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

ABSTRACT: 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.

ORGANISM(S): Fragaria x ananassa

PROVIDER: GSE48055 | GEO | 2013/07/07

SECONDARY ACCESSION(S): PRJNA208799

REPOSITORIES: GEO

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Project description:The pink-flowered strawberry is very popular in China due to its appreciation and economic benefits and its flower has rich red petal with varying degrees, which is provided by anthocyanins accumulation. To better understand the functions of miRNAs, sRNAome, transcriptome and degradome sequencing were used to explore the target genes of miRNAs in flower development and coloring of pink-flowered strawberry. Nine small RNA libraries and a mixed degradome library from flower petals at different developmental stages were constructed and sequenced in this study. A total of 739 known miRNAs and 964 newly identified miRNAs were identified via small RNA sequencing, and their 2816 target genes were cleaved by 639 miRNAs based on the degradome data. There were 317 different expression miRNAs among flower development in pink-flowered strawberry regulated 2134 different expression target genes, which significantly enriched in the transcriptional regulation, phenylpropanoid biosynthesis and plant hormone signal transduction. Furthermore, integrated microRNAomic and transcriptomic analyses suggested that 98 miRNAs were targeted several transcription factors related to anthocyanin accumulation, in which 26 were targeted to MYBs, 12 bHLHs, 14 NACs, and 19 SPLs. And that, twenty seven different expression miRNAs may affect anthocyanin biosynthesis by regulating 23 targets participated in hormone signal transduction pathway in pink-flowered strawberry. The qRT-PCR analysis confirmed the expression changes of 21 miRNA-target pairs showed an opposite trend. Moreover, a co-expression regulatory network was constructed based on differentially expressed miRNA-targets according to the degradome data. Overall, we conducted a comparative analysis uncovered the regulatory functions of microRNAs in flower development and color changes of pink-flowered strawberry via multiple factors, including anthocyanin biosynthesis, hormone signaling and regulation factors. This work not only expands the knowledge of miRNAs affecting the coloration in strawberry, but also provides rich resources for future functional studies.

Project description:Background: A long juvenile period between germination and flowering is a common characteristic among fruit trees, including Malus hupehensis (Pamp.) Rehd., which is an apple rootstock widely used in China. microRNAs (miRNAs) play an important role in the regulation of phase transition and reproductive growth processes. Results: M. hupehensis RNA libraries, one adult and one juvenile phase, were constructed using tree leaves and underwent high-throughput sequencing. We identified 42 known miRNA families and 172 novel miRNAs. We also identified 127 targets for 25 known miRNA families and 168 targets for 35 unique novel miRNAs using degradome sequencing. The identified miRNA targets were categorized into 58 biological processes, and the 123 targets of known miRNAs were associated with phase transition processes. The KEGG analysis revealed that these targets were involved in starch and sucrose metabolism, and plant hormone signal transduction. Expression profiling of miRNAs and their targets indicated multiple regulatory functions in the phase transition. The higher expression level of mdm-miR156 and lower expression level of mdm-miR172 in the juvenile phase leaves implied that these two small miRNAs regulated the phase transition. mdm-miR160 and miRNA393, which regulate genes involved in auxin signal transduction, could also be involved in controlling this process. The identification of known and novel miRNAs and their targets provides new information on this regulatory process in M. hupehensis, which will contribute to the understanding of miRNA functions during growth, phase transition and reproduction in woody fruit trees. Conclusions: A comprehensive study on M. hupehensis miRNAs related to the juvenile to adult phase transition was performed. The combination of sRNA and degradome sequencing can be used to better illustrate the profiling of hormone-regulated miRNAs and miRNA targets involving complex regulatory networks, which will contribute to the understanding of miRNA functions during growth, phase transition and reproductive growth in perennial woody fruit trees.

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

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