Grynberg Priscila, Coiti Togawa Roberto, Dias de Freitas Leticia, Antonino Jose Dijair, Rancurel Corinne, Mota do Carmo Costa Marcos, Grossi-de-Sa Maria Fatima, Miller Robert N G, Brasileiro Ana Cristina Miranda, Messenberg Guimaraes Patricia, Danchin Etienne G J
Embrapa Genetic Resources and Biotechnology, Brasília DF 70770-917, Brazil.
National Institute of Science and Technology-INCT PlantStress Biotech-EMBRAPA, Brasília DF 70770-917, Brazil.
Genes (Basel). 2020 Nov 13;11(11):1347. doi: 10.3390/genes11111347.
Plant-parasitic nematodes cause extensive annual yield losses to worldwide agricultural production. Most cultivated plants have no known resistance against nematodes and the few bearing a resistance gene can be overcome by certain species. Chemical methods that have been deployed to control nematodes have largely been banned from use due to their poor specificity and high toxicity. Hence, there is an urgent need for the development of cleaner and more specific control methods. Recent advances in nematode genomics, including in phytoparasitic species, provide an unprecedented opportunity to identify genes and functions specific to these pests. Using phylogenomics, we compared 61 nematode genomes, including 16 for plant-parasitic species and identified more than 24,000 protein families specific to these parasites. In the genome of , one of the most devastating plant parasites, we found ca. 10,000 proteins with orthologs restricted only to phytoparasitic species and no further homology in protein databases. Among these phytoparasite-specific proteins, ca. 1000 shared the same properties as known secreted effectors involved in essential parasitic functions. Of these, 68 were novel and showed strong expression during the endophytic phase of the nematode life cycle, based on both RNA-seq and RT-qPCR analyses. Besides effector candidates, transcription-related and neuro-perception functions were enriched in phytoparasite-specific proteins, revealing interesting targets for nematode control methods. This phylogenomics analysis constitutes a unique resource for the further understanding of the genetic basis of nematode adaptation to phytoparasitism and for the development of more efficient control methods.
植物寄生线虫每年给全球农业生产造成巨大的产量损失。大多数栽培植物对线虫没有已知的抗性，少数带有抗性基因的植物也可能被某些线虫物种克服。由于特异性差和毒性高，过去用于控制线虫的化学方法大多已被禁止使用。因此，迫切需要开发更清洁、更具特异性的控制方法。线虫基因组学的最新进展，包括植物寄生线虫物种的基因组学进展，为识别这些害虫特有的基因和功能提供了前所未有的机会。通过系统发育基因组学，我们比较了61个线虫基因组，其中包括16个植物寄生线虫物种的基因组，并鉴定出24000多个这些寄生虫特有的蛋白质家族。在最具破坏性的植物寄生虫之一的基因组中，我们发现约10000种蛋白质，其直系同源物仅局限于植物寄生线虫物种，在蛋白质数据库中没有进一步的同源性。在这些植物寄生虫特有的蛋白质中，约1000种与已知参与基本寄生功能的分泌效应子具有相同的特性。其中，基于RNA测序和逆转录定量PCR分析，有68种是新的，并且在线虫生命周期的内生阶段表现出强烈的表达。除了效应子候选物外，转录相关和神经感知功能在植物寄生虫特有的蛋白质中富集，揭示了线虫控制方法的有趣靶点。这种系统发育基因组学分析为进一步了解线虫适应植物寄生的遗传基础以及开发更有效的控制方法提供了独特的资源。
