Citrus trifoliata
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA279929 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR1947310.fastq.gz | Fastqsanger.gz | |||
| SRR1947311.fastq.gz | Fastqsanger.gz | |||
| SRR1947307_1.fastq.gz | Fastqsanger.gz | |||
| SRR1947307_2.fastq.gz | Fastqsanger.gz | |||
| SRR1947308.fastq.gz | Fastqsanger.gz |
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Project description:Salt stress, especially saline-alkali stress, has seriously negative effect on citrus production. Ziyang xiangcheng (Citrus junos Sieb.) (Cj) has been reported as a saline-alkali stress and iron deficiency tolerant citrus rootstock. However, the molecular mechanism of its saline-alkali stress tolerance is still not clear. Two citrus rootstocks and one navel orange scion, Cj, Poncirus trifoliate (Poncirus trifoliata (L.) Raf.) (Pt) and ‘Lane Late’ navel orange (Citrus sinensis (L.) Osb.) (LL), were used in this study. The grafted materials Cj+LL and Pt+LL grown in calcareous soil were used to identify genes and pathways responsive to saline-alkali stress using RNA-seq. The seedlings of Cj and Pt grown in the solutions with different gradient pH value were used to perform a supplement experiment. Comprehensively analyzing the data of RNA-seq, physiology and biochemistry, agronomic traits and mineral elements of Cj+LL, Pt+LL, Cj and Pt, several candidate pathways and genes were identified to be highly regulated under saline-alkali stress. Here, we propose citrate is important for the tolerance to iron deficiency and the jasmonate (JA) biosynthesis and signal transduction pathway may play a crucial role in tolerance to saline-alkali stress in citrus by interacting with other plant hormones, calcium signaling, ROS scavenging system and lignin biosynthesis.
2018-07-06 | GSE98996 | GEO
Project description:Transcription profiling of citrus rootstock Poncirus trifoliata (L.) Raf. Keywords: Abiotic stress (Iron chlorosis) Total RNA from four replicates for each sample category (Poncirus trifoliata (L.) Raf watered for 60 days with 18 uM Fe-EDDHA or without Fe-EDDHA) were generated and compared.
2010-05-19 | E-GEOD-17255 | biostudies-arrayexpress
Project description:In 1976, a spontaneous mutant derived from Poncirus trifoliata (L.) Raf with short juvenile phase, namely, precocious trifoliate orange, was found in Yichang, Hubei province, China. Compared with 6 to 8 years of the wild-type trifoliate orange, almost all of the seedlings germinated from precocious trifoliate orange only have 1 to 2 years’ juvenile period, and 20% seedlings even flowered in the year after germination. Therefore, precocious trifoliate orange is an ideal material for studying the role of miRNAs involved in citrus juvenile and adult developmental stages. To characterize these miRNAs expressed at the juvenile and adult development stages of citrus, Affymetrix miRNA arrays were used to generate miRNA profiles of shoot meristems of trifoliate orange, the results revealed that some miRNAs were down-regulated expressed at adult stage compared with juvenile stage. Detailed comparison of the expression patterns of miRNAs and corresponding target genes revealed the negative correlation between them, while few of them are positively correlated.
2016-03-04 | GSE28363 | GEO
Project description:Transcription profiling of citrus rootstock Poncirus trifoliata (L.) Raf. Keywords: Abiotic stress (Iron chlorosis)
2009-12-01 | GSE17255 | GEO
Project description:Solexa sequencing was performed at different developmental stages both an early flowering mutant of trifoliate orange (precocious trifoliate orange, Poncirus trifoliata L. Raf.) and its wild-type in this study, resulting in the obtainment of a total of 143 known miRNAs belonging to 99 families and 75 novel miRNAs in four libraries. A total of 317 potential target genes were predicted based on the 50 novel miRNAs families, GO and KEGG annotation revealed that high ranked miRNA-target genes are those implicated in diverse cellular processes in plants, including development, transcription, protein degradation and cross adaptation. To characterize those miRNAs expressed at the juvenile and adult development stages of the mutant and its wild-type, further analysis on the expression profiles of several miRNAs through real-time PCR was performed. The results revealed that most miRNAs were down-regulated at adult stage compared with juvenile stage both the mutant and its wild-type. These results indicate that both conserved and novel miRNAs may play important roles in citrus growth and development, stress responses and other physiological processes.
