Mapping of known effector genes on five Meloidogyne genomes

Based on the literature, we established a manually curated list of M. incognita genes specifically expressed in sub-ventral or dorsal secretory gland cells. We started from the list published in (Truong, Nguyen, Abad, Quentin, Favery, 2015) and manually checked the figures associated with the cited references to only keep genes with evidence for specific expression via in-situ hybridization. We completed this list with the Mi-PNF3 gene published more recently (Leelarasamee, Zhang, Gleason, 2018) and eliminated redundancy between the sequences at the protein level. We retrieved the corresponding CDS sequences and aligned them to the M. incognita, M. arenaria, M. javanica, M. enterolobii and M. hapla genome sequences (Blanc-Mathieu et al., 2017; Koutsovoulos et al., 2020, Opperman et al. 2008) using the splice aware aligner SPALN (Iwata Gotoh, 2012) with the following parameters. 'spaln -Q7 -O4 -M -d Mi.mfa CDS > input.gff -M = report multiple hits and only the best -Q4= DP mode, 5-7 = maximum number of reported hsp -O4= megablast-like format We performed this operation for the subventral (SvG) and (DG) subsets, separtely and provide a summary of the results in MS Word and PDF Format.