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Incompletely fused carpels ovary development revealed by miRNAs and target genes analysis in maize. (smallRNA-Seq and degradome-Seq)

ABSTRACT: To identify miRNAs involved in carpels fusion development in maize, four independent small RNA libraries and two degradome libraries from WT and IFC ovaries were constructed at the carpels fusion deficiency just being observed. A total of 162 known miRNAs distributed in 33 faimilies were identified, of which 20 known miRNAs were differentially expressed. In addition, 19 novel miRNAs were shown difference in expression levels between IFC and WT ovaries. By degradome analysis, totals of 113 and 78 target genes were predicted for known and novel miRNAs, respectively. 24 (60%) target genes of the differentially expressed known miRNAs coded for transcription factors, among which target genes encoding auxin response factors (ARF), TB1-CYC-PCFs (TCP), APETALA2 (AP2), growth regulating factor (GRF), MYB, NAC and NF-YA were classified as Class I. These target genes showed opposite expression patterns with their corresponding miRNAs according to quantitative real-time PCR results. The results suggested that the incomplete carpels fusion may partly due to the differential expression of these miRNAs and their target genes

ORGANISM(S): Zea mays

PROVIDER: GSE80998 | GEO | 2017/06/13

SECONDARY ACCESSION(S): PRJNA320257

REPOSITORIES: GEO

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Project description:microRNAs (miRNAs) play vital roles in plants regulating a panoply of biological processes, such as development, hormone signaling, and the stress response, by inhibiting target genes at the post-transcriptional level. However, the roles of miRNAs in Betula luminifera remain elusive. To mine for B. luminifera miRNAs and targets, we used a deep sequencing approach to analyze the sRNAs and degradome sequencing of mixed samples, including roots, stems, and leaves. A total of 114 known miRNAs or miRNA*s from 44 families, and 24 novel miRNAs and 17 miRNA*s plus 15 plausible miRNA candidates were identified, of which 36 known miRNAs, 29 miRNA*s, and all novel miRNAs had precursor sequences. Additionally, 49 targets for 19 known miRNA families and seven miRNA*s, and seven targets for novel miRNAs were identified using a high-throughput degradome-sequencing approach. The conserved miRNA targets were mainly transcription factors, whereas the miRNA* targets were mainly protein-coding genes, with preferential propensity to functional enzymes. A Gene Ontology analysis showed that the predicted targets were classified into 62 biological processes, 20 cellular components, and 28 molecular functions, respectively. We found two different targets for 396a* and miR396c*, and the target changed when the miR156d precursor cleavage site was shifted toward the 5′-end by two nucleotides, indicating the diverse regulatory roles of MIRNA genes. Furthermore, three targets identified by degradome sequencing were validated further through 5′ rapid amplification of cDNA ends. The expression patterns of the randomly selected miRNAs varied among different tissues. miR164 expression was induced under nitrogen starvation, with tissue-specific expression patterns, and was negatively correlated with the NAC1 target gene in roots and leaves, but not in stems. This study is a transcriptome-based analysis of miRNAs and the degradome in a B. luminifera pre-model tree and provides useful information to explore the functions of miRNAs and their target genes in B. luminifera.

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Incompletely fused carpels ovary development revealed by miRNAs and target genes analysis in maize. (smallRNA-Seq and degradome-Seq)

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