Exploring miRNAs involved in citrus nucellar embryo initiation by high-throughput small RNA sequencing
Ontology highlight
ABSTRACT:
OTHER RELATED OMICS DATASETS IN: PRJNA300206PRJNA299149
ORGANISM(S): Citrus reticulata Citrus x clementina Citrus x paradisi Citrus maxima
PROVIDER: GSE74132 | GEO | 2016/09/16
SECONDARY ACCESSION(S): PRJNA299149
REPOSITORIES: GEO
Similar Datasets
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: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: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:Exploring miRNAs involved in citrus nucellar embryo initiation by high-throughput small RNA sequencing
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Project description:Citrus australasica cultivar:cultivars Genome sequencing
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Project description:To identify genes associated with citrus peel development and manifestation of peel disorders, we analyzed flavedo, albedo and juice sac tissues from five types of citrus fruit including, mandarin orange, navel orange, valencia orange, grapefruit and lemon. Fruits of five different citrus cultivars. Mature, healthy fruits of five different citrus cultivars (M-bM-^@M-^\ValenciaM-bM-^@M-^] and M-bM-^@M-^\NavelM-bM-^@M-^] orange [Citrus sinensis], mandarin [Citrus reticulata], lemon [Citrus M-CM-^W limon], grapefruit [Citrus M-CM-^W paradisi]) were purchased from a food market located in Davis, CA, USA. For all five types of fruit, three tissues (flavedo, albedo, and juice sacs) were compared separately. Each of the three tissues from each of the five types of fruit were sampled in three biological replicates, for a total of 45 samples. Samples were prepared from a 1 cm-thick equatorial disc and four sections (N, S, E, and W) were cut. Each section of flavedo, albedo, and juice sac tissue was dissected. gene expression variation underlying quality trait, different genotypes
2014-01-01 | E-GEOD-50384 | biostudies-arrayexpress
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:Ovule developmental arrest is one of the early phenotypes of seed abortion. However, the molecular mechanism underlying ovule developmental arrest of citrus is still unclear. In this study, laser capture microdissection (LCM) was used to accurately divide the ovules of seedless Ponkan ‘Huagan NO.4’ (Citrus reticulata) (MT) and seeded Ponkan ‘Egan NO.1’ (Citrus reticulata) (WT) into nucellus and integument tissues. The captured tissues were used for subsequent RNA-seq. Moreover, single-molecule real-time (SMRT) sequencing was used to generate full-length transcripts of WT, which were used as reference transcripts for RNA-seq. These data can be utilized to analyse the causes of citrus seedlessness formation and the molecular regulatory network in the process of ovule abortion.
2024-09-01 | GSE183639 | 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:Citrus species are among the most important fruit crops. However, gene regulation and signaling pathways related to etiolation in this crop remain unknown. Using Illumina sequencing technology, modification of global gene expression in two hybrid citrus cultivars—Huangguogan and Shiranuhi, respectively—were investigated. More than 834.16 million clean reads and 125.12 Gb of RNA-seq data were obtained, more than 91.37% reads had a quality score of Q30 (sequencing error rate, 0.1%). 124,952 unigenes were finally generated with a mean length of 1,189 bp. Of these unigenes, 98,904 (79.15%), 105,408 (84.35%), 42,016 (33.62%), 78,872 (63.12%), 72,068 (57.67%), 72,464 (57.99%), 72464 (57.99%) and 46,308 (37.06%) had been annotated in NR, NT, KO, SwissProt, PFAM, GO and KOG databases, respectively. Further, we identified 604 differentially expressed genes (DEGs) in multicoloured and etiolated seedlings of Shiranuhi, including 180 up-regulated genes and 424 down-regulated genes. While in Huangguogan, we found 1,035 DEGs, 271 of which were increasing and the others were decreasing. 7 DEGs were commonly up-regulated, and 59 DEGs down-regulated in multicoloured and etiolated seedlings of these two cultivars, suggesting that some genes play fundamental roles in two hybrid citrus seedlings during etiolation. Functional classification of the DEGs in two cultivars using GO term indicated that biological process, cellular component and molecular function were three major groups. Our study is the first to provide the transcriptome sequence resource for seedlings etiolation of Shiranuhi and Huangguogan, and advance our knowledge of the genes involved in the complex regulatory networks of seedling etiolation.
2017-06-13 | GSE90935 | GEO