AUTHOR=Gao Xue , Cui Qi , Cao Qin-Zheng , Liu Qiang , He Heng-Bin , Zhang Dong-Mei , Jia Gui-Xia 

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

JOURNAL=Frontiers in Plant Science

VOLUME=8

YEAR=2017

URL=https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2017.00753

DOI=10.3389/fpls.2017.00753

ISSN=1664-462X

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