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Citrus trifoliata

ABSTRACT: Identifying the genome-wide genetic variation between precocious trifoliate orange and its wild type and developing new markers for genetics research

PROVIDER: PRJNA314020 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR3199131_1.fastq.gz	Fastqsanger.gz
	SRR3199131_2.fastq.gz	Fastqsanger.gz
	SRR3199132_1.fastq.gz	Fastqsanger.gz
	SRR3199132_2.fastq.gz	Fastqsanger.gz

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Project description:Identifying the genome-wide genetic variation between precocious trifoliate orange and its wild type and developing new markers for genetics research

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Project description:To investigate the role of lncRNAs in citrus flowering, paired-end strand-specific RNA sequencing was performed between precocious trifoliate orange and its wild-type. Total 6,584 potential lncRNAs were identified, 51.6% of which came from intergenic regions. It was also observed that 555 lncRNAs were significantly up-regulated, and 276 lncRNAs were down-regulated in precocious trifoliate orange, indicating that lncRNAs could be involved in the regulation of citrus flowering.

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Project description:miRNA expression data of shoot meristems of trifoliate orange

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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.

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Project description:Deep sequencing-based characterization of transcriptome and transcriptional profiling of trifoliate orange (Poncirus trifoliata (L.) Raf.) in response to cold stress

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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

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.

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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).

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