Ontology highlight
ABSTRACT:
PROVIDER: PRJNA861377 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR20504701_1.fastq.gz | Fastqsanger.gz | |||
| SRR20504701_2.fastq.gz | Fastqsanger.gz | |||
| SRR20504702_1.fastq.gz | Fastqsanger.gz | |||
| SRR20504702_2.fastq.gz | Fastqsanger.gz | |||
| SRR20504703_1.fastq.gz | Fastqsanger.gz |
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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. The aim of this study is to investigate the small RNA transcriptome in Cunninghamia lanceolata. Total RNAs of seeds and calli were extracted using RNAiso-mate for plant tissue and RNAiso plus (Takara, Dalian, Liaoning, China), whereas total RNAs of seedlings, adult leaves and stems were isolated with the Concert Plant RNA Reagent (Invitrogen, Carlsbad, CA, USA), and were then treated with RNase-free DNase I (Promega, Madison, WI, USA). Equal amount of total RNAs from the 5 different samples were mixed to form a single RNA pool. Twenty micrograms of total RNAs from the pool 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 1G Genome Analyzer at the Beijing Genomics Institute, Shenzhen, China.
2012-06-27 | E-GEOD-24226 | biostudies-arrayexpress
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 an excellent fast-growing timber species occurring in southern China and has significant value in the forestry industry. In order to enhance the phosphorus utilization efficiency in Chinese fir, four clones named X6, S3, S39 and FK were used, and low phosphorus (LP) stress experiments were performed to analyze the response of different clones to phosphorus deficiency. According to the results on seedling height, maximum root length, leaf blade aspect ratio, root ratio, malondialdehyde content, acid phosphates activity, proline content, soluble protein level, and chlorophyll a and b levels of the tested clones, compared to the control groups (CK), the phosphorus high efficiency clone X6 was screen out for transcriptome sequencing experiments. De novo RNA-seq was then used to sequence the root transcriptomes of X6 under LP stress and CK, and we then compared the gene expression differences under the two conditions. A total of 3416 SDEGs were obtained by comparing the LP and CK groups, among which 1742 were up-regulated and 1682 were down-regulated. All SDEGs obtained from the LP and CK treated samples were subjected to KEGG annotation and classification. Through classification statistical analysis using WEGO software, 607 SDEGs obtained KEGG pathway annotations, which were related to 206 metabolic pathways. In Chinese fir subjected to LP stress, 53 SDEGs related with phosphorus metabolism, and phosphate uptake and transport were obtained from our transcriptome data. Based on the phosphorus metabolism pathway obtained by KEGG classification, combined with previously report on gene annotation related with phosphorus metabolism, the enzymes encoded by SDEG related with phosphorus metabolism and their expression pattern were mapped onto phosphorus metabolism pathway.
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Project description:Chinese fir (Cunninghamia lanceolate)
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Project description:Microbial communities in the rhizosphere make significant contributions to crop health and nutrient cycling. However, their ability to perform important biogeochemical processes remains uncharacterized. Important functional genes, which characterize the rhizosphere microbial community, were identified to understand metabolic capabilities in the maize rhizosphere using GeoChip 3.0-based functional gene array method. Triplicate samples were taken for both rhizosphere and bulk soil, in which each individual sample was a pool of four plants or soil cores. To determine the abundance of functional genes in the rhizosphere and bulk soils, GeoChip 3.0 was used.
2014-12-10 | E-MTAB-2920 | biostudies-arrayexpress