2016-01-25 | GSE37115 | GEO
Project description:Deep sequencing discovery of novel and conserved microRNAs in trifoliate orange (Citrus trifoliata)
| PRJNA128941 | ENA
Project description:Identification and comparative profiling of microRNAs in an early flowering mutant of trifoliate orange (Poncirus trifoliata (L.) Raf.) and its wild type by genome-wide high throughput sequencing
| PRJNA158273 | ENA
Project description:MicroRNAs (miRNAs) play a critical role in post-transcriptional gene regulation. miRNAs have been shown to control many genes involved in various biological and metabolic processes. Deep sequencing technologies have facilitated identification of species-specific or lowly expressed as well as conserved or highly expressed miRNAs in plants. In this research, we used Solexa sequencing to discover new microRNAs in trifoliate orange (Citrus trifoliata) an important rootstock of citrus. A total of 13,106,753 reads representing 4,876,395 distinct sequences were obtained from a short RNA library generated from small RNA extracted from C. trifoliata flower and fruit tissues, Based on sequence similarity and hairpin structure prediction, we found that 178,102 reads representing 89 sequences from 42 highly conserved miRNA families, have perfect matches to known miRNAs. We also identified 10 novel miRNA candidates, whose precursors were all potentially generated from citrus ESTs. And of them five miRNA* sequences were also sequenced. These sequences had not been described in other plant species and accumulation of these 10 novel miRNAs were confirmed by qRT-PCR analysis. Potential target genes were predicted for most conserved and novel miRNAs. Moreover, four target genes included one encoding IRX12 copper ion binding/ oxidoreductase and three genes encoding NB-LRR disease resistance protein have been experimentally verified by detection of the miRNA-mediated mRNA cleavage in C. trifoliata.
2010-08-18 | GSE22089 | GEO
Project description:MicroRNAs (miRNAs) play a critical role in post-transcriptional gene regulation. miRNAs have been shown to control many genes involved in various biological and metabolic processes. Deep sequencing technologies have facilitated identification of species-specific or lowly expressed as well as conserved or highly expressed miRNAs in plants. In this research, we used Solexa sequencing to discover new microRNAs in trifoliate orange (Citrus trifoliata) an important rootstock of citrus. A total of 13,106,753 reads representing 4,876,395 distinct sequences were obtained from a short RNA library generated from small RNA extracted from C. trifoliata flower and fruit tissues, Based on sequence similarity and hairpin structure prediction, we found that 178,102 reads representing 89 sequences from 42 highly conserved miRNA families, have perfect matches to known miRNAs. We also identified 10 novel miRNA candidates, whose precursors were all potentially generated from citrus ESTs. And of them five miRNA* sequences were also sequenced. These sequences had not been described in other plant species and accumulation of these 10 novel miRNAs were confirmed by qRT-PCR analysis. Potential target genes were predicted for most conserved and novel miRNAs. Moreover, four target genes included one encoding IRX12 copper ion binding/ oxidoreductase and three genes encoding NB-LRR disease resistance protein have been experimentally verified by detection of the miRNA-mediated mRNA cleavage in C. trifoliata. Size fractionated small RNAs (16-30 bp) from total RNA extracts was ligated to 5' and 3' adapters, and reverse transcribed. After PCR amplification the sample was subjected to Solexa sequencing. The resultant 35nt sequence data were filtered according to base quality value. The remained sequences were used to trim 5' and 3' adaptors. The clean tags were used for further analysis.
2010-08-17 | E-GEOD-22089 | biostudies-arrayexpress
Project description:A microarray containing 62,876 unigenes selected from CitEST database and prepared by Nimblegen Systems was used for identifying candidate resistance genes against P. parasitica at 48 hours after inoculation Four resistant and four susceptible F1 hybrids were selected from the population derived from the cross between Citrus sunki Hort. ex. Tan. and Poncirus trifoliate (L.) Raf cv. Rubidoux, respectively susceptible and resistant to P. parasitica. It was proposed that differentially expressed genes between resistant and susceptible hybrids and their parents provide essential candidates for identifying transcripts involved in disease resistance A total of 62,876 unigenes (18,712 unigenes of Citrus sinensis; 31,583 unigenes of Citrus reticulata and 12,581 unigenes of Poncirus trifoliate) selected from CitEST database assembled from the EST submitted to NCBI (Genebank accession number EY649559 to EY842485) were used to construct genome-wide oligonucleotide cDNA microarrays by Roche NimbleGen Systems using a multi-step approach to select probes with optimal predicted hybridization characteristics. Three probes were selected per unigene, comprising a probe set, and each probe set is represented on the final array by two replicates. All probes were designed as ‘‘perfect match’’ (PM) oligonucleotides (oligos).
2010-02-19 | E-GEOD-20412 | biostudies-arrayexpress