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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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Small RNAs from female and male flower libraries in andromonoecious poplar.(A) Distribution of unique sRNA annotation categories. (B) Size distribution of small RNA reads.
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pone-0062681-g001: Small RNAs from female and male flower libraries in andromonoecious poplar.(A) Distribution of unique sRNA annotation categories. (B) Size distribution of small RNA reads.

Mentions: Two small RNA (sRNA) libraries were constructed from female (F) and male (M) flowers of andromonoecious P. tomentosa. A total of 58,517,150 (F) and 47,918,351 (M) raw reads were generated from these libraries, respectively, using the Solexa sequencing technology (Table 1). After removing contaminant reads, clean reads were obtained and screened against rRNA, tRNA, snRNA, snoRNA, and mRNA in the Rfam 9.1 and NCBI GenBank databases, resulting in 50,782,479 (F) and 42,837,470 (M) reads remaining for further analyses. Conserved miRNAs were identified by alignment to data in miRBase 19.0 with ±2 nt mismatch; a total of 4,789,550 (F) and 4,306,015 (M) reads that could form characteristic hairpin structures were identified. 4,459,932 (F) and 3,810,615 (M) unannotated unique sRNA sequences, which were further analyzed to predict novel miRNAs. The sequenced sRNAs were then mapped to the Populus genome, miRBase19.0, the NCBI GenBank database, and the Rfam database, and classified into six categories: rRNA, known miRNA (miRNAs in miRBase 19.0), exon, intron, repeat associated RNA, and unknown sRNA. More than 60% of the sequences were unknown sRNAs (Figure 1A). The majority of total sRNA reads were either 21 or 24 nt for both libraries (Figure 1B). In female flower libraries, the 21-nt sRNAs were the most abundant, making up 41.4% of total sequence reads. The 24-nt sRNAs were the second most abundant class at 17.3% of total sequence reads. In male flower libraries, the 21 and 24 nt sRNAs were not significantly different, making up 29.9% and 29.7%, respectively.


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)

Small RNAs from female and male flower libraries in andromonoecious poplar.(A) Distribution of unique sRNA annotation categories. (B) Size distribution of small RNA reads.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0062681-g001: Small RNAs from female and male flower libraries in andromonoecious poplar.(A) Distribution of unique sRNA annotation categories. (B) Size distribution of small RNA reads.
Mentions: Two small RNA (sRNA) libraries were constructed from female (F) and male (M) flowers of andromonoecious P. tomentosa. A total of 58,517,150 (F) and 47,918,351 (M) raw reads were generated from these libraries, respectively, using the Solexa sequencing technology (Table 1). After removing contaminant reads, clean reads were obtained and screened against rRNA, tRNA, snRNA, snoRNA, and mRNA in the Rfam 9.1 and NCBI GenBank databases, resulting in 50,782,479 (F) and 42,837,470 (M) reads remaining for further analyses. Conserved miRNAs were identified by alignment to data in miRBase 19.0 with ±2 nt mismatch; a total of 4,789,550 (F) and 4,306,015 (M) reads that could form characteristic hairpin structures were identified. 4,459,932 (F) and 3,810,615 (M) unannotated unique sRNA sequences, which were further analyzed to predict novel miRNAs. The sequenced sRNAs were then mapped to the Populus genome, miRBase19.0, the NCBI GenBank database, and the Rfam database, and classified into six categories: rRNA, known miRNA (miRNAs in miRBase 19.0), exon, intron, repeat associated RNA, and unknown sRNA. More than 60% of the sequences were unknown sRNAs (Figure 1A). The majority of total sRNA reads were either 21 or 24 nt for both libraries (Figure 1B). In female flower libraries, the 21-nt sRNAs were the most abundant, making up 41.4% of total sequence reads. The 24-nt sRNAs were the second most abundant class at 17.3% of total sequence reads. In male flower libraries, the 21 and 24 nt sRNAs were not significantly different, making up 29.9% and 29.7%, respectively.

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