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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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Summary of common and specific sequences between female and male libraries. (A) Conserved sRNAs and (B) Novel sRNAs.
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pone-0062681-g002: Summary of common and specific sequences between female and male libraries. (A) Conserved sRNAs and (B) Novel sRNAs.

Mentions: To date, 46 conserved and non-conserved miRNA families have been discovered in the Populus genome [20]. In the two libraries sequenced in our study, 134 unique miRNA sequences were identified belonging to 38 conserved miRNA families (Table 2). The expression levels of a few miRNA families, such as miR166 and miR472, were extraordinarily high in both libraries (Table 2). miR166 was the most abundant, with 2,157,665 (F) and 142, 916 (M) reads accounting for 62.5% and 47.1% of all conserved miRNA reads, respectively. Several miRNA families, such as miR156, miR159, miR169, miR319, miR396, and miR1447, had moderate expression levels (Table 2). By contrast, some miRNA families showed very low levels of expression, with fewer than 200 reads. Different members in the same miRNA family displayed drastically different expression levels. For example, miR166 members varied in abundance from 695 to 2,157,665 reads. Also, 38 unique miRNA sequences belonging to 38 conserved miRNA families were produced from 134 loci (Table S1). Of these miRNA sequences, 11 were encoded by a single locus in the Populus genome, whereas the other 27 sequences had multiple loci. Most of these had 2–6 loci in the genome, and only a few had more than eight loci. For example, Pto-miR166a–l and Pto-miR169a–m had 12 and 13 loci, respectively. Thus, the size of miRNA families varies in andromonoecious P. tomentosa. Among these conserved miRNAs, miR6459 was only expressed in the female library. By contrast, two miRNAs, miRNA397 and miRNA6462, were detected as having male-specific expression (Figure 2).


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)

Summary of common and specific sequences between female and male libraries. (A) Conserved sRNAs and (B) Novel sRNAs.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0062681-g002: Summary of common and specific sequences between female and male libraries. (A) Conserved sRNAs and (B) Novel sRNAs.
Mentions: To date, 46 conserved and non-conserved miRNA families have been discovered in the Populus genome [20]. In the two libraries sequenced in our study, 134 unique miRNA sequences were identified belonging to 38 conserved miRNA families (Table 2). The expression levels of a few miRNA families, such as miR166 and miR472, were extraordinarily high in both libraries (Table 2). miR166 was the most abundant, with 2,157,665 (F) and 142, 916 (M) reads accounting for 62.5% and 47.1% of all conserved miRNA reads, respectively. Several miRNA families, such as miR156, miR159, miR169, miR319, miR396, and miR1447, had moderate expression levels (Table 2). By contrast, some miRNA families showed very low levels of expression, with fewer than 200 reads. Different members in the same miRNA family displayed drastically different expression levels. For example, miR166 members varied in abundance from 695 to 2,157,665 reads. Also, 38 unique miRNA sequences belonging to 38 conserved miRNA families were produced from 134 loci (Table S1). Of these miRNA sequences, 11 were encoded by a single locus in the Populus genome, whereas the other 27 sequences had multiple loci. Most of these had 2–6 loci in the genome, and only a few had more than eight loci. For example, Pto-miR166a–l and Pto-miR169a–m had 12 and 13 loci, respectively. Thus, the size of miRNA families varies in andromonoecious P. tomentosa. Among these conserved miRNAs, miR6459 was only expressed in the female library. By contrast, two miRNAs, miRNA397 and miRNA6462, were detected as having male-specific expression (Figure 2).

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