@article{fdi:010064926,
  title = {{Q}ue{TAL} : a suite of tools to classify and compare {TAL} effectors functionally and phylogenetically},
  author = {{P}erez-{Q}uintero, {A}lvaro and {L}amy, {L}. and {G}ordon, {J}. {L}. and {E}scalon, {A}. and {C}unnac, {S}{\'e}bastien and {S}zurek, {B}oris and {G}agnevin, {L}.},
  editor = {},
  language = {{ENG}},
  abstract = {{T}ranscription {A}ctivator-{L}ike ({TAL}) effectors from {X}anthomonas plant pathogenic bacteria can bind to the promoter region of plant genes and induce their expression. {DNA}-binding specificity is governed by a central domain made of nearly identical repeats, each determining the recognition of one base pair via two amino acid residues (a.k.a. {R}epeat {V}ariable {D}i-residue, or {RVD}). {K}nowing how {TAL} effectors differ from each other within and between strains would be useful to infer functional and evolutionary relationships, but their repetitive nature precludes reliable use of traditional alignment methods. {T}he suite {Q}ue{TAL} was therefore developed to offer tailored tools for comparison of {TAL} effector genes. {T}he program {D}is{TAL} considers each repeat as a unit, transforms a {TAL} effector sequence into a sequence of coded repeats and makes pair-wise alignments between these coded sequences to construct trees. {T}he program {F}unc{TAL} is aimed at finding {TAL} effectors with similar {DNA}-binding capabilities. {I}t calculates correlations between position weight matrices of potential target {DNA} sequence predicted from the {RVD} sequence, and builds trees based on these correlations. {T}he programs accurately represented phylogenetic and functional relationships between {TAL} effectors using either simulated or literature-curated data. {W}hen using the programs on a large set of {TAL} effector sequences, the {D}is{TAL} tree largely reflected the expected species phylogeny. {I}n contrast, {F}unc{TAL} showed that {TAL} effectors with similar binding capabilities can be found between phylogenetically distant taxa. {T}his suite will help users to rapidly analyse any {TAL} effector genes of interest and compare them to other available {TAL} genes and should improve our understanding of {TAL} effectors evolution.},
  keywords = {{TAL} effectors ; phylogeny ; {R}alstonia ; {X}anthomonas ; functional convergence ; {EBE}},
  booktitle = {},
  journal = {{F}rontiers in {P}lant {S}cience},
  volume = {6},
  numero = {},
  pages = {art. 545 [16 p.]},
  ISSN = {1664-462{X}},
  year = {2015},
  DOI = {10.3389/fpls.2015.00545},
  URL = {https://www.documentation.ird.fr/hor/fdi:010064926},
}