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Sexual dimorphism floral microRNA profiling and target gene expression in andromonoecious poplar (Populus tomentosa).

Song Y, Ma K, Ci D, Zhang Z, Zhang D - PLoS ONE (2013)

Bottom Line: The conserved and novel miRNA locations were annotated in the Populus trichocarpa genome.Among these, miRNA Pto-F70 and 4 targets are located in the sex-determination regions of chromosome XIX.Furthermore, two novel miRNAs, Pto-F47 and Pto-F68, were shown for the first time to be regulatory factors in phytohormone interactions.

View Article: PubMed Central - PubMed

Affiliation: National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China.

ABSTRACT
Although the molecular basis of poplar sex-specific flower development remains largely unknown, increasing evidence indicates an essential role for microRNAs (miRNAs). The specific miRNA types and precise miRNA expression patterns in dioecious plant flower development remain unclear. Here, we used andromonoecious poplar, an exceptional model system, to eliminate the confounding effects of genetic background of dioecious plants. This system, combined with high-throughput sequencing and computational analysis, allowed us to characterize sex-specific miRNAomes from female and male flowers. Comparative miRNAome analysis combined with quantitative real-time PCR revealed the expression patterns of 27 miRNAs in poplar flower and showed that the targets of these miRNAs are involved in flower organogenesis, Ca(2+) transport, phytohormone synthesis and metabolism, and DNA methylation. This paper describes a complex regulatory network consisting of these miRNAs expressed in sex-specific flower development in a dioecious plant. The conserved and novel miRNA locations were annotated in the Populus trichocarpa genome. Among these, miRNA Pto-F70 and 4 targets are located in the sex-determination regions of chromosome XIX. Furthermore, two novel miRNAs, Pto-F47 and Pto-F68, were shown for the first time to be regulatory factors in phytohormone interactions. To our knowledge, this report is the first systematic investigation of sex-specific flower-related miRNAs and their targets in poplar, and it deepens our understanding of the important regulatory functions of miRNAs in female and male flower development in this dioecious plant.

Show MeSH
AgriGO analysis of target genes for statistically enriched GO terms in the ‘Biological process’ ontology.Coloring of GO term nodes is proportional to their significance as indicated by the scale.
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pone-0062681-g005: AgriGO analysis of target genes for statistically enriched GO terms in the ‘Biological process’ ontology.Coloring of GO term nodes is proportional to their significance as indicated by the scale.

Mentions: To understand the functions of sex-specific flower development related miRNAs, the first step is to predict and experimentally validate their targets. Consequently, we predicted 25 target genes for Pto-miR156, Pto-miR159, Pto-miR172 and Pto-miR319 that were different from the previously defined Populus miRNA targets (miRBase 19.0), and a total of 464 targets were identified for the 78 novel miRNAs (Table S3). The number of predicted targets varied from 1 to 15 per miRNA. The categorization of female and male-specific miRNA target genes according to biological process is shown in Figure 5. After putative functional annotation by BLAST searches against the TAIR, NCBI and JGI protein datasets, all targets of female and male-specific miRNAs that had a greater than twofold difference in expression between the sexes (Ratio≧2or≦0.5) were identified as candidate genes for gene functional enrichment analysis. All the target genes between the sexes were functionally characterized using enrichment analysis of gene sets, mostly as described by Gene Ontology terms (Figure 5). GO analysis showed that response to hormone stimulus, negative regulation of gene expression, regulation of flower development, and organ formation were significantly enriched terms for biological processes.


Sexual dimorphism floral microRNA profiling and target gene expression in andromonoecious poplar (Populus tomentosa).

Song Y, Ma K, Ci D, Zhang Z, Zhang D - PLoS ONE (2013)

AgriGO analysis of target genes for statistically enriched GO terms in the ‘Biological process’ ontology.Coloring of GO term nodes is proportional to their significance as indicated by the scale.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3646847&req=5

pone-0062681-g005: AgriGO analysis of target genes for statistically enriched GO terms in the ‘Biological process’ ontology.Coloring of GO term nodes is proportional to their significance as indicated by the scale.
Mentions: To understand the functions of sex-specific flower development related miRNAs, the first step is to predict and experimentally validate their targets. Consequently, we predicted 25 target genes for Pto-miR156, Pto-miR159, Pto-miR172 and Pto-miR319 that were different from the previously defined Populus miRNA targets (miRBase 19.0), and a total of 464 targets were identified for the 78 novel miRNAs (Table S3). The number of predicted targets varied from 1 to 15 per miRNA. The categorization of female and male-specific miRNA target genes according to biological process is shown in Figure 5. After putative functional annotation by BLAST searches against the TAIR, NCBI and JGI protein datasets, all targets of female and male-specific miRNAs that had a greater than twofold difference in expression between the sexes (Ratio≧2or≦0.5) were identified as candidate genes for gene functional enrichment analysis. All the target genes between the sexes were functionally characterized using enrichment analysis of gene sets, mostly as described by Gene Ontology terms (Figure 5). GO analysis showed that response to hormone stimulus, negative regulation of gene expression, regulation of flower development, and organ formation were significantly enriched terms for biological processes.

Bottom Line: The conserved and novel miRNA locations were annotated in the Populus trichocarpa genome.Among these, miRNA Pto-F70 and 4 targets are located in the sex-determination regions of chromosome XIX.Furthermore, two novel miRNAs, Pto-F47 and Pto-F68, were shown for the first time to be regulatory factors in phytohormone interactions.

View Article: PubMed Central - PubMed

Affiliation: National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China.

ABSTRACT
Although the molecular basis of poplar sex-specific flower development remains largely unknown, increasing evidence indicates an essential role for microRNAs (miRNAs). The specific miRNA types and precise miRNA expression patterns in dioecious plant flower development remain unclear. Here, we used andromonoecious poplar, an exceptional model system, to eliminate the confounding effects of genetic background of dioecious plants. This system, combined with high-throughput sequencing and computational analysis, allowed us to characterize sex-specific miRNAomes from female and male flowers. Comparative miRNAome analysis combined with quantitative real-time PCR revealed the expression patterns of 27 miRNAs in poplar flower and showed that the targets of these miRNAs are involved in flower organogenesis, Ca(2+) transport, phytohormone synthesis and metabolism, and DNA methylation. This paper describes a complex regulatory network consisting of these miRNAs expressed in sex-specific flower development in a dioecious plant. The conserved and novel miRNA locations were annotated in the Populus trichocarpa genome. Among these, miRNA Pto-F70 and 4 targets are located in the sex-determination regions of chromosome XIX. Furthermore, two novel miRNAs, Pto-F47 and Pto-F68, were shown for the first time to be regulatory factors in phytohormone interactions. To our knowledge, this report is the first systematic investigation of sex-specific flower-related miRNAs and their targets in poplar, and it deepens our understanding of the important regulatory functions of miRNAs in female and male flower development in this dioecious plant.

Show MeSH