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1. Deep sequencing identifies tissue-specific microRNAs and their target genes involving in the biosynthesis of tanshinones in Salvia miltiorrhiza.

Author

Xiangbin Xu, Qinghua Jiang, Xiuyan Ma, Qicai Ying, Bo Shen, Yongsheng Qian, Hongmiao Song, and Huizhong Wang

Subjects
Medicine, Science
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. The finding of microRNAs (miRNAs) and their target genes will help understand their biological role on the biosynthesis of tanshinones in S. miltiorrhiza. In the present study, a total of 452 known miRNAs corresponding to 589 precursor miRNAs (pre-miRNAs), and 40 novel miRNAs corresponding to 24 pre-miRNAs were identified in different tissues of S. miltiorrhiza by high-throughput sequencing, 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 cleaved by miR5072, and involved in the biosynthesis of tanshinones. This study provided valuable information for understanding the tissue-specific expression patterns of miRNAs in S. miltiorrhiza, and offered a foundation for future studies of the miRNA-mediated biosynthesis of tanshinones.

Published
2014
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2. High-throughput sequencing and degradome analysis identify miRNAs and their targets involved in fruit senescence of Fragaria ananassa.

Author

Xiangbin Xu, Lili Yin, Qicai Ying, Hongmiao Song, Dawei Xue, Tongfei Lai, Maojun Xu, Bo Shen, Huizhong Wang, and Xuequn Shi

Subjects
Medicine, Science
Abstract

In non-climacteric fruits, the respiratory increase is absent and no phytohormone is appearing to be critical for their ripening process. They must remain on the parent plant to enable full ripening and be picked at or near the fully ripe stage to obtain the best eating quality. However, huge losses often occur for their quick post-harvest senescence. To understanding the complex mechanism of non-climacteric fruits post-harvest senescence, we constructed two small RNA libraries and one degradome from strawberry fruit stored at 20°C for 0 and 24 h. A total of 88 known and 1224 new candidate miRNAs, and 103 targets cleaved by 19 known miRNAs families and 55 new candidatemiRNAs were obtained. These targets were associated with development, metabolism, defense response, signaling transduction and transcriptional regulation. Among them, 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. The present study provided valuable information for understanding the quick senescence of strawberry fruit, and offered a foundation for studying the miRNA-mediated senescence of non-climacteric fruits.

Published
2013
Full Text
View/download PDF

3. Deep Sequencing Identifies Tissue-Specific MicroRNAs and Their Target Genes Involving in the Biosynthesis of Tanshinones in Salvia miltiorrhiza

Author

Xiuyan Ma, Qicai Ying, Bo Shen, Hongmiao Song, Huizhong Wang, Qinghua Jiang, Yongsheng Qian, and Xiangbin Xu

Subjects
Agricultural Biotechnology, lcsh:Medicine, Datasets as Topic, Salvia miltiorrhiza, Computational biology, Biology, Deep sequencing, chemistry.chemical_compound, Biosynthesis, Gene Expression Regulation, Plant, Plant Products, microRNA, Genetics, Tissue specific, Cluster Analysis, RNA, Messenger, lcsh:Science, Gene, Gene Library, Multidisciplinary, Gene Expression Profiling, lcsh:R, Biology and Life Sciences, Computational Biology, High-Throughput Nucleotide Sequencing, Agriculture, Molecular biology, Agronomy, MicroRNAs, chemistry, Organ Specificity, Abietanes, Protocatechuic aldehyde, lcsh:Q, RNA Interference, RNA extraction, Research Article, Biotechnology
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. The finding of microRNAs (miRNAs) and their target genes will help understand their biological role on the biosynthesis of tanshinones in S. miltiorrhiza. In the present study, a total of 452 known miRNAs corresponding to 589 precursor miRNAs (pre-miRNAs), and 40 novel miRNAs corresponding to 24 pre-miRNAs were identified in different tissues of S. miltiorrhiza by high-throughput sequencing, 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 cleaved by miR5072, and involved in the biosynthesis of tanshinones. This study provided valuable information for understanding the tissue-specific expression patterns of miRNAs in S. miltiorrhiza, and offered a foundation for future studies of the miRNA-mediated biosynthesis of tanshinones.

Published
2014

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

Author

Qicai Ying, Dawei Xue, Hongmiao Song, Xuequn Shi, Lili Yin, Huizhong Wang, Bo Shen, Tongfei Lai, Xiangbin Xu, and Maojun Xu

Subjects
Senescence, Small RNA, Time Factors, Transcription, Genetic, lcsh:Medicine, Crops, Biology, Real-Time Polymerase Chain Reaction, Fragaria, Fruits, Molecular Genetics, RNA interference, Auxin, Gene Expression Regulation, Plant, Genome Analysis Tools, Vegetables, Transcriptional regulation, Genetics, MYB, Gene Regulation, Genome Sequencing, lcsh:Science, Transcription factor, Gene Library, chemistry.chemical_classification, Multidisciplinary, lcsh:R, Temperature, food and beverages, High-Throughput Nucleotide Sequencing, Computational Biology, Ripening, Agriculture, Genomics, MicroRNAs, chemistry, RNA, Plant, Fruit, lcsh:Q, Gene expression, Sequence Analysis, Genome, Plant, Signal Transduction, Transcription Factors, Research Article
Abstract

In non-climacteric fruits, the respiratory increase is absent and no phytohormone is appearing to be critical for their ripening process. They must remain on the parent plant to enable full ripening and be picked at or near the fully ripe stage to obtain the best eating quality. However, huge losses often occur for their quick post-harvest senescence. To understanding the complex mechanism of non-climacteric fruits post-harvest senescence, we constructed two small RNA libraries and one degradome from strawberry fruit stored at 20°C for 0 and 24 h. A total of 88 known and 1224 new candidate miRNAs, and 103 targets cleaved by 19 known miRNAs families and 55 new candidatemiRNAs were obtained. These targets were associated with development, metabolism, defense response, signaling transduction and transcriptional regulation. Among them, 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. The present study provided valuable information for understanding the quick senescence of strawberry fruit, and offered a foundation for studying the miRNA-mediated senescence of non-climacteric fruits.

Published
2013

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