Meloidogyne luci gene predictions

Results of EuGene annotation on the M. luci genome. Predictions of gene models in M. incognita, M. javanica, M. arenaria and M. luci genomes were done with the fully automated pipeline EuGene-EP version 1.6.5 (Sallet et al., 2019). EuGene has been configured to integrate similarities with known proteins of Caenorhabditis elegans (PRJNA13758) downloaded from Wormbase ParaSite (Howe et al., 2017) as well as the “nematoda” section of UniProtKB/Swiss-Prot library (UniProt Consortium, 2018), with the prior exclusion of proteins that were similar to those present in RepBase (Bao et al., 2015). We used as transcriptional evidence, transcriptome data for M. incognita, as it is the Meloidogyne species with the most comprehensive expression data available. RNA-seq data from pre-parasitic J2, J2-J3 and adult female stages (Blanc-Mathieu et al., 2017) were assembled de novo using Trinity (Haas et al., 2013) followed by a cleanup that retains for each trinity locus only the transcript that gives the longest ORF. The dataset of M. incognita assembled transcriptome was aligned on the genomes of the four Meloidogyne species using Gmap (Wu and Watanabe, 2005) and except for M. incognita the option "cross-species" was used. Only alignments spanning 30% of the transcript length with at least 97% identity were retained. The EuGene default configuration was edited to set the “preserve” parameter to 1 for all datasets, the “gmap_intron_filter” parameter to 1, the minimum intron length to 35 bp, and to allow the non-canonical donor splice site “GC”. Finally, the Nematode specific Weight Array Method matrices were used to score the splice sites (available at this URL: http://eugene.toulouse.inra.fr/Downloads/WAM_nematodes_20171017.tar.gz).