Transcriptome-wide identification and profiling of miRNAs in a stress-tolerant conifer Sabina chinensis. Hu, X., Zhou, S., Yang, Y., Liu, H., Anil, S., Wang, Q., Zhao, W., Gao, Q., El-Kassaby, Y. A., Wang, T., Li, Y., & Mao, J. Journal of Biosciences, 45(1):41, February, 2020. ![Transcriptome-wide identification and profiling of miRNAs in a stress-tolerant conifer Sabina chinensis [link]](https://bibbase.org/img/filetypes/link.svg "link")
Paper doi abstract bibtex miRNAs are important regulatory components involving in many biological processes, including plant development, vegetative and reproductive growth, and stress response. However, identification and characterization of miRNAs still remain limited for conifer species. In this study, with deep sequencing, we obtained 1,314,450 unique reads with 18–30 nt length from a stress-tolerant conifer, Sabina chinensis. We identified 37 conserved and 103 novel miRNAs, their unique characteristics were further analyzed, and 10 randomly selected were validated by qRT-PCR. Through miRNA target predictions and annotations, we found miRNA may have several targets as well a target could be regulated by several miRNAs, and a total of 2,397 mRNAs were predicted to be targets of the 140 miRNAs. These targets included not only important transcription factors such as auxin response factors, but also indispensable non-transcriptional factor proteins. Pathway-based analysis showed that S. chinensis miRNAs are involved in 172 metabolic pathways, of which 3 were discovered in adaptation-related pathways, indicating their possible relevance to the species’ stress-tolerance characteristics. This study is expected to lay the foundation for exploring the regulative roles of miRNAs in development, growth, and response to environmental stresses of S. chinensis.
@article{hu_transcriptome-wide_2020,
title = {Transcriptome-wide identification and profiling of {miRNAs} in a stress-tolerant conifer {Sabina} chinensis},
volume = {45},
issn = {0973-7138},
url = {https://doi.org/10.1007/s12038-020-0002-4},
doi = {10.1007/s12038-020-0002-4},
abstract = {miRNAs are important regulatory components involving in many biological processes, including plant development, vegetative and reproductive growth, and stress response. However, identification and characterization of miRNAs still remain limited for conifer species. In this study, with deep sequencing, we obtained 1,314,450 unique reads with 18–30 nt length from a stress-tolerant conifer, Sabina chinensis. We identified 37 conserved and 103 novel miRNAs, their unique characteristics were further analyzed, and 10 randomly selected were validated by qRT-PCR. Through miRNA target predictions and annotations, we found miRNA may have several targets as well a target could be regulated by several miRNAs, and a total of 2,397 mRNAs were predicted to be targets of the 140 miRNAs. These targets included not only important transcription factors such as auxin response factors, but also indispensable non-transcriptional factor proteins. Pathway-based analysis showed that S. chinensis miRNAs are involved in 172 metabolic pathways, of which 3 were discovered in adaptation-related pathways, indicating their possible relevance to the species’ stress-tolerance characteristics. This study is expected to lay the foundation for exploring the regulative roles of miRNAs in development, growth, and response to environmental stresses of S. chinensis.},
language = {en},
number = {1},
urldate = {2023-04-27},
journal = {Journal of Biosciences},
author = {Hu, Xian-Ge and Zhou, Shan-Shan and Yang, Ying and Liu, Hui and Anil, Shrestha and Wang, Qing and Zhao, Wei and Gao, Qiong and El-Kassaby, Yousry A. and Wang, Tongli and Li, Yue and Mao, Jian-Feng},
month = feb,
year = {2020},
keywords = {Sabina chinensis, miRNA, miRNA target, pathway},
pages = {41},
}
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In this study, with deep sequencing, we obtained 1,314,450 unique reads with 18–30 nt length from a stress-tolerant conifer, Sabina chinensis. We identified 37 conserved and 103 novel miRNAs, their unique characteristics were further analyzed, and 10 randomly selected were validated by qRT-PCR. Through miRNA target predictions and annotations, we found miRNA may have several targets as well a target could be regulated by several miRNAs, and a total of 2,397 mRNAs were predicted to be targets of the 140 miRNAs. These targets included not only important transcription factors such as auxin response factors, but also indispensable non-transcriptional factor proteins. Pathway-based analysis showed that S. chinensis miRNAs are involved in 172 metabolic pathways, of which 3 were discovered in adaptation-related pathways, indicating their possible relevance to the species’ stress-tolerance characteristics. 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However, identification and characterization of miRNAs still remain limited for conifer species. In this study, with deep sequencing, we obtained 1,314,450 unique reads with 18–30 nt length from a stress-tolerant conifer, Sabina chinensis. We identified 37 conserved and 103 novel miRNAs, their unique characteristics were further analyzed, and 10 randomly selected were validated by qRT-PCR. Through miRNA target predictions and annotations, we found miRNA may have several targets as well a target could be regulated by several miRNAs, and a total of 2,397 mRNAs were predicted to be targets of the 140 miRNAs. These targets included not only important transcription factors such as auxin response factors, but also indispensable non-transcriptional factor proteins. Pathway-based analysis showed that S. chinensis miRNAs are involved in 172 metabolic pathways, of which 3 were discovered in adaptation-related pathways, indicating their possible relevance to the species’ stress-tolerance characteristics. This study is expected to lay the foundation for exploring the regulative roles of miRNAs in development, growth, and response to environmental stresses of S. chinensis.},\n\tlanguage = {en},\n\tnumber = {1},\n\turldate = {2023-04-27},\n\tjournal = {Journal of Biosciences},\n\tauthor = {Hu, Xian-Ge and Zhou, Shan-Shan and Yang, Ying and Liu, Hui and Anil, Shrestha and Wang, Qing and Zhao, Wei and Gao, Qiong and El-Kassaby, Yousry A. and Wang, Tongli and Li, Yue and Mao, Jian-Feng},\n\tmonth = feb,\n\tyear = {2020},\n\tkeywords = {Sabina chinensis, miRNA, miRNA target, pathway},\n\tpages = {41},\n}\n\n","author_short":["Hu, X.","Zhou, S.","Yang, Y.","Liu, H.","Anil, S.","Wang, Q.","Zhao, W.","Gao, Q.","El-Kassaby, Y. 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