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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.

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First nucleotide bias of novel candidate miRNAs in andromonoecious poplar female and male flower libraries.
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pone-0062681-g003: First nucleotide bias of novel candidate miRNAs in andromonoecious poplar female and male flower libraries.

Mentions: The characteristic hairpin structure of miRNA precursors was used to predict novel miRNAs. In total, 78 unique sRNA sequences were identified including 8 sRNAs with complementary miRNA*s (Table 3, 4 and 5). The majority of these novel miRNA candidates had lengths of 21 and 22 nt, and started with a 5′ U (Figure 3). The 78 sRNA sequences were transcribed from 85 loci; most were only produced from one locus, but Pto-F2, Pto-F13, Pto-F31 and Pto-F31 were each generated from 3 loci. The length of the predicted novel miRNA precursors ranged from 76 to 303 nt, with an average of 140 nt. The average minimum free energy (MFE) value was −55.58 kcal/mol, with a range of −21.2 to −177.4 kcal/mol. The structures of the 78 novel miRNA precursors are shown in Figure S2. Most of them showed differential expression in the two libraries. For instance, the mature miRNA counts ranged from 63 to 8,480,860. Among those 78 miRNAs, only 6 sRNAs were found both in female and male libraries. 61 female-specific sRNAs and 11 male-specific sRNAs were detected, suggesting that more kinds of sRNA are involved in female floral development than in male development. To investigate whether these novel miRNA sequences were conserved across plant species, we used them as query sequences to perform BLASTN searches against the Arabidopsis thaliana, Brassica rapa, Citrus sinensis, Medicago truncatula, Oryza sativa, Ricinus communis, Prunus persica, Vitis vinifera and Zea mays genome databases in Phytozome v7.0. A large proportion of the novel sRNAs identified in andromonoecious P. tomentosa did not have perfect matches in different genome databases. Only 6 male-specific sRNA and 5 female-specific sRNAs were detected in other species (Table S2).


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)

First nucleotide bias of novel candidate miRNAs in andromonoecious poplar female and male flower libraries.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0062681-g003: First nucleotide bias of novel candidate miRNAs in andromonoecious poplar female and male flower libraries.
Mentions: The characteristic hairpin structure of miRNA precursors was used to predict novel miRNAs. In total, 78 unique sRNA sequences were identified including 8 sRNAs with complementary miRNA*s (Table 3, 4 and 5). The majority of these novel miRNA candidates had lengths of 21 and 22 nt, and started with a 5′ U (Figure 3). The 78 sRNA sequences were transcribed from 85 loci; most were only produced from one locus, but Pto-F2, Pto-F13, Pto-F31 and Pto-F31 were each generated from 3 loci. The length of the predicted novel miRNA precursors ranged from 76 to 303 nt, with an average of 140 nt. The average minimum free energy (MFE) value was −55.58 kcal/mol, with a range of −21.2 to −177.4 kcal/mol. The structures of the 78 novel miRNA precursors are shown in Figure S2. Most of them showed differential expression in the two libraries. For instance, the mature miRNA counts ranged from 63 to 8,480,860. Among those 78 miRNAs, only 6 sRNAs were found both in female and male libraries. 61 female-specific sRNAs and 11 male-specific sRNAs were detected, suggesting that more kinds of sRNA are involved in female floral development than in male development. To investigate whether these novel miRNA sequences were conserved across plant species, we used them as query sequences to perform BLASTN searches against the Arabidopsis thaliana, Brassica rapa, Citrus sinensis, Medicago truncatula, Oryza sativa, Ricinus communis, Prunus persica, Vitis vinifera and Zea mays genome databases in Phytozome v7.0. A large proportion of the novel sRNAs identified in andromonoecious P. tomentosa did not have perfect matches in different genome databases. Only 6 male-specific sRNA and 5 female-specific sRNAs were detected in other species (Table S2).

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