Cunninghamia lanceolata
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA233997 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR1104931.fastq.gz | Fastqsanger.gz | |||
| SRR1104932.fastq.gz | Fastqsanger.gz | |||
| SRR1104933.fastq.gz | Fastqsanger.gz |
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Project description:We sequenced mRNA from dormant, reactivating, and actively growing C. lanceolata vascular cambium using tangential cryosections to generate the first transcriptome dynamics that may serve as a gene expression profile blueprint for cambium development and wood formation in the conifer.
2014-03-31 | GSE37152 | GEO
Project description:We sequenced mRNA from dormant, reactivating, and actively growing C. lanceolata vascular cambium using tangential cryosections to generate the first transcriptome dynamics that may serve as a gene expression profile blueprint for cambium development and wood formation in the conifer. Examination of mRNA levels in dormant, reactivating, and actively growing C. lanceolata vascular cambium, respectively
2014-03-31 | E-GEOD-37152 | biostudies-arrayexpress
Project description:Chinese fir (Cunninghamia lanceolate)
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Project description:Chinese fir Transcriptome or Gene expression
| PRJNA208414 | ENA
Project description:Identification and characterization of small non-coding RNAs from Chinese fir by high throughput sequencing
| PRJNA132921 | ENA
Project description:MicroRNAs (miRNAs) are small noncoding regulatory RNAs that play key roles in the process of plant development. To date, extensive studies of miRNAs have been performed in a few model plants, but few efforts have focused on small RNAs in conifers because of the lack of reference sequences for these enormous genomes. In this study, Solexa sequencing of three small RNA libraries obtained from dormant, reactivating, and active vascular cambium in Chinese fir samples identified 76 known miRNAs from 27 miRNA families and 18 new potential miRNAs, of which 15 novel miRNA precursors were validated by RT-PCR and sequencing. More than half of these novel miRNAs displayed stage-specific expression patterns in the vascular cambium. Furthermore, analyzing the 103 miRNAs and their predicted targets indicated that 30% of miRNAs appeared to negatively regulate their targets, of which 4 target genes involved in the regulation of cambial cell division were validated via RNA ligase-mediated rapid amplification of 5’ cDNA ends (RLM 5’-RACE). Interestingly, miRNA156 and miRNA172 may regulate the phase transition in vascular cambium from dormancy to active growth. These results provide new insights into the important regulatory functions of miRNAs in vascular cambium development and wood formation in conifers. The aim of this study is to investigate the small RNA transcriptome in different stages of vascular cambium development in Cunninghamia lanceolata. We herein conducted our comprehensive analysis of a plant sRNAome during development of the vascular cambium in Chinese fir using cryosectioning to isolate cambial meristem, which allowed a higher cellular resolution for defining small RNA profiles and overcomed the limitations resulting from the mixed samples in many previous investigations. Total RNAs of dormant, reactivating, and active cambial meristem, respectively were isolated using the Concert Plant RNA Reagent (Invitrogen, Carlsbad, CA, USA), and were then treated with RNase-free DNase I (Promega, Madison, WI, USA). Twenty micrograms of total RNAs were used and 16 to 30-nt sRNAs were purified using Novex 15% TBE-¬Urea gel (Invitrogen). Two adaptors were sequentially ligated to the 5' and 3' ends of purified sRNAs. The ligation products were further purified from Novex 10% TBE-Urea gel. Reverse transcriptase SuperScript II (Invitrogen) and high-fidelity DNA polymerase Phusion (New England Biolabs, Ipswich, MA, USA) were used in the following RT-PCR reaction. The amplification products were cut from Novex 6% TBE-Urea gel. The purified DNA fragments were used for sequencing on an Illumina 2G Genome Analyzer at the Beijing Genomics Institute, Shenzhen, China.
2015-04-07 | E-GEOD-53933 | biostudies-arrayexpress
Project description:MicroRNAs (miRNAs) are small noncoding regulatory RNAs that play key roles in the process of plant development. To date, extensive studies of miRNAs have been performed in a few model plants, but few efforts have focused on small RNAs in conifers because of the lack of reference sequences for these enormous genomes. In this study, Solexa sequencing of three small RNA libraries obtained from dormant, reactivating, and active vascular cambium in Chinese fir samples identified 76 known miRNAs from 27 miRNA families and 18 new potential miRNAs, of which 15 novel miRNA precursors were validated by RT-PCR and sequencing. More than half of these novel miRNAs displayed stage-specific expression patterns in the vascular cambium. Furthermore, analyzing the 103 miRNAs and their predicted targets indicated that 30% of miRNAs appeared to negatively regulate their targets, of which 4 target genes involved in the regulation of cambial cell division were validated via RNA ligase-mediated rapid amplification of 5’ cDNA ends (RLM 5’-RACE). Interestingly, miRNA156 and miRNA172 may regulate the phase transition in vascular cambium from dormancy to active growth. These results provide new insights into the important regulatory functions of miRNAs in vascular cambium development and wood formation in conifers.
2015-04-07 | GSE53933 | GEO
Project description: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. 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. 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.
2012-06-28 | GSE24226 | GEO
Project description:Chinese fir (Cunninghamia lanceolata) is one of southern China's most important native tree species, which has experienced noticeable climate-induced changes. Published papers (1978-2020) on tree growth of Chinese fir forests in China were collected and critically reviewed. After that, a comprehensive growth data set was developed from 482 sites, which are distributed between 102.19° and 130.07°E in longitude, between 21.87° and 37.24°N in latitude and between 5 and 2260 m in altitude. The dataset consists of 2265 entries, including mean DBH (cm), mean H (m), volume (m3), biomass (dry weight) (kg) (stem (over bark) biomass, branches biomass, leaves biomass, bark biomass, aboveground biomass, roots biomass, total trees biomass) and related information, i.e. geographical location (Country, province, study site, longitude, latitude, altitude, slope, and aspect), climate (mean annual precipitation-MAP and mean annual temperature-MAT), stand description (origin, age, canopy density and stand density), and sample regime (plot size, number and investigation year). Our results showed that (1) the best prediction of height was obtained using nonlinear composite model Height = [Formula: see text], (R2 = 0.8715, p < 0.05), (2) the equation Volume = DBH2/(387.8 + 19,190/Height) (R2 = 0.9833, p < 0.05) was observed to be the most suitable model for volume estimation. Meanwhile, when the measurements of the variables are difficult to carry out, the volume model Volume = 0.03957 - 0.01215*DBH + 0.00118*DBH2 (R2 = 0.9573, p < 0.05) is determined from DBH only has a practical advantage, (3) the regression equations of component biomass against DBH explained more significant than 86% variability in almost all biomass data of woody tissues, which were ranked as total trees (97.25%) > aboveground (96.55%) > stems (with bark) (96.17%) > barks (88.95%) > roots (86.71%), and explained greater than 64% variability in branch biomass. The foliage biomass equation was the poorest among biomass components (R2 = 0.6122). The estimation equations derived in this study are particularly suitable for the Chinese fir forests in China. This dataset can provide a theoretical basis for predicting and assessing the potential of carbon sequestration and afforestation activities of Chinese fir forests on a national scale.
| S-EPMC9616935 | biostudies-literature
Project description:Cunninghamia lanceolata Transcriptome or Gene expression
| PRJNA156945 | ENA