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Identification of differentially expressed microRNAs from a male sterile Ponkan mandarin (Citrus reticulata Blanco) and its fertile wild type by small RNA and degradome sequencing

ABSTRACT: High-throughput small RNA and degradome sequencing were performed to identify a large number of miRNAs and their targets. Differential expression of several miRNAs reveals that miRNA regulatory network was closely linked to gametophyte development and male sterility in Ponkan mandarin. The expression profiles of miR156 and miR167 as well as their targets demonstrated their contribution in male sterility in the Ponkan seedless type. This study provides valuable information for better understanding of miRNAs network in plant anther development and lays a foundation to future research on male sterility in citrus and even other species.

ORGANISM(S): Citrus reticulata

PROVIDER: GSE53389 | GEO | 2014/12/08

SECONDARY ACCESSION(S): PRJNA231900

REPOSITORIES: GEO

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Identification of differentially expressed microRNAs from a male sterile Ponkan mandarin (Citrus reticulata Blanco) and its fertile wild type by small RNA and degradome sequencing

Project description:High-throughput small RNA and degradome sequencing were performed to identify a large number of miRNAs and their targets. Differential expression of several miRNAs reveals that miRNA regulatory network was closely linked to gametophyte development and male sterility in Ponkan mandarin. The expression profiles of miR156 and miR167 as well as their targets demonstrated their contribution in male sterility in the Ponkan seedless type. This study provides valuable information for better understanding of miRNAs network in plant anther development and lays a foundation to future research on male sterility in citrus and even other species. small RNA and degradome sequencing of seedy M-bM-^@M-^XEgan No.1M-bM-^@M-^Y and its male sterile and seedless mutant M-bM-^@M-^XQianyang seedlessM-bM-^@M-^Y

2014-12-08 | E-GEOD-53389 | biostudies-arrayexpress

Comparative transcript profiling of gene expression between seedless Ponkan mandarin (Citrus reticulata Blanco) and its seedy wild type during floral organ development

Project description:Seedlessness is an important agronomic trait for citrus, and male sterility (MS) is one main cause of seedless citrus fruit. However, the molecular mechanism of citrus seedlessness remained not well explored. An integrative strategy combining SSH (suppression subtractive hybridization) library with cDNA microarray was employed to study the underlying mechanism of seedlessness of a Ponkan mandarin seedless mutant (Citrus reticulate Blanco). Screening with custom microarray, a total of 279 differentially expressed clones were identified, and 133 unigenes (43 contigs and 90 singletons) were obtained after sequencing. Gene Ontology (GO) distribution showed that the majority of differential genes involved in metabolic process, responded to stimulus and functioned as DNA/RNA binding, catalytic activity and oxidoreductase activity. Expression dynamics of some candidate clones revealed a gene encoding male sterility protein 2 was highly up-regulated, while several transcription factors (TFs) such as AP2/EREBP, MYB, WRKY, NAC and C2C2-GATA zinc-finger domain TFs were specifically down-regulated in the seedless mutant compared with the wild type. Our research highlighted some candidate pathways that participated in the citrus male gametophyte development and could be beneficial for seedless citrus breeding in the future.

2012-05-22 | GSE38094 | GEO

Comparative transcript profiling of gene expression between seedless Ponkan mandarin (Citrus reticulata Blanco) and its seedy wild type during floral organ development

2012-05-21 | E-GEOD-38094 | biostudies-arrayexpress

Citrus reticulata strain:Ponkan mandarin

Project description:Citrus reticulata strain:Ponkan mandarin Genome sequencing

| PRJNA225963 | ENA

Citrus reticulata strain:Ponkan mandarin

Project description:Citrus reticulata strain:Ponkan mandarin Transcriptome or Gene expression

| PRJNA157945 | ENA

Citrus hybrid cultivar cultivar:Ponkan mandarin

Project description:Ponkan mandarin methylation

| PRJNA545866 | ENA

Transcriptome profiling for seed abortion in Ponkan (Citrus reticulata)

Project description:Seed developmental arrest is one of the early phenotypes of seed abortion. However, the molecular mechanism underlying seed developmental arrest of citrus is still unclear. In this study, laser capture microdissection (LCM) was used to accurately divide the seeds of seedless Ponkan ‘Huagan No.4’ (Citrus reticulata) (HG) and seeded Ponkan ‘Egan No.1’ (Citrus reticulata) (EG) into nucellus and integument/seed coat 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 EG, 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 seed abortion.

2023-05-08 | GSE197716 | GEO

Citrus reticulata strain:Egan No.1 | cultivar:Ponkan mandarin

Project description:Citrus reticulata strain:Egan No.1 | cultivar:Ponkan mandarin Transcriptome or Gene expression

| PRJNA261374 | ENA

Citrus hybrid cultivar cultivar:Ponkan mandarin

Project description:Citrus hybrid cultivar cultivar:Ponkan mandarin Raw sequence reads

| PRJNA545864 | ENA

Expression data from postharvest Ponkan (Citrus reticulata Blanco) fruit under cold storage

Project description:Low temperature storage of citrus fruits are susceptible to chilling disorder symptoms that impact fruit quality. Understanding the molecular frame underlying the cold storage process will provide a basic guidance for practical control. We used Affymetrix Citrus GeneChip to examine the transcriptional changes in cold-stored Citrus reticulata Blanco cv. ‘Ponkan’ pulp tissue for three successive months.

2009-12-18 | GSE19543 | GEO

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