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PPN-specific genes in M. incognita
Identification of genes specific to plant-parasitic nematodes (PPN) in the genome of the root-knot nematode Meloidogyne incognita.
The identification is based on an orthofinder analysis of 63 species (61 nematodes + 2 tardigrades). Specificity to PPN is verified by a Diamond similarity search against the NCBI's nr library.
The identified genes are then annotated and filtered according to various different criteria.
This dataverse gathers all the intermediate results and further annotations.
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1 to 10 of 15 Results
Jul 3, 2020
Danchin, Etienne; Da Rocha, Martine, 2020, "M. incognita protein-coding genes expression patterns", https://doi.org/10.15454/YM2DHE, Portail Data INRAE, V1
M. incognita protein-coding genes expression values across 4 life stages in triplicates. Life stages are as follows: - W: eggs - J2: pre-parasitic infective juveniles - J3: infective juveniles (mic of late J2, J3 and J4) - Fem: adult female Two tables are given, one with the raw...
Aug 18, 2020
Danchin, Etienne; Rancurel, Corinne, 2020, "Horizontal gene transfer candidates in M. incognita", https://doi.org/10.15454/W6SWZH, Portail Data INRAE, V1, UNF:6:wuWOjB++Puk5yJOSrDfxWw== [fileUNF]
Analysis of horizontal gene transfer (HGT) candidates on the M. incognita predicted proteins from (Blanc-Mathieu et al. 2017), using Alienness (Rancurel et al. 2017) on a Diamond search against the NCBI's nr library. The following parameters were used in Alienness Taxonomic group...
Aug 18, 2020
Danchin, Etienne, 2020, "Meloidogyne incognita Interproscan annotation", https://doi.org/10.15454/9BFFKG, Portail Data INRAE, V1
Interproscan annotation on the 43,718 predicted proteins in the genome of the root-knot nematode Meloidogyne incognita (Blanc-Mathieu et al. 2017, PLoS Genetics). vesrion used: interproscan-5.29-68.0 options used: -dp Disables use of the precalculated match lookup service = all m...
Aug 18, 2020
Danchin, Etienne, 2020, "M. incongnita proteins specific to plant-parasitic nemaotdes", https://doi.org/10.15454/I9MWRS, Portail Data INRAE, V1
Accession numbers of M. incognita predicted proteins having predicted homologs only in other plant-parasitic nematodes (PPN) or being M. incognita-specific.
Aug 18, 2020
Danchin, Etienne; Rancurel, Corinne; Togawa, Roberto, 2020, "Taxonomic distribution of M. incognita Diamond hits against the NCBI's nr library", https://doi.org/10.15454/FROF42, Portail Data INRAE, V1
Taxonomic distribution of M. incognita Diamond hits against the NCBI's nr library. The taxonomy has been determined by Diamond LCA algorithm via outformat 102. Two reports are available: 1- all the M. incognita proteins as queries 2- PPN-specific M. incognita proteins as queries...
Aug 18, 2020
Danchin, Etienne, 2020, "PPN-specific M. incognita proteins with no hits against NR", https://doi.org/10.15454/48436V, Portail Data INRAE, V1
Accession numbers of M. incognita proteins specific to plant-parasitic nematodes as determined by the orthofinder analysis and returning no significant hits against the NCBI's NR according to Diamond.
Aug 18, 2020
Danchin, Etienne, 2020, "MERCI effector-enriched motifs in the 100 first amino acids of M. incognita proteins", https://doi.org/10.15454/LMY6LV, Portail Data INRAE, V1
MERCI effector-enriched motifs in the 100 first amino acids of M. incognita proteins M. incognita proteins with at least one of the 4 motifs identified as enriched in the known effector proteins as described in (Vens, Rosso, Danchin, Bioinformatics, 2011)
Aug 18, 2020
Danchin, Etienne, 2020, "M. incognita candidate effector proteins", https://doi.org/10.15454/CSTXU2, Portail Data INRAE, V1
Accession numbers of M. incognita candidate effectors. These proteins are predicted to be secreted based on the presence of a signal peptide for secretion and absence of transmembrane domains. Furthermore at least one motif known to be enriched in effector proteins is present in...
Aug 18, 2020
Danchin, Etienne; Grynberg, Priscila; Togawa, Roberto, 2020, "Annotated list of species used in this study", https://doi.org/10.15454/IIAQOW, Portail Data INRAE, V1
Annotated list of the 63 species used in the Orthofinder comparative analysis of nematodes (61 species) and two tardigrade species as out-groups. Description: Lines 1-64, definition of columns - Abbrev Species: abbreviated species name. Species identifiers used in all the Orthofi...
Aug 18, 2020
Danchin, Etienne; Grynberg, Priscila; Togawa, Roberto, 2020, "Orthofinder rooted species tree", https://doi.org/10.15454/MBMOQC, Portail Data INRAE, V1
Rooted phylogenomics species tree performed by Orthofinder on the 63 species, in Newick format. An annotated version of the tree in PDF format, produced with iTOL is also available.
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