Contribution of Lateral Gene Transfers to the Genome Composition and Parasitic Ability of Root-Knot Nematodes
This simplified representation highlights the three main steps used to detect potential lateral gene transfers of non-metazoan origin in root-knot nematodes. The three bioinformatics steps are represented within blue rectangles while initial, intermediate and final results are represented within white rectangles. Starting from 34,780 root-knot nematode proteins, step 1 consisted in eliminating redundancy at 100% identity and detecting orthologs in proteomes of 14 other metazoan species. Step 2 consisted in “blasting” all proteins that passed step 1 against the NCBI’s NR database completed with the whole proteomes of the two root-knot nematodes. Only proteins that returned at least 50% of non-metazoan hits among their 10 best blast hits were kept at this stage. Proteins that showed more than 80% identity with non-metazoan hits on at least half of their length were considered as contaminants and eliminated. All proteins passing step 2 were sent for automated phylogenetic analysis using FIGENIX pipeline. Topologies compatible with a lateral gene transfer were automatically searched among all generated trees using PhyloPattern. At the end of step 2 and of step 3, the total number of M. incognita protein-coding genes of non-metazoan origin, (including gene duplicates) and the proportion of the whole gene set are indicated in bold.