Ontology highlight
ABSTRACT:
PROVIDER: PRJNA578261 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR10317100.fastq.gz | Fastqsanger.gz | |||
| SRR10317101.fastq.gz | Fastqsanger.gz | |||
| SRR10317102.fastq.gz | Fastqsanger.gz | |||
| SRR10317103.fastq.gz | Fastqsanger.gz | |||
| SRR10317104.fastq.gz | Fastqsanger.gz |
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Project description:Wheat, an important human food crop, is very sensitive to temperature changes. Thermosensitive sterile lines (TMS) is a natural material for exploring the effects of anther development and temperature changes on male fertility. In order to study the possible molecular mechanism of regulating protein activity during anther fertility alteration, proteomics analysis based on high resolution mass spectrometry were used to study the binuclear anther of wheat YS3038.
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Project description:Anther development is a complex process, and the study of its molecular mechanism has an important impact on plant breeding. This study aims to identify microRNA (miRNA), mRNA, long non-coding RNA (lncRNA), and circular RNA (circRNA) related to anther development of Chinese cabbage, so as to construct competitive endogenous RNA (ceRNA) regulatory networks and provide valuable knowledge for the exploration of pollen development mechanism of Chinese cabbage. A total of 9055 mRNA, 585 miRNA, 1344 lncRNA, and 165 circRNA were identified as differentially expressed in the anther of Chinese cabbage compared with Mix (roots, stems and leaves) by whole-transcriptome sequencing. The anther-related ceRNA-miRNA-target gene regulatory network through miRNA targeting relationships was constructed and 450 pairs of ceRNA relationships, including 97 DEmiRNA-DEmRNA, 281 DEmiRNA-DElncRNA, and 23 DEmiRNA-DEcircRNA interactions were obtained in Chinese cabbage. The genes in the ceRNA network were enriched in the pathways including starch and sucrose metabolism, carbon metabolism, pyruvate metabolism and carbon fixation in photosynthetic organisms, plant hormone signal transduction, and RNA degradation. This study identified some important genes and their interaction lncRNAs, circRNAs, and miRNAs involved in microsporogenesis (BraA06g035480.3C), tapetum and callose layer development (BraA09g009280.3C, BraA04g028920.3C, and BraA10g022680.3C etc), pollen wall formation (BraA06g000980.3C, BraA02g023130.3C, and BraA10g029650.3C etc), and anther dehiscence (BraA10g027200.3C, BraA04g023740.3C, and BraA04g030860.3C etc). Additionally, we analyzed the promoter activity of six anther predominant expression genes, and the results showed that they were all expressed specifically in the anther of Chinese cabbage. This study lay the foundation for further research on the molecular mechanism of anther growth and development.
2022-02-23 | GSE171706 | GEO
Project description:Anther development is a complex process, and the study of its molecular mechanism has an important impact on plant breeding. This study aims to identify microRNA (miRNA), mRNA, long non-coding RNA (lncRNA), and circular RNA (circRNA) related to anther development of Chinese cabbage, so as to construct competitive endogenous RNA (ceRNA) regulatory networks and provide valuable knowledge for the exploration of pollen development mechanism of Chinese cabbage. A total of 9055 mRNA, 585 miRNA, 1344 lncRNA, and 165 circRNA were identified as differentially expressed in the anther of Chinese cabbage compared with Mix (roots, stems and leaves) by whole-transcriptome sequencing. The anther-related ceRNA-miRNA-target gene regulatory network through miRNA targeting relationships was constructed and 450 pairs of ceRNA relationships, including 97 DEmiRNA-DEmRNA, 281 DEmiRNA-DElncRNA, and 23 DEmiRNA-DEcircRNA interactions were obtained in Chinese cabbage. The genes in the ceRNA network were enriched in the pathways including starch and sucrose metabolism, carbon metabolism, pyruvate metabolism and carbon fixation in photosynthetic organisms, plant hormone signal transduction, and RNA degradation. This study identified some important genes and their interaction lncRNAs, circRNAs, and miRNAs involved in microsporogenesis (BraA06g035480.3C), tapetum and callose layer development (BraA09g009280.3C, BraA04g028920.3C, and BraA10g022680.3C etc), pollen wall formation (BraA06g000980.3C, BraA02g023130.3C, and BraA10g029650.3C etc), and anther dehiscence (BraA10g027200.3C, BraA04g023740.3C, and BraA04g030860.3C etc). Additionally, we analyzed the promoter activity of six anther predominant expression genes, and the results showed that they were all expressed specifically in the anther of Chinese cabbage. This study lay the foundation for further research on the molecular mechanism of anther growth and development.
2022-02-23 | GSE171705 | GEO
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:The small RNA transcriptomes of bread wheat (Triticum aestivum L.) and its emerging model (Brachypodium distachyon (L.) Beauv) were obtained by using deep sequencing technology. Small RNA compositions were analyzed in these two species. In addition to 70 conserved microRNAs (miRNA) from 25 families, 23 novel wheat miRNAs were identified. For Brachypodium, 12 putative miRNAs were predicted from a limited number of ESTs, of which one was a potential novel miRNA. Also, 94 conserved miRNAs from 28 families were identified in this species. Expression validation was performed for several novel wheat miRNAs. RNA ligase-mediated 5' RACE experiments demonstrated their capability to cleave predicted target genes including three disease resistant gene analogs. Differential expression of miRNAs was observed between Brachypodium vegetative and reproductive tissues, suggesting their different roles at the two growth stages. Our work significantly increases the novel miRNA numbers in wheat and provides the first set of small RNAs in Brachypodium distachyon. Keywords: Small RNA
2009-06-08 | GSE16177 | GEO
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.
2012-03-29 | GSE36867 | GEO
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.
2012-04-11 | GSE37134 | GEO
Project description:We aimed to identify targets of miRNAs during wheat grain development by using degradome sequencing approach. Two degradome libraries were constructed from wheat grains. Verification of miRNA targets from two degradome libraries in developing wheat grains.
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