Abstract
BackgroundPhasiRNAs (phased secondary siRNAs) play important regulatory roles in the development processes and biotic or abiotic stresses in plants. Some of phasiRNAs involve in the reproductive development in grasses, which include two categories, 21-nt (nucleotide) and 24-nt phasiRNAs. They are triggered by miR2118 and miR2275 respectively, in premeiotic and meiotic anthers of rice, maize and other grass species. Wheat (Triticum aestivum) with three closely related subgenomes (subA, subB and subD), is a model of allopolyploid in plants. Knowledge about the role of phasiRNAs in the inflorescence development of wheat is absent until now, and the evolution of PHAS loci in polyploid plants is also unavailable.ResultsUsing 261 small RNA expression datasets from various tissues, a batch of PHAS (phasiRNA precursors) loci were identified in the young spike of wheat, most of which were regulated by miR2118 and miR2275 in their target site regions. Dissection of PHAS and their trigger miRNAs among the diploid (AA and DD), tetraploid (AABB) and hexaploid (AABBDD) genomes of Triticum indicated that distribution of PHAS loci were dominant randomly in local chromosomes, while miR2118 was dominant only in the subB genome. The diversity of PHAS loci in the three subgenomes of wheat and their progenitor genomes (AA, DD and AABB) suggested that they originated or diverged at least before the occurrence of the tetraploid AABB genome. The positive correlation between the PHAS loci or the trigger miRNAs and the ploidy of genome indicated the expansion of genome was the major drive force for the increase of PHAS loci and their trigger miRNAs in Triticum. In addition, the expression profiles of the PHAS transcripts suggested they responded to abiotic stresses such as cold stress in wheat.ConclusionsAltogether, non-coding phasiRNAs are conserved transcriptional regulators that display quick plasticity in Triticum genome. They may be involved in reproductive development and abiotic stress in wheat. It could be referred to molecular research on male reproductive development in Triticum.
Highlights
IntroductionPhasiRNAs (phased secondary siRNAs) play important regulatory roles in the development processes and biotic or abiotic stresses in plants
PhasiRNAs play important regulatory roles in the development processes and biotic or abiotic stresses in plants
Identification of 21- and 24-PhasiRNA precursors (PHAS) in wheat To identify the PHAS loci in wheat, we downloaded 261 small RNA datasets from the GEO database (Table 1), which included 12 seedling samples, 128 leaf samples, 12 root samples, one stem sample, one shoot sample, 29 young spike samples, two anther samples, one embryo sample, 17 spikelet samples, 12 rachis samples, grain samples, seed samples, 6 callus samples, and one mixed tissue sample. By comparing these small RNAs to the wheat genome using the Shortstack package [19] following the flowchart as shown in Supplementary Fig. 1, a batch of PHAS loci were identified with phased scores greater than 15, 20, 25 or 30
Summary
PhasiRNAs (phased secondary siRNAs) play important regulatory roles in the development processes and biotic or abiotic stresses in plants. There is a particular class of small RNAs generated in 21- or 24-nt (nucleotide) intervals with a ‘head-to-tail’ pattern from their precursor transcripts, which are called phased, secondary, small interfering RNAs (phasiRNAs) [1,2,3]. In plants, phased siRNAs play a series of roles in abiotic and biotic stresses [5, 6], seed germination [7] and reproductive development [3, 8,9,10]. MiRNAs [12,13,14] can trigger 21-nt phasiRNA generation from NB-LRR transcripts, and most of them are species-
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