Transcriptome-Wide Analysis of Botrytis elliptica Responsive microRNAs and Their Targets in Lilium Regale Wilson by High-Throughput Sequencing and Degradome Analysis

Abstract

MicroRNAs, as master regulators of gene expression, have been widely identified and play crucial roles in plant-pathogen interactions. A fatal pathogen, Botrytis elliptica, causes the serious folia disease of lily, which reduces production because of the high susceptibility of most cultivated species. However, the miRNAs related to Botrytis infection of lily, and the miRNA-mediated gene regulatory networks providing resistance to B. elliptica in lily remain largely unexplored. To systematically dissect B. elliptica-responsive miRNAs and their target genes, three small RNA libraries were constructed from the leaves of Lilium regale, a promising Chinese wild Lilium species, which had been subjected to mock B. elliptica treatment or B. elliptica infection for 6 and 24 h. By high-throughput sequencing, 71 known miRNAs belonging to 47 conserved families and 24 novel miRNA were identified, of which 18 miRNAs were downreguleted and 13 were upregulated in response to B. elliptica. Moreover, based on the lily mRNA transcriptome, 22 targets for 9 known and 1 novel miRNAs were identified by the degradome sequencing approach. Most target genes for elliptica-responsive miRNAs were involved in metabolic processes, few encoding different transcription factors, including ELONGATION FACTOR 1 ALPHA (EF1a) and TEOSINTE BRANCHED1/CYCLOIDEA/PROLIFERATING CELL FACTOR 2 (TCP2). Furthermore, the expression patterns of a set of elliptica-responsive miRNAs and their targets were validated by quantitative real-time PCR. This study represents the first transcriptome-based analysis of miRNAs responsive to B. elliptica and their targets in lily. The results reveal the possible regulatory roles of miRNAs and their targets in B. elliptica interaction, which will extend our understanding of the mechanisms of this disease in lily.

Transcriptome-based identification of genes related to resistance against Botrytis elliptica in Lilium regale

“…Signal transduction via phytohormones is a crucial requirement of plant immunity. The positive role of the JA pathway in L. regale resistance to B. elliptica has been reported by Gao et al (2017), who found that several JA biosynthetic genes regulated by miRNAs influenced disease resistance. Based on our RNA-seq data, DEGs encoding JA biosynthetic enzymes (AOS, AOC and OPR3) and JA signaling responsive factors (COI1 and MYC2) were upregulated.…”

“…Rich germplasm resources for Lilium spp. are available in China, some of which (e.g., Lilium regale Wilson) are resistant to B. elliptica infection (Du et al 2014;Gao et al 2017). However, the molecular basis of lily resistance to this fungus remains unclear, although several studies have provided insights.…”

“…Moreover, a new report revealed that multiple microRNA-mediated silencing cascades regulated gene expression in the L. regale-B. elliptica interaction (Gao et al 2017).…”

Comparative transcriptome profiling uncovers a Lilium regale NAC transcription factor, LrNAC35, contributing to defence response against cucumber mosaic virus and tobacco mosaic virus

“…In recent reports, differentially expressed transcripts in L. regale response to F. oxysporum have been identified using the SSH method (Rao et al , ). Transcriptome‐wide identification has also been performed to characterize the microRNAs (Gao et al , ) and genes (Cui et al , ) with significantly changed expression in Botrytis elliptica ‐infected L. regale , and two TFs, LrWRKY4 and LrWRKY12 , have been characterized as important regulators of resistance to B. cinerea (Cui et al , ). In this study, we employed a comparative transcriptome approach to dissect the antiviral molecular mechanism in L. regale .…”

Integrated analysis of small RNA, transcriptome and degradome sequencing provides new insights into floral development and abscission in yellow lupine (Lupines luteus L.)

“…Therefore, we believe that the pathways controlling these processes deserve intensive research focus. The commonly used NGS technique allows for comprehensive analyses of sRNAoms, transcriptoms, and degradomes, as well as identification of sRNAs and their target genes in both model and non-model plants, for example: tomato [58], soybean [59], Arabidopsis [60,61], oilseed rape [62], Brassica juncea [63], lily [64,65], peanut [66], orchardgrass [67] or wheat [68,69].…”