649250_1.fastq.gz	Fastqsanger.gz
	SRR1649250_2.fastq.gz	Fastqsanger.gz
	SRR1649260.fastq.gz	Fastqsanger.gz
	SRR1649251.fastq.gz	Fastqsanger.gz
	SRR1649261.fastq.gz	Fastqsanger.gz

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Comprehensive transcriptome analysis of phytohormone pathway genes and miRNAs in ABA initiated strawberry receptacle ripening

2016-10-27 | GSE63224 | GEO

Comprehensive transcriptome analysis of phytohormone pathway genes and miRNAs in ABA initiated strawberry receptacle ripening

Project description:We used Illumina sequencing to investigate the global transcriptomic expression of hormonal pathway genes in ABA initiated strawberry receptacle ripening. Expression profiles of hormone synthetic and signaling genes further demonstrated the positive roles of ABA and GA, and the negative role of auxin in receptacle ripening. We also evaluated the transcript profiling of ethylene and JA pathway genes, and the results suggested that both ethylene and JA participated in receptacle ripening. Furthermore, two novel miRNAs and three conserved miRNAs were identified and validated to target genes in ABA and auxin pathways, respectively. Our analyses reveal the molecular mechanism of hormonal regulation during strawberry receptacle ripening. The data also provide an abundant of genetic information for molecular manipulation on non-climacteric fruit ripening. Sample 1: CK0 (Strawberry fruit two weeks after athesis treated with water, set as day 0); Sample 2: CK5 (fruit treated with water on day 5); Sample 3: CK8 (fruit treated with water on day 8); Sample 4: ABA5 (fruit treated with ABA on day 5); Sample 5: ABA8 (fruit treated with ABA on day 5); Sample 6: NDGA5 (fruit treated with water on day 5); Sample 7: NDGA8 (fruit treated with NDGA on day 8).

2016-10-27 | E-GEOD-63224 | biostudies-arrayexpress

Central role of FaGAMYB in the transition of the strawberry receptacle from development to ripening

Project description:The study assigns a key regulatory role of FaGAMYB in the initiation of strawberry receptacle ripening and acting upstream of the known regulator ABA. Down-regulation of FaGAMYB caused an arrest in the ripening of receptacle and inhibited colour formation. Consistent with this, several transcription factors associated to the regulation of flavonoids biosynthetic pathway showed altered expression. FaGAMYB silencing also caused a reduction of ABA biosynthesis and sucrose content. Interestingly exogenous ABA application to RNAi transformed receptacle reversed most defects caused by FaGAMYB down53 regulation. Transient silencing of FaGAMYB using RNAi and further determination of changes in (1) global gene expression by RNAseq, and (2) composition of primary and secondary metabolites has been used to investigate the role played by this gene during the development of the receptacle.

2015-04-14 | E-MTAB-3496 | biostudies-arrayexpress

The NAC transcription factor FaRIF controls fruit ripening in strawberry

Project description:In contrast to climacteric fruits such as tomato, the knowledge on key regulatory genes controlling the ripening of strawberry, a non-climacteric fruit, is still limited. NAC transcription factors mediate different developmental processes in plants. Here, we identified and characterized FaRIF (Ripening Inducing Factor), a NAC transcription factor that is highly expressed and induced in strawberry receptacles during ripening. Functional analyses based on stable transgenic lines aimed at silencing FaRIF by RNA interference, either from a constitutive promoter or the ripe receptacle-specific EXP2 promoter, as well as overexpression lines showed that FaRIF controls critical ripening-related processes such as fruit softening and pigment and sugar accumulation. Physiological, metabolome and transcriptome analyses of receptacles of FaRIF-silenced and overexpression lines point to FaRIF as a key regulator of strawberry fruit ripening from early developmental stages, controlling abscisic acid (ABA) biosynthesis and signaling, cell wall degradation and modification, the phenylpropanoid pathway, volatiles production, and the balance of the aerobic/anaerobic metabolism. FaRIF is therefore a target to be modified/edited to control the quality of strawberry fruits.

