microRNAs from the parasitic plant Cuscuta target host messenger RNAs

My lab has a long-standing interest in the evolution, function, and genomics of small silencing RNAs in plants, including microRNAs and short interfering RNAs (siRNAs). We developed the 'degradome' sequencing method and supporting software, which allows genome-wide experimental discovery of microRNA targets. We have also developed a widely used program, 'ShortStack', which performs robust genome alignments and annotations of small RNA genes using high-throughput small RNA-seq data as input. Using ShortStack we are currently annotating small RNA-producing genes from dozens of plant species. We, along with our collaborators, have also recently discovered that parasitic plants in the genus Cuscuta specifically induce the expression of several microRNAs at the haustorial interface. These microRNAs can target host messenger RNAs. Several of the targeted host mRNAs function in defense responses or phloem function, and some target mutants support increased growth of Cuscuta. We hypothesize that Cuscuta microRNAs act as virulence factors by targeting key host transcripts. We have also recently discovered that Cuscuta microRNAs appear to have rapidly diversified within the Cuscuta genus