Meloidogyne enterolobii E1834 gene prediction

Results of EuGene annotation on the M. enterolobii E1834 nuclear genome. Gene models prediction was done with the fully automated pipeline EuGene-EP (v1.6.5, Sallet et al., 2019). EuGene has been configured to integrate similarities with known proteins of Caenorhabditis elegans (PRJNA13758) from WormBase Parasite (Howe et al., 2017) and “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). The dataset of Meloidogyne enterolobii transcribed sequences (Koutsovoulos et al., 2020) was aligned on the genome and used by EuGene as transcription evidence. Only the alignments of datasets on the genome 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 and the minimum intron length to 35 bp. Finally, the Nematodes-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). Using the automated Eugene-EP pipeline, a total of 49,870 genes were predicted, with 45,924 being protein-coding genes and 3,946 being non-protein-coding genes such as rRNA, tRNA, and splice leader genes.