@article{fdi:010087584,
  title = {{A}ssembling highly repetitive {X}anthomonas {TAL}omes using {O}xford {N}anopore sequencing},
  author = {{E}rkes, {A}. and {G}rove, {R}. {P}. and {Z}arkovic, {M}. and {K}rautwurst, {S}. and {K}oebnik, {R}alf and {M}organ, {R}. {D}. and {W}ilson, {G}. {G}. and {H}olzer, {M}. and {M}arz, {M}. and {B}och, {J}. and {G}rau, {J}.},
  editor = {},
  language = {{ENG}},
  abstract = {{B}ackground {M}ost plant-pathogenic {X}anthomonas bacteria harbor transcription activator-like effector ({TALE}) genes, which function as transcriptional activators of host plant genes and support infection. {T}he entire repertoire of up to 29 {TALE} genes of a {X}anthomonas strain is also referred to as {TAL}ome. {T}he {DNA}-binding domain of {TALE}s is comprised of highly conserved repeats and {TALE} genes often occur in gene clusters, which precludes the assembly of {TALE}-carrying {X}anthomonas genomes based on standard sequencing approaches. {R}esults {H}ere, we report the successful assembly of the 5 {M}bp genomes of five {X}anthomonas strains from {O}xford {N}anopore {T}echnologies ({ONT}) sequencing data. {F}or one of these strains, {X}anthomonas oryzae pv. oryzae ({X}oo) {PXO}35, we illustrate why {I}llumina short reads and longer {P}ac{B}io reads are insufficient to fully resolve the genome. {W}hile {ONT} reads are perfectly suited to yield highly contiguous genomes, they suffer from a specific error profile within homopolymers. {T}o still yield complete and correct {TAL}omes from {ONT} assemblies, we present a computational correction pipeline specifically tailored to {TALE} genes, which yields at least comparable accuracy as {I}llumina-based polishing. {W}e further systematically assess the {ONT}-based pipeline for its multiplexing capacity and find that, combined with computational correction, the complete {TAL}ome of {X}oo {PXO}35 could have been reconstructed from less than 20,000 {ONT} reads. {C}onclusions {O}ur results indicate that multiplexed {ONT} sequencing combined with a computational correction of {TALE} genes constitutes a highly capable tool for characterizing the {TAL}omes of huge collections of {X}anthomonas strains in the future.},
  keywords = {{B}acteria ; {G}enome assembly ; {T}ranscription activator-like effectors ; {S}equencing technologies ; {O}xford {N}anopore {T}echnologies},
  booktitle = {},
  journal = {{BMC} {G}enomics},
  volume = {24},
  numero = {1},
  pages = {151 [18 ]},
  ISSN = {1471-2164},
  year = {2023},
  DOI = {10.1186/s12864-023-09228-1},
  URL = {https://www.documentation.ird.fr/hor/fdi:010087584},
}