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ABSTRACT: Wild strawberry (Fragaria vesca) green stage and white stage fruit transcriptome

PROVIDER: PRJNA360594 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR5155710.fastq.gz	Fastqsanger.gz
	SRR5155711.fastq.gz	Fastqsanger.gz
	SRR5155712.fastq.gz	Fastqsanger.gz
	SRR5155713.fastq.gz	Fastqsanger.gz
	SRR5155714.fastq.gz	Fastqsanger.gz

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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.

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Project description:With the development of high throughput sequencing technologies, plenty of non-coding RNAs (ncRNAs) have been discovered to play important roles in diverse plant biological processes. Although these ncRNAs extensively exist in plant, their biological functions are still remained to characterize. To obtain a comprehensive understanding of long non-coding RNA (lncRNA) function in strawberry fruit ripening progress, we performed transcriptomic analyses on the diploid strawberry Fragaria vesca in a time-course during fruit ripening. Here, we have identified 25,613 lncRNAs based on RNA-seq data from poly(A)-depleted libraries and rRNA-depleted libraries. Among them, most of lncRNAs exhibit stage-specific expression pattern. Functional analysis on F.vesca endogenous FRUIT RIPENING-RELATED LONG ANTISENSE INTERGENIC RNA (FRILAIR) in octaploid strawberry Falandi, we found that overexpression FRILAIR can compete miR397 to regulate its target laccase genes (LACs), and it may contribute to strawberry ripening. Our findings demonstrate that FRILAIR can act as a competing endogenous RNA (ceRNA) by disturbing miR397 to repress expression level of LACs, and would be valuable for strawberry ripening.

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Deep small RNA and degradome sequencing identifies new miRNAs-target pairs and novel PhasiRNAs in F-box regulatory networks in diploid strawberry

Project description:The wild strawberry Fragaria vesca has recently emerged as an excellent model for investigating flower and fruit traits in economically important fruit crops. Its history of physiological studies combined with sequenced genome and full complements of molecular genetic tools facilitate investigations into mechanisms of its unique biological processes such as fleshy fruit development from the enlarged stem tip called receptacle. Sequencing of nine small RNA libraries encompassing vegetative, flower, and fruit tissues led to the identification of 22 conserved and 10 less-conserved miRNAs as well as 41 novel miRNAs that are likely specific to the strawberry. High throughput Parallel Analyses of RNA ends (PARE) were performed to identify miRNA-guided cleavage events and corresponding target genes. We found that most conserved miRNAs developed species-specific target genes in addition to conserved targets, highlighting the dynamic and fluid nature of the miRNA_target relations. Significantly, we discovered two novel clusters of miRNAs, which together target up to 94 F-box genes. Within one of the clusters is a 22 nt novel miRNA, miRN39, that was expressed preferentially in the developing receptacle fruit and triggered phased siRNA production from six primary FBX PHAS loci. This miRN39-phasiFBX pathway may be involved in regulating disease resistance in the receptacle fruit. In addition, a modified “two-hit” mode of tasiRNA processing was identified in F. vesca, suggesting flexibility in applying previously set rules. A major theme that emerges from this work is that novel miRNAs and miRNA-phasiRNA networks may have evolved to regulate recently expanded gene families so as to control species-specific biological or physiological processes.

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