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.
Project description:Global transcriptome analysis and identification of differentially expressed genes after infection of the diploid strawberry Fragaria vesca with powdery mildew pathogen(Podosphaera aphanis)using Illumina HiSeq2000 platform
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.
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.
Project description:In order to discover novel small RNAs expressed in mature sperm, we isolated mature sperm from mouse cauda epididymis, comparing with data from adult tesis and uterus. The small RNA fraction (18-40nt) was cloned and sequenced from total RNA of mature sperm, testis and uterus of mice. RNAs extracted from mature sperm, adult testis and uterus were used for high throughput sequencing analysis
Project description:In order to discover novel small RNAs expressed in mature sperm, we isolated mature sperm from mouse cauda epididymis, comparing with data from adult tesis and uterus. The small RNA fraction (18-40nt) was cloned and sequenced from total RNA of mature sperm, testis and uterus of mice.
Project description:In plants, microRNAs (miRNAs) play a critical role in post-transcriptional gene regulation and have been shown to control many genes involved in various biological and metabolic processes. Deep sequencing technologies have facilitated identification of species-specific or lowly expressed as well as conserved or highly expressed miRNAs in plants. Strawberry is one of the most economically important fruit throughout the world.Although miRNAs have been extensively studied in the past five years, limited systematic study of miRNAs has been performed on the Fragaria genus. These results show that regulatory miRNAs exist in agronomically important strawberry and may play an important role in strawberry growth, development, and response to disease. High throughput sequencing was employed to identify miRNAs in strawberry and try to describe their functions in strawberry growth and development