Project description:microRNAs (miRNAs) play important roles in responses to abiotic stresses, including nutrition stress, by regulating target gene expression. Phosphate (Pi) is often lacking in natural and agro-climatic environments, and plants have developed strategies to cope with low Pi (LP) availability. However, the miRNA-mediated regulation of these adaptive responses and their underlying coordinating signals are still poorly understood in forestry trees such as Betula luminifera. Four small RNA (sRNA) libraries, a mixed degradome cDNA library, and four transcriptomic libraries of B. luminifera roots and shoots treated under LP and normal conditions (CK) were constructed and sequenced using next-generation deep sequencing. sRNA sequencing analyses indicated that 66 and 60 miRNAs were differentially expressed in roots and shoots, respectively, under LP conditions. A total of 109 and 112 miRNA–target pairs were further validated in the roots and shoots, respectively, using degradome sequencing, including several novel target genes that were cleaved by isomiRNAs with lengths of 18 or 19 nucleotides, which were only differentially expressed in roots. Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis of differential miRNA targets indicated that the “ascorbate and aldarate metabolism” pathway responded to LP, and “circadian rhythm – plant” was specifically enriched in shoots. A comprehensive B. luminifera transcriptome derived from its roots and shoots was constructed, and a total of 76,899 unigenes were generated. A comparison of transcriptome identified 8,095 and 5,584 differentially expressed genes in roots and shoots, respectively, under LP conditions. Integrated analysis uncovered 14 and 16 miRNA–target pairs that showed negatively correlated expression profiles in roots and shoots, respectively. Moreover, a putative model of miRNA–target interaction involved in plant responses to LP stress is proposed. These results suggest that comprehensive analyses of sRNAs, degradome, and transcriptome provide a useful platform for investigating LP stress in B. luminifera, and may provide new insights into the genetic engineering of high use efficiency of Pi in forestry trees.

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Integrated analysis of microRNA and mRNA expression profiles of rice seedlings in response to zinc deficiency and recovery (mRNA-seq)

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