Project description:To characterize the site-specific methylation landscape of the Mandarin fish ranavirus (MRV) genome, whole-genome bisulfite sequencing (WGBS) was conducted on an isolated MRV strain.

2024-04-02 | GSE262554 | GEO

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

Genome-wide genetic variation identification and fruit-associated trait comparisons between kumquat (Fortunella japonica) and Clementine mandarin

Project description:We performed whole genome re-sequencing to reveal the comprehensive genetic variation of the fruit development between kumquat (Fortunella japonica) and Clementine mandarin. Total 5,865,235 single-nucleotide polymorphisms (SNPs) and 414,447 insertion/deletion (InDels) were identified in the two citrus species. Meanwhile, a total of 640,801 SNPs and 20,733 InDels were identified based on integrative analysis of genome and transcriptome of fruit. The variation feature, genomic distribution, functional effect and other characteristics of these genetic variation were explored. Total 1,090 differentially expressed genes (DEGs) were found during fruit development process of kumquat and Clementine mandarin by RNA-sequencing. Gene Ontology revealed that these genes were involved in various molecular functional and biological processes. Meanwhile, the genetic variation of 939 DEGs and 74 multiple fruit development pathway genes from previous reported were also identified. In addition, a global survey of genes splicing events identified 24,237 specific alternative splicing (AS) events in the two citrus species and showed that intron retention is the most prevalent pattern of alternative splicing.

2018-02-01 | GSE107812 | GEO

Comparison of transcriptomes in five varieties of citrus fruit

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.

2014-01-01 | GSE50384 | GEO

RNA-sequencing for peel roughing disorder of Satsuma mandarin fruit.

Project description:Roughing disorder (RD) is a significant quality barrier in citrus fruit, occurring more easily on easy-peeling mandarins. As RD is not yet well understood, this study aimed to examine the changes and synergic molecular processes involved. Peel with RD was induced by severely defruiting Satsuma mandarin trees. Morphology observations, RNA-sequencing and untargeted and targeted metabolic analyses were conducted.

2017-12-06 | GSE100512 | GEO

Citrus hybrid cultivar cultivar:Ponkan mandarin

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

| PRJNA545864 | ENA

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.

2014-12-08 | GSE53389 | GEO

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