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Identification and characterization of small non-coding RNAs from Chinese fir by high throughput sequencing
BACKGROUND: Small non-coding RNAs (sRNAs) play key roles in plant development, growth and responses to biotic and abiotic stresses. At least four classes of sRNAs have been well characterized in plants, including repeat-associated siRNAs (rasiRNAs), microRNAs (miRNAs), trans-acting siRNAs (tasiRNAs)...
Autores principales: | , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2012
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3462689/ https://www.ncbi.nlm.nih.gov/pubmed/22894611 http://dx.doi.org/10.1186/1471-2229-12-146 |
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author | Wan, Li-Chuan Wang, Feng Guo, Xiangqian Lu, Shanfa Qiu, Zongbo Zhao, Yuanyuan Zhang, Haiyan Lin, Jinxing |
author_facet | Wan, Li-Chuan Wang, Feng Guo, Xiangqian Lu, Shanfa Qiu, Zongbo Zhao, Yuanyuan Zhang, Haiyan Lin, Jinxing |
author_sort | Wan, Li-Chuan |
collection | PubMed |
description | BACKGROUND: Small non-coding RNAs (sRNAs) play key roles in plant development, growth and responses to biotic and abiotic stresses. At least four classes of sRNAs have been well characterized in plants, including repeat-associated siRNAs (rasiRNAs), microRNAs (miRNAs), trans-acting siRNAs (tasiRNAs) and natural antisense transcript-derived siRNAs. Chinese fir (Cunninghamia lanceolata) is one of the most important coniferous evergreen tree species in China. No sRNA from Chinese fir has been described to date. RESULTS: To obtain sRNAs in Chinese fir, we sequenced a sRNA library generated from seeds, seedlings, leaves, stems and calli, using Illumina high throughput sequencing technology. A comprehensive set of sRNAs were acquired, including conserved and novel miRNAs, rasiRNAs and tasiRNAs. With BLASTN and MIREAP we identified a total of 115 conserved miRNAs comprising 40 miRNA families and one novel miRNA with precursor sequence. The expressions of 16 conserved and one novel miRNAs and one tasiRNA were detected by RT-PCR. Utilizing real time RT-PCR, we revealed that four conserved and one novel miRNAs displayed developmental stage-specific expression patterns in Chinese fir. In addition, 209 unigenes were predicted to be targets of 30 Chinese fir miRNA families, of which five target genes were experimentally verified by 5' RACE, including a squamosa promoter-binding protein gene, a pentatricopeptide (PPR) repeat-containing protein gene, a BolA-like family protein gene, AGO1 and a gene of unknown function. We also demonstrated that the DCL3-dependent rasiRNA biogenesis pathway, which had been considered absent in conifers, existed in Chinese fir. Furthermore, the miR390-TAS3-ARF regulatory pathway was elucidated. CONCLUSIONS: We unveiled a complex population of sRNAs in Chinese fir through high throughput sequencing. This provides an insight into the composition and function of sRNAs in Chinese fir and sheds new light on land plant sRNA evolution. |
format | Online Article Text |
id | pubmed-3462689 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2012 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-34626892012-10-03 Identification and characterization of small non-coding RNAs from Chinese fir by high throughput sequencing Wan, Li-Chuan Wang, Feng Guo, Xiangqian Lu, Shanfa Qiu, Zongbo Zhao, Yuanyuan Zhang, Haiyan Lin, Jinxing BMC Plant Biol Research Article BACKGROUND: Small non-coding RNAs (sRNAs) play key roles in plant development, growth and responses to biotic and abiotic stresses. At least four classes of sRNAs have been well characterized in plants, including repeat-associated siRNAs (rasiRNAs), microRNAs (miRNAs), trans-acting siRNAs (tasiRNAs) and natural antisense transcript-derived siRNAs. Chinese fir (Cunninghamia lanceolata) is one of the most important coniferous evergreen tree species in China. No sRNA from Chinese fir has been described to date. RESULTS: To obtain sRNAs in Chinese fir, we sequenced a sRNA library generated from seeds, seedlings, leaves, stems and calli, using Illumina high throughput sequencing technology. A comprehensive set of sRNAs were acquired, including conserved and novel miRNAs, rasiRNAs and tasiRNAs. With BLASTN and MIREAP we identified a total of 115 conserved miRNAs comprising 40 miRNA families and one novel miRNA with precursor sequence. The expressions of 16 conserved and one novel miRNAs and one tasiRNA were detected by RT-PCR. Utilizing real time RT-PCR, we revealed that four conserved and one novel miRNAs displayed developmental stage-specific expression patterns in Chinese fir. In addition, 209 unigenes were predicted to be targets of 30 Chinese fir miRNA families, of which five target genes were experimentally verified by 5' RACE, including a squamosa promoter-binding protein gene, a pentatricopeptide (PPR) repeat-containing protein gene, a BolA-like family protein gene, AGO1 and a gene of unknown function. We also demonstrated that the DCL3-dependent rasiRNA biogenesis pathway, which had been considered absent in conifers, existed in Chinese fir. Furthermore, the miR390-TAS3-ARF regulatory pathway was elucidated. CONCLUSIONS: We unveiled a complex population of sRNAs in Chinese fir through high throughput sequencing. This provides an insight into the composition and function of sRNAs in Chinese fir and sheds new light on land plant sRNA evolution. BioMed Central 2012-08-15 /pmc/articles/PMC3462689/ /pubmed/22894611 http://dx.doi.org/10.1186/1471-2229-12-146 Text en Copyright ©2012 Wan et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Research Article Wan, Li-Chuan Wang, Feng Guo, Xiangqian Lu, Shanfa Qiu, Zongbo Zhao, Yuanyuan Zhang, Haiyan Lin, Jinxing Identification and characterization of small non-coding RNAs from Chinese fir by high throughput sequencing |
title | Identification and characterization of small non-coding RNAs from Chinese fir by high throughput sequencing |
title_full | Identification and characterization of small non-coding RNAs from Chinese fir by high throughput sequencing |
title_fullStr | Identification and characterization of small non-coding RNAs from Chinese fir by high throughput sequencing |
title_full_unstemmed | Identification and characterization of small non-coding RNAs from Chinese fir by high throughput sequencing |
title_short | Identification and characterization of small non-coding RNAs from Chinese fir by high throughput sequencing |
title_sort | identification and characterization of small non-coding rnas from chinese fir by high throughput sequencing |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3462689/ https://www.ncbi.nlm.nih.gov/pubmed/22894611 http://dx.doi.org/10.1186/1471-2229-12-146 |
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