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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. 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

ORGANISM(S): Citrus reticulata

SUBMITTER: Yan-ni Fang

PROVIDER: E-GEOD-53389 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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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.

2014-12-08 | GSE53389 | GEO

Genome-wide profiling of miRNAs and their target genes during somatic embryogenesis in cotton by small RNA and degradome sequencing

Project description:MicroRNAs (miRNAs) are endogenous non-coding ~21 nucleotide (nt) RNAs that regulate gene expression at transcriptional and post-transcriptional levels in plants and animals. They play an important role in development, abiotic stress responses or pathogen responses. miRNAs with their related target genes have been widely studied in model plants?and increasing studies have been performed on some crops?however, the number of identified miRNAs in cotton was limited, and global identification of related targets through degradome sequencing has not been developed previously. In this study, we globally identified small RNAs and their related target genes during cotton somatic embryogenesis by the high throughput small RNA and degradome sequencing technology using fresh hypocotyls and EC (embryogenic calli) of Gossypium hirsutum YZ1. A total of 36 differentially expressed conserved miRNA families of which 19 miRNA families represented by 29 precursors and 25 novel miRNAs were identified, with star sequences of 20 known miRNAs and 2 novel miRNAs discovered. 234 genes in EC and 322 genes in CK were identified as targets of 23 and 30 known miRNA families, and 16 genes were found as targets of 8 novel miRNAs. The expression profiles of several miRNAs and their targets were verified by qRT-PCR and 5’RACE were further used to validate the sliced sites of the targets. Interestingly, four TAS3 D6 and D7 were also found in both degradome libaries which can perfectly match their precursors. The profiling of the miRNAs and their target genes provides more information about the regulatory network of miRNAs during somatic embryogenesis in cotton. small RNA and degradome sequencing of CK(fresh hypocotyls) and EC (embryogenic calli) of Gossypium hirsutum YZ1

2013-03-08 | E-GEOD-41132 | 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

Uncovering small RNA-mediated responses to cold stress in a wheat thermosensitive genic male sterile line by deep sequencing (Degradome-Seq)

Project description:The male sterility of thermosensitive genic male sterile (TGMS) lines of wheat (Triticum aestivum) is strictly controlled by temperature. The early phase of anther development is especially susceptible to cold stress. MicroRNAs (miRNA) play an important role in plant development and in responses to environmental stress. In this study, deep sequencing of small RNA (smRNA) libraries obtained from spike tissues of the TGMS line under cold and control conditions identified a total of 81 unique miRNA sequences from 30 families, and trans-acting small interfering RNAs (tasiRNAs) derived from two TAS3 genes. To identify smRNA targets in the wheat TGMS line, we applied the degradome sequencing method, which globally and directly identifies the remnants of smRNA-directed target cleavage. We identified 26 targets of 16 miRNA families and three targets of tasiRNAs. Comparing smRNA sequencing datasets and TaqMan qPCR results, we identified six miRNAs and one tasiRNA (tasiRNA-ARF) as cold stress-responsive smRNAs in spike tissues of the TGMS line. We also determined the expression profiles of target genes that encode transcription factors in response to cold stress. Interestingly, expressions of cold-stress responsive smRNAs integrated in the auxin-signaling pathway and their target genes were largely anticorrelated. We investigated tissue-specific expression of smRNAs using a tissue microarray approach. Our data indicated that miR167 and tasiRNA-ARF play roles in regulating the auxin-signaling pathway, and possibly in the developmental response to cold stress. These data provide evidence that smRNA regulatory pathways are linked with male sterility in the TGMS line during cold stress. Examination of 2 mRNA degradome libraries in spike tissues during cold and control condition

2012-04-11 | E-GEOD-37134 | biostudies-arrayexpress

Project description:male sterility in seedless citrus Raw sequence reads

| PRJNA430529 | ENA

Uncovering small RNA-mediated responses to cold stress in a wheat thermosensitive genic male sterile line by deep sequencing (Degradome-Seq)

2012-04-11 | GSE37134 | GEO

Comparative expression profiling of miRNA during anther development in genetic male sterile and wild type cotton [degradome]

