@article{fdi:010079030,
  title = {{E}volutionarily conserved plant genes responsive to root-knot nematodes identified by comparative genomics},
  author = {{M}ota, {A}. {P}. {Z}. and {F}ernandez, {D}iana and {A}rraes, {F}. {B}. {M}. and {P}etitot, {A}nne-{S}ophie and de {M}elo, {B}. {P}. and de {S}a, {M}. {E}. {L}. and {G}rynberg, {P}. and {S}araiva, {M}. {A}. {P}. and {G}uimaraes, {P}. {M}. and {B}rasileiro, {A}. {C}. {M}. and {A}lbuquerque, {E}. {V}. {S}. and {D}anchin, {E}. {G}. {J}. and {G}rossi-de-{S}a, {M}. {F}.},
  editor = {},
  language = {{ENG}},
  abstract = {{R}oot-knot nematodes ({RKN}s, genus {M}eloidogyne) affect a large number of crops causing severe yield losses worldwide, more specifically in tropical and sub-tropical regions. {S}everal plant species display high resistance levels to {M}eloidogyne, but a general view of the plant immune molecular responses underlying resistance to {RKN}s is still lacking. {C}ombining comparative genomics with differential gene expression analysis may allow the identification of widely conserved plant genes involved in {RKN} resistance. {T}o identify genes that are evolutionary conserved across plant species, we used {O}rtho{F}inder to compared the predicted proteome of 22 plant species, including important crops, spanning 214 {M}yr of plant evolution. {O}verall, we identified 35,238 protein orthogroups, of which 6,132 were evolutionarily conserved and universal to all the 22 plant species ({PLA}nts {C}ommon {O}rthogroups-{PLACO}). {T}o identify host genes responsive to {RKN} infection, we analyzed the {RNA}-seq transcriptome data from {RKN}-resistant genotypes of a peanut wild relative ({A}rachis stenosperma), coffee ({C}offea arabica {L}.), soybean ({G}lycine max {L}.), and {A}frican rice ({O}ryza glaberrima {S}teud.) challenged by {M}eloidogyne spp. using {E}dge{R} and {DES}eq tools, and we found 2,597 ({O}. glaberrima), 743 ({C}. arabica), 665 ({A}. stenosperma), and 653 ({G}. max) differentially expressed genes ({DEG}s) during the resistance response to the nematode. {DEG}s' classification into the previously characterized 35,238 protein orthogroups allowed identifying 17 orthogroups containing at least one {DEG} of each resistant {A}rachis, coffee, soybean, and rice genotype analyzed. {O}rthogroups contain 364 {DEG}s related to signaling, secondary metabolite production, cell wall-related functions, peptide transport, transcription regulation, and plant defense, thus revealing evolutionarily conserved {RKN}-responsive genes. {I}nterestingly, the 17 {DEG}s-containing orthogroups (belonging to the {PLACO}) were also universal to the 22 plant species studied, suggesting that these core genes may be involved in ancestrally conserved immune responses triggered by {RKN} infection. {T}he comparative genomic approach that we used here represents a promising predictive tool for the identification of other core plant defense-related genes of broad interest that are involved in different plant-pathogen interactions.},
  keywords = {{T}ranscriptome ; {M}eloidogyne ; {A}rachis ; {S}oybean ; {C}offee ; {R}ice},
  booktitle = {},
  journal = {{M}olecular {G}enetics and {G}enomics},
  volume = {295},
  numero = {4},
  pages = {1063--1078},
  ISSN = {1617-4615},
  year = {2020},
  DOI = {10.1007/s00438-020-01677-7},
  URL = {https://www.documentation.ird.fr/hor/fdi:010079030},
}