Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Deep sequencing identify tissue-specific microRNAs and their target genes involved in tanshinones biosynthesis in Salvia miltiorrhiza

ABSTRACT: Salvia miltiorrhiza is one of the most popular traditional medicinal herbs in Asian nations. Its dried root contains a number of tanshinones, protocatechuic aldehyde, salvianolic acid B and rosmarinic, and is used for the treatment of various diseases. To make clear the molecular mechanism of tanshinones biosynthesis in S. miltiorrhiza, the tissue-specific miRNAs and their target genes were identified by high-throughput sequencing and degradome analysis. A total of 452 known miRNAs corresponding to 589 pre-miRNAs, and 40 novel miRNAs corresponding to 24 pre-miRNAs were identified in different tissues of S. miltiorrhiza, respectively. Among them, 62 miRNAs express only in root, 95 miRNAs express only in stem, 19 miRNAs express only in leaf, and 71 miRNAs express only in flower, respectively. By the degradome analysis, 69 targets potentially cleaved by 25 miRNAs were identified. Among them, Acetyl-CoA C-acetyltransferase was identified in S. miltiorrhiza, which was cleaved by miR5072 and involved in the biosynthesis of tanshinones. This study provided valuable information for understanding the tissues expression patterns of miRNAs, and offered a foundation for future studies of the miRNA-mediated tanshinones biosynthesis in S. miltiorrhiza. The tissue-specific miRNAs and their target genes were identified by high-throughput sequencing and degradome analysis.

ORGANISM(S): Salvia miltiorrhiza

SUBMITTER: Xiangbin Xu

PROVIDER: E-GEOD-60757 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Enhancing grain production of rice (Oryza sativa L.) is a top priority in ensuring food security for human being. One approach to increase yield is to delay leaf senescence and to extend the available time for photosynthesis. microRNAs (miRNAs) are key regulators for aging and cellular senescence in eukayotes. However, miRNAs and their roles in rice leaf senescence remain unexplored. Here, we report identification of miRNAs and their putative target genes by deep sequencing of six small RNA libraries, six RNA-seq libraries and two degradome libraries from the leaves of two super hybrid rice, Nei-2-You 6 (N2Y6, age-resistant rice) and Liang-You-Pei 9 (LYP9, age-sensitive rice). Totally 372 known miRNAs and 162 miRNA candidates were identified, and 1145 targets were identified. Compared with the expression of miRNAs in the leaves of LYP9, the numbers of miRNAs up-regulated and down-regulated in the leaves of N2Y6 were 47 and 30 at early stage of grain-filling, 21 and 17 at the middle stage, and 11 and 37 at the late stage, respectively. Six miRNA families, osa-miR159, osa-miR160 osa-miR164, osa-miR167, osa-miR172 and osa-miR1848, targeting the genes encoding APETALA2 (AP2), zinc finger proteins, salicylic acid-induced protein 19 (SIP19), Auxin response factors (ARF) and NAC transcription factors, respectively, were found to be involved in leaf senescence through phytohormone signaling pathways. These results provided valuable information for understanding the miRNA-mediated leaf senescence of rice, and offered an important foundation for rice breeding. [miRNA] sample 1:The flag leaves at early stage of grain-filling of N2Y6 rice; sample 2: The flag leaves at middle stage of grain-filling of N2Y6 rice;sample 3:The flag leaves at late stage of grain-filling of N2Y6 rice; sample 4:The flag leaves at early stage of grain-filling of LYP9 rice; sample 5: The flag leaves at middle stage of grain-filling of LYP9 rice;sample 6:The flag leaves at late stage of grain-filling of LYP9 rice. [DGE]: samples 7-12 [degradome (targets)]: samples 13:The flag leaves at mixed stages of grain-filling of N2Y6 rice; sample 14:The flag leaves at mixed stages of grain-filling of LYP9 rice

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.

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Deep sequencing identify tissue-specific microRNAs and their target genes involved in tanshinones biosynthesis in Salvia miltiorrhiza

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