Project description:In this study, in order to identify miRNA targets, a degradome library derived from anthers of the WT and GMS (Genetic Male Sterility) mutant representing three stages of development was constructed and sequenced, resulting in the generation of 24.6 million raw reads. After removal of low quality sequences and adapter sequences, 24.4 million clean reads were obtained and 98% were 20 or 21 nt in length as expected in that normally length distribution peak of degradome fragment is between 20 and 21 nt [Addo-Quaye C, Eshoo TW, Bartel DP, Axtell MJ: Endogenous siRNA and miRNA targets identified by sequencing of the Arabidopsis degradome. Curr Biol 2008, 18:758-762]. Identification of miRNA targets in the WT and GMS muant anthers. Anthers of the WT and GMS mutant representing three stages of development [the meiosis stage (WT: Mar-F-1; mutant: Mar-S-1) and tetrad stage (WT: Mar-F-2; mutant: Mar-S-2), together with the uninucleate microspore stage (WT: Mar-F-3; mutant: Mar-S-3) from the GMS M-bM-^@M-^XDong AM-bM-^@M-^Y mutant and its fertile wild type] were collected during early mornings.

2013-07-28 | E-GEOD-43389 | biostudies-arrayexpress

Identification of chilling stress-responsive tomato microRNAs and their target genes by high-throughput sequencing and degradome analysis

Project description:To identify tomato miRNAs involved in chilling response, two small RNA libraries and two degradome libraries from chilling-treated(4M-BM-0C/4M-BM-0C for 1hM-oM-<M-^L4h, 8h, 12h, 24h and 48h) and non-chilling-treated (25M-BM-0C/20M-BM-0C for 1hM-oM-<M-^L4h, 8h, 12h, 24h and 48h)leaves of LA1777M-bM-^@M-^Y (S. habrochaites) seedlings were constructed. A total of 4342604 and 7231609 clean reads were obtained by high-throughput sequencing of the two libraries, respectively. 161 conserved miRNAs and 236 novel miRNAs were identified in the two librayies. Of these miRNAs, 192 were upregulated, whereas 205 were downregulated in response to chilling stress. Among these, 23 miRNAs and 26 miRNAs were significantly upregulated and downregulated in response to chilling stress, respectively.Through degradome sequencing,62 target genes were cleaved by 42 conserved miRNAs, while nine target genes were cleaved by nine novel miRNAs. Target gene functional analysis revealed that most target genes played positive role in the chilling response, primarily by regulating the expression of anti-stress proteins, antioxidant enzymes and genes involved in cell wall formation. tomato miRNA-seq and Degradome-seq after chilling

2015-03-03 | E-GEOD-57335 | biostudies-arrayexpress

Uncovering small RNA-mediated responses to cold stress in a wheat thermosensitive genic male sterile line by deep sequencing

Project description:The male sterility of thermosensitive genic male sterile (TGMS) lines of wheat (Triticum aestivum) is strictly controlled by temperature. The early phase of anther development is especially susceptible to cold stress. MicroRNAs (miRNA) play an important role in plant development and in responses to environmental stress. In this study, deep sequencing of small RNA (smRNA) libraries obtained from spike tissues of the TGMS line under cold and control conditions identified a total of 81 unique miRNA sequences from 30 families, and trans-acting small interfering RNAs (tasiRNAs) derived from two TAS3 genes. We identified 26 targets of 16 miRNA families and three targets of tasiRNAs. Comparing smRNA sequencing datasets and TaqMan qPCR results, we identified six miRNAs and one tasiRNA (tasiRNA-ARF) as cold stress-responsive smRNAs in spike tissues of the TGMS line. We also determined the expression profiles of target genes that encode transcription factors in response to cold stress. Interestingly, expressions of cold-stress responsive smRNAs integrated in the auxin-signaling pathway and their target genes were largely anticorrelated. We investigated tissue-specific expression of smRNAs using a tissue microarray approach. Our data indicated that miR167 and tasiRNA-ARF play roles in regulating the auxin-signaling pathway, and possibly in the developmental response to cold stress. These data provide evidence that smRNA regulatory pathways are linked with male sterility in the TGMS line during cold stress. Examination of 7 small RNA libraries in spike tissues during cold and control condition

2012-03-29 | E-GEOD-36867 | biostudies-arrayexpress

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