Abstract
BackgroundPhosphorus is an important macronutrient that is severely lacking in soils. In plants, specific microRNAs (miRNAs) essential for nutrient management and the regulation of stress responses are responsible for the control of many phosphate starvation responses. Further understanding of conserved and species-specific microRNA species has potential implications for the development of crops tolerant to soils with low phosphate.ResultsThis study identified and characterised phosphate starvation-responsive miRNAs in the native Australian tobacco Nicotiana benthamiana. Small RNA libraries were constructed and sequenced from phosphate-starved plant leaves, stems and roots. Twenty-four conserved miRNA families and 36 species-specific miRNAs were identified. The majority of highly phosphate starvation-responsive miRNAs were highly conserved, comprising of members from the miR399, miR827, and miR2111 families. In addition, two miRNA-star species were identified to be phosphate starvation-responsive. A total of seven miRNA targets were confirmed using RLM-5’RACE to be cleaved by five miRNA families, including two confirmed cleavage targets for Nbe-miR399 species, one for Nbe-miR2111, and two for Nbe-miR398. A number of N. benthamiana-specific features for conserved miRNAs were identified, including species-specific miRNA targets predicted or confirmed for miR399, miR827, and miR398.ConclusionsOur results give an insight into the phosphate starvation-responsive miRNAs of Nicotiana benthamiana, and indicate that the phosphate starvation response pathways in N. benthamiana contain both highly conserved and species-specific components.
Highlights
IntroductionSpecific microRNAs (miRNAs) essential for nutrient management and the regulation of stress responses are responsible for the control of many phosphate starvation responses
Phosphorus is an important macronutrient that is severely lacking in soils
Analysis of small RNA sequencing reads Deep sequencing of supplemented phosphate is inaccessible to theSmall RNAs (sRNAs) from N. benthamiana leaves, stems, and roots grown under phosphate-sufficient (+P) or phosphate starvation (-P) conditions yielded a total of 40,047,335 input reads (Table 1)
Summary
Specific microRNAs (miRNAs) essential for nutrient management and the regulation of stress responses are responsible for the control of many phosphate starvation responses. Further understanding of conserved and species-specific microRNA species has potential implications for the development of crops tolerant to soils with low phosphate. Phosphorus is the second-most important plant macronutrient after nitrogen, and a major limiting factor for agricultural production [1, 2]. Natural soil phosphorus is low and declining, and artificial application of phosphate fertilisers is heavily relied upon, in order to maintain current agricultural production [3]. RNA (mRNA precursors), known as primary miRNAs (pri-miRNAs), which are transcribed from defined promoter-containing loci within the plant genome and contain a stem-loop structure enzymatically processed into a duplex composed of the mature miRNA and a near-complementary passenger or miRNA-star (miRNA*) strand. The mature miRNA strand is separated from the miRNA* and loaded into an ARGONAUTE family member protein, which recognises transcripts near-complementary to the miRNA sequence and effects transcript cleavage or translational repression of the transcript, resulting in gene silencing [5, 6]
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