Exploring miRNAs involved in citrus nucellar embryo initiation by high-throughput small RNA sequencing
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ABSTRACT:
PROVIDER: PRJNA299149 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR2722830.fastq.gz | Fastqsanger.gz | |||
| SRR2722840.fastq.gz | Fastqsanger.gz | |||
| SRR2722831.fastq.gz | Fastqsanger.gz | |||
| SRR2722841.fastq.gz | Fastqsanger.gz | |||
| SRR2722832.fastq.gz | Fastqsanger.gz |
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Project description:To identify miRNAs related nucellar embryo intiation (NEI) in citrus, we performed small RNA sequencing in ovules of two pairs of poly- and mono-embryonic cultivars right prior to and at NEI stages. Nearly 150 miRNAs including ~90 conserved and ~60 novel miRNAs were identified in ovules of each cultivar pair.
2016-09-16 | GSE74132 | GEO
Project description:Nucellar embryony is a form of apomixis found in citrus where somatic nucellar cells differentiate into embryos and are included in the seed resulting from the normal sexual process. The nucellar cells giving rise to adventive embryo start proliferating prior to anthesis and fully differentiate obtaining nourishment from sexually derived endosperm. To identify transcripts differentially expressed during nucellar embryo initiation we have taken RNA samplesfrom different developing stages of ovules from polyembryonic (cv. Vaniglia Sanguigno) and monoembryonic (cv. Temple) cultivars. We used microarray for a detailed analysis of global gene expression during nucellar embryony initiation and development. We have further validated the differentially expressed genes using qRT-PCR.
2012-03-01 | GSE36188 | GEO
Project description:Nucellar embryony is a form of apomixis found in citrus where somatic nucellar cells differentiate into embryos and are included in the seed resulting from the normal sexual process. The nucellar cells giving rise to adventive embryo start proliferating prior to anthesis and fully differentiate obtaining nourishment from sexually derived endosperm. To identify transcripts differentially expressed during nucellar embryo initiation we have taken RNA samplesfrom different developing stages of ovules from polyembryonic (cv. Vaniglia Sanguigno) and monoembryonic (cv. Temple) cultivars. We used microarray for a detailed analysis of global gene expression during nucellar embryony initiation and development. We have further validated the differentially expressed genes using qRT-PCR. Citrus ovules were harvested from the excised ovaries of different flower developmental stages. These developing stages were decided on the basis of morphological and histological characteristics of flower and female gametophyte, respectively. We selected, Pre anthesis, post anthesis, and initial fruit set stage of flower to excise ovules from Polyembryonic cultivar Vaniglia Sanguigno and Monoembryonic cultivar Temple. Leaf tissue of Vaniglia Sanguigno was used to check the overall transcriptome level differences between leaf and ovule tissues. For each sample, three technical replicates were used.
2012-03-01 | E-GEOD-36188 | biostudies-arrayexpress
Project description:DNA methylomes in laser microdissection (LMD) captured apomictic cells to delineate nucellar embryogenesis initiation of citrus
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Project description:Fruit ripening in Citrus is not well understood at the molecular level. Knowledge of the regulatory mechanism of citrus fruit ripening at the post-transcriptional level in particular is lacking. Here, we comparatively analyzed the miRNAs and their targeted genes in a spontaneous late-ripening mutant, ?Fengwan? sweet orange (MT) (Citrus sinensis L. Osbeck), and its wild-type counterpart ('Fengjie 72-1', WT). Using high-throughput sequencing of small RNAs and RNA degradome tags, we identified 107 known and 21 novel miRNAs, as well as 225 target genes. A total of 24 miRNAs (16 known miRNAs and 8 novel miRNAs) were shown to be differentially expressed between MT and WT. The expression pattern of several key miRNAs and their target genes during citrus fruit development and ripening stages was examined. Csi-miR156k, csi-miR159 and csi-miR166d suppressed specific transcription factors (GAMYBs, SPLs and ATHBs) that are supposed to be important regulators involved in citrus fruit development and ripening. In the present study, miRNA-mediated silencing of target genes was found under complicated and sensitive regulation in citrus fruit. The identification of miRNAs and their target genes provide new clues for future investigation of mechanisms that regulate citrus fruit ripening.
