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Identification and characterization of small non-coding RNAs from Chinese fir by high throughput sequencing

Authors :
Wan Li-Chuan
Wang Feng
Guo Xiangqian
Lu Shanfa
Qiu Zongbo
Zhao Yuanyuan
Zhang Haiyan
Lin Jinxing
Source :
BMC Plant Biology, Vol 12, Iss 1, p 146 (2012)
Publication Year :
2012
Publisher :
BMC, 2012.

Abstract

Abstract 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.

Details

Language :
English
ISSN :
14712229
Volume :
12
Issue :
1
Database :
Directory of Open Access Journals
Journal :
BMC Plant Biology
Publication Type :
Academic Journal
Accession number :
edsdoj.2fba36dd5cea4d2cb3d4f5e78313ccec
Document Type :
article
Full Text :
https://doi.org/10.1186/1471-2229-12-146