2021-02-20 | GSE167107 | GEO

High-throughput sequencing and degradome analysis identify miRNAs and their targets involved in fruit senescence of Fragaria ananassa

Project description:To identify miRNAs involved in senescence of strawberry fruit, two independent small RNA libraries and one degradome library from strawberry fruits stored at 20 M-BM-0C for 0 and 24 h were constructed. A total of 18,759,735 and 20,293,492 mappable small RNA sequences were generated in the two small RNA libraries, respectively, and 88 known and 1224 new candidate miRNAs were obtained. Among them, 94 miRNAs were up-regulated and 64 were down-regulated in the senescence of strawberry fruit. Through degradome sequencing, 103 targets cleaved by 19 known miRNAs families and 55 new candidate miRNAs were identified. 14 targets, including NAC transcription factor, Auxin response factors (ARF) and Myb transcription factors, cleaved by 6 known miRNA families and 6 predicted candidates, were found to be involved in regulating fruit senescence. sample 1: Examination of small RNA in strawberry fruits stored at 20 M-BM-0C for 0; sample 2: Examination of small RNA in strawberry fruits stored at 20 M-BM-0C for 24 h

2013-07-07 | E-GEOD-48055 | biostudies-arrayexpress

Fragaria x ananassa

Project description:Identification of miRNAs in strawberry

| PRJNA150259 | ENA

Comprehensive transcriptomic dataset for early stage fruit development in woodland strawberry Fragaria vesca

Project description:Fragaria vesca, a diploid woodland strawberry with a small and sequenced genome, is an excellent model for studying fruit development. The strawberry fruit is unique in that the edible flesh is actually enlarged receptacle tissue. The true fruit are the numerous dry achenes dotting the receptacleM-^Rs surface. Auxin produced from the achene is essential for the receptacle fruit set, a paradigm for studying crosstalk between hormone signaling and development. To investigate the molecular mechanism underlying strawberry fruit set, next-generation sequencing was employed to profile early-stage fruit development with five fruit tissue types and five developmental stages from floral anthesis to enlarged fruits. This two-dimensional data set provides a systems-level view of molecular events with precise spatial and temporal resolution.

2013-10-01 | E-MTAB-1902 | biostudies-arrayexpress

Fragaria vesca

Project description:Strawberry receptacle transcriptome

| PRJNA320931 | ENA

High-throughput sequencing and degradome analysis identify miRNAs and their targets involved in fruit senescence of Fragaria ananassa

Project description:To identify miRNAs involved in senescence of strawberry fruit, two independent small RNA libraries and one degradome library from strawberry fruits stored at 20 °C for 0 and 24 h were constructed. A total of 18,759,735 and 20,293,492 mappable small RNA sequences were generated in the two small RNA libraries, respectively, and 88 known and 1224 new candidate miRNAs were obtained. Among them, 94 miRNAs were up-regulated and 64 were down-regulated in the senescence of strawberry fruit. Through degradome sequencing, 103 targets cleaved by 19 known miRNAs families and 55 new candidate miRNAs were identified. 14 targets, including NAC transcription factor, Auxin response factors (ARF) and Myb transcription factors, cleaved by 6 known miRNA families and 6 predicted candidates, were found to be involved in regulating fruit senescence.

2013-07-07 | GSE48055 | GEO

Role of Fragaria FaPRE1 in fruit ripening [FaPRE1-RNAi]

Project description:The role played by transcription factors in the regulation of strawberry fruit ripening process is scant. We have identified and functionally characterized FaPRE1, a non-DNA-binding bHLH transcription factor. FaPRE1 is a ripening-related transcription factor that regulates genes involved in cell architecture in strawberry fruit receptacles.

2019-10-18 | GSE125995 | GEO

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