2017-02-10 | GSE84191 | GEO
Project description:Somatic embryogenesis in nucellar tissues is widely recognized to induce polyembryony in major citrus varieties such as sweet oranges, satsuma mandarins and lemons. This capability for apomixis is attractive in agricultural production systems using hybrid seeds, and many studies have been performed to elucidate the molecular mechanisms of various types of apomixis. To identify the gene responsible for somatic embryogenesis in citrus, a custom oligo-DNA microarray including predicted genes in the citrus polyembryonic locus was used to compare the expression profiles in reproductive tissues between monoembryonic and polyembryonic varieties. The full length of CitRKD1, which was identified as a candidate gene responsible for citrus somatic embryogenesis, was isolated from satsuma mandarin and its molecular function was investigated using transgenic ‘Hamlin’ sweet orange by antisense-overexpression. The candidate gene CitRKD1, predominantly transcribed in reproductive tissues of polyembryonic varieties, is a member of the plant RWP-RK domain proteins. CitRKD1 of satsuma mandarin comprised two alleles (CitRKD1-mg1 and CitRKD1-mg2) at the polyembryonic locus controlling embryony type (mono/polyembryony) that were structurally divided into two types with or without a miniature inverted-repeat transposable element (MITE)-like insertion in the upstream region. CitRKD1-mg2 with the MITE insertion was the predominant transcript in flowers and young fruits where somatic embryogenesis of nucellar cells occurred. Loss of CitRKD1 function by antisense-overexpression abolished somatic embryogenesis in transgenic sweet orange and the transgenic T1 plants were confirmed to derive from zygotic embryos produced by self-pollination by DNA diagnosis. Genotyping PCR analysis of 95 citrus traditional and breeding varieties revealed that the CitRKD1 allele with the MITE insertion (polyembryonic allele) was dominant and major citrus varieties with the polyembryonic allele produced polyembryonic seeds.
2018-05-31 | GSE115082 | GEO
Project description:Comparative analysis of citrus polyembryonic and monoembryonic ovule transcriptomes identifies candidate transcripts related to nucellar embryony initiation
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Project description:Next-generation sequencing was employed to compare transcriptomic profiling of ovules at and prior to the appearance of nucellar embryony initial cells. To exclude the unwanted genetic background noise and variations among years, two biological replicates for each sample were set by sampling in two consecutive years from two pairs of polyembryonic and monoembryonic cultivars, i.e. one pair of mandarin and the other of grapefruit/pummelo. In that manner, 71 embryo-type enriched transcripts were determined by overlaying differentially expressed transcripts, derived from pairwise comparisons between polyembryonic and monoembryonic cultivars in each basic taxa, which revealed commonly genes that indeed regulated nucellar embryogenesis. Transcriptome profiling indicated that cell wall remodelling transcripts, such as pectinesterase, endochitinase, glucan endo-1,3-β-glucosidase precursor, UDP-glucosyltransferase and laccase were significantly enriched in the polyembryonic cultivars. The expression of transcription factors containing AP2/ERF and WRKY domains were also up-regulated in polyembryonic cultivars compared with monoembryonic cultivars. In addition, the embryo-type enriched transcripts were associated with hormone regulation and signal transduction, as well as carbohydrate metabolism.
2016-12-01 | GSE74384 | GEO
Project description:An antifungal aroma substance, 2-phenylethanol (PEA), was isolated from antagonistic yeast strain Kloeckera apiculata extract. Microarry were used to analyse its role citrus. We used microarrays to detail the global programme of gene expression underlying Citrus were treated with 1.0x108 cells/ml K. apiculata (KA), PEA (0.15%), the extract (1000xdilute) and control (CK) for 24 h,
2014-01-01 | GSE45680 | GEO
Project description:An antifungal aroma substance, 2-phenylethanol (PEA), was isolated from antagonistic yeast strain Kloeckera apiculata extract. Microarry were used to analyse its role citrus. We used microarrays to detail the global programme of gene expression underlying Citrus were treated with 1.0x108 cells/ml K. apiculata (KA), PEA (0.15%), the extract (1000xdilute) and control (CK) for 24 h, An antifungal aroma substance, 2-phenylethanol, was isolated from antagonistic yeast strain Kloeckera apiculata. To analyse its role in Citrus response,Citrus were treated with K. apiculata , 2-phenylethano (0.15%), the extract (1000xdilute) and control (CK) for 24 h, respectively. The fresh epicarp of citrus was separated by knife and directly frozen in liquid nitrogen for RNA extraction and hybridization on Affymetrix microarrays.
2014-01-01 | E-GEOD-45680 | biostudies-arrayexpress