Characterization of microRNAs in the cyst nematode <i>Heterodera glycines</i> identifies possible candidates involved in cross-kingdom interactions with its host <i>Glycine max</i>

The soybean cyst nematode (SCN – <i>Heterodera glycines</i>) is one of the most damaging pests to the cultivated soybean worldwide. Using a wide array of stylet-secreted effector proteins, this nematode can restructure its host cells into a complex and highly active feeding structure called the syncytium. Tight regulation of these proteins is thought to be essential to the successful formation of this syncytium. To date, multiple mechanisms have been proposed to regulate the expression of these proteins including through post-transcriptional regulation. MicroRNAs (miRNAs) are a class of small, roughly 22-nucleotide-long, non-coding RNA shown to regulate gene expression through its interaction with the 3’ untranslated region of genes. These same small RNAs have also been hypothesized to be able to cross over kingdom barriers and regulate genes in other species in a process called cross-kingdom interactions. In this study, we characterized the miRNome of the SCN via sequencing of small-RNAs isolated from whole nematodes and exosomes representing all developmental stages. We identified 121 miRNA loci encoding 96 distinct miRNA families including multiple lineage- and species-specific candidates. Using a combination of plant- and animal-specific miRNA target predictors, we generated a unique repertoire of miRNA:mRNA interacting partners in the nematode and its host plant leading to the identification of a set of nine probable cross-kingdom miRNA candidates.大豆胞囊线虫（soybean cyst nematode，简称SCN——*Heterodera glycines*）是全球范围内危害栽培大豆最为严重的害虫之一。该线虫可借助多种口针分泌效应蛋白（stylet-secreted effector proteins），将宿主细胞重构成结构复杂且高度活跃的取食结构——合胞体（syncytium）。学界普遍认为，对这些效应蛋白的严格调控是合胞体成功形成的必要前提。迄今为止，已有多种调控此类蛋白表达的机制被提出，其中包括转录后调控（post-transcriptional regulation）途径。微小RNA（microRNAs，缩写miRNAs）是一类长度约为22个核苷酸的小型非编码RNA，可通过与靶基因的3'非翻译区（3’ untranslated region）结合调控基因表达。这类小型RNA还被推测能够跨越生物界界限，在其他物种中调控基因表达，这一过程被称为跨界相互作用（cross-kingdom interactions）。在本研究中，我们通过对取自完整大豆胞囊线虫虫体以及涵盖其所有发育阶段的外泌体（exosomes）中分离得到的小RNA进行测序，对该线虫的miRNA组（miRNome）进行了系统表征。我们共鉴定出121个miRNA基因座，编码96个不同的miRNA家族，其中包含多个线虫谱系及物种特异性的候选miRNA。结合植物与动物专属的miRNA靶标预测工具（miRNA target predictors），我们构建了该线虫与其宿主植物之间独特的miRNA与mRNA互作伴侣库，最终鉴定出9个潜在的跨界miRNA候选分子。