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Parasitic nematodes that attack agronomically important cultivars are responsible for immense agricultural losses worldwide. Among the different control strategies, RNA interference (RNAi) has been shown to be viable and efficient. This is possible because RNAi allows vital and essential genes to be identified, given the functional annotation of proteins and analysis of differential expression, so that the complete development of all stages of these animals' lives. Bioinformatic approaches applied to genomic and transcriptomic analyses are fundamental for the identification of essential genes. The search for target genes by transcriptomic analysis requires the development of bioinformatics pipelines. Depending on the context of the data, this development can be initiated through the de novo assembly (or reference) of the transcriptome, functional annotation of the transcripts, calculation of differential gene expression in the different experimental conditions of interest, cluster analysis of gene families in search for targets that do not have paralogs, among others. The main goal of this project is to develop a pipeline of genomics and transcriptomics data analysis for the identification of target genes for silencing. Root-knot nematodes (genus Meloidogyne) are major contributors to crop losses caused by nematodes, and reduce the productivity of crops worldwide by 5 to 10% per year (including: cotton, various vegetables, spices and coffee). These nematodes secrete effector proteins in the plant, derived from two sets of pharyngeal gland cells, to manipulate the physiology and immunity of the host. Details of how root-knot nematodes regulate transcription remain sparse. The focus of this project is the identification of essential genes in the endoparasite Meloidogyne incognita, through a multi-omic approach for silencing via RNAi. For this, we considered different public data of M. incognita genome, transcriptome of different life stages (egg, J2/3/4, female/adult, with 3 replicas) and low coverage sequencing (DNA-seq) of 11 pathogens of Brazilian cultivars from different regions of the country. Initially, we search for genes in M. incognita that are significantly expressed in the J2 life (the infective phase by the Meloidogyne adult female – formation of galls). We then performed phylogenomic analysis of 10 organisms phylogenetically close to M. incognita, to select single copy genes, to avoid function compensation after the target gene’ silencing. After, were evaluated the sequence conservation of these genes among 11 Brazilian cultivars of M. incognita to select a set of highly conserved genes (95% of conservation). Finally, these genes were filters for essential functions in model organisms related to M. incognita, such as Caenorhabditis elegans and Saccharomyces cerevisiae. This analysis resulted in a list of four candidate genes (differentially expressed in J2, single copy orthologs, conserved between cultivars and essential in model organisms). We will now validate our multi-omic approach for finding essential genes as RNAi candidates by performing gene silencing assays in C. elegans. We believe that it is possible to apply our pipeline for agricultural pest control beyond the scope of this project, which can reduce the numerous damages caused by parasitic nematodes around the world.

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1	Giovana Oliveira(g235517@dac.unicamp.br,)
2	Maria Fernanda Campanari(m264554@dac.unicamp.br)
3	Marcelo Carazzolle(mcarazzo@unicamp.br)
4	Henrique Marques-Souza(hmsouza@unicamp.br)

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