Identification and characterization of wheat long non-protein coding RNAs responsive to powdery mildew infection and heat stress by using microarray analysis and SBS sequencing

In this study, by using computational analysis and experimental approach we identified 125 putative wheat stress responsive long npcRNAs, which are not conserved among plant species. Among them, some were precursors of small RNAs such as microRNAs and siRNAs, two long npcRNAs were identified as signal recognition particle (SRP) 7S RNA variants, and three were characterized as U3 snoRNAs. We found that wheat long npcRNAs showed tissue dependent expression patterns and were responsive to powdery mildew infection and heat stress.Our results indicated that diverse sets of wheat long npcRNAs were responsive to powdery mildew infection and heat stress, and could function in wheat responses to both biotic and abiotic stresses, which provided a starting point to understand their functions and regulatory mechanisms in the future.The developmental and physiological complexity of eukaryotes could not be explained solely by the number of protein-coding genes [1]. For example, the Drosophila melanogaster genome contains only twice as many genes as some bacterial species, although the former is far more complex in its genome organization than the latter. Similarly, the number of protein-coding genes in human and nematode is extremely close. A portion of this paradox can be resolved through alternative pre-mRNA splicing [2]. In addition, post-translational modifications can also contribute to the increased complexity and diversity of protein species [3].Recent studies suggest that most of the genome are transcribed, among the transcripts only a small portion encode for proteins, whereas a large portion of the transcripts do not encode any proteins, which are generally termed non-protein coding RNAs (npcRNA). For example, transcriptome profiling in rice (Oryza sativa) indicates that there are about 8400 putative npcRNAs, which do not overlap with any predicted open reading frames (ORFs) [4]. These npcRNAs are subdivided as housekeeping npcRNAs (such as transfer and ribosomal RNAs)