biostudies-literatureErkes AAgence Nationale de la RechercheDeutsche ForschungsgemeinschaftThüringer Ministerium für Wirtschaft, Wissenschaft und Digitale GesellschaftMartin-Luther-Universität Halle-Wittenberg151https://www.ebi.ac.uk/biostudies/studies/S-EPMC10045945biostudies-literatureUnknown24(1)<h4>Background</h4>Most plant-pathogenic Xanthomonas bacteria harbor transcription activator-like effector (TALE) genes, which function as transcriptional activators of host plant genes and support infection. The entire repertoire of up to 29 TALE genes of a Xanthomonas strain is also referred to as TALome. The DNA-binding domain of TALEs is comprised of highly conserved repeats and TALE genes often occur in gene clusters, which precludes the assembly of TALE-carrying Xanthomonas genomes based on standard sequencing approaches.<h4>Results</h4>Here, we report the successful assembly of the 5 Mbp genomes of five Xanthomonas strains from Oxford Nanopore Technologies (ONT) sequencing data. For one of these strains, Xanthomonas oryzae pv. oryzae (Xoo) PXO35, we illustrate why Illumina short reaBMC genomicsAssembling highly repetitive Xanthomonas TALomes using Oxford Nanopore sequencing.PMC10045945DigLeben-5575/10-9ANR-2010-BLAN-1723GR 4587/1-2FZT 118/2BO 1496/8-2Krautwurst SWilson GGErkes AZarkovic MMorgan RDHolzer MGrau JBoch JMarz MGrove RPKoebnik RfalseAssembling highly repetitive Xanthomonas TALomes using Oxford Nanopore sequencing.<h4>Background</h4>Most plant-pathogenic Xanthomonas bacteria harbor transcription activator-like effector (TALE) genes, which function as transcriptional activators of host plant genes and support infection. The entire repertoire of up to 29 TALE genes of a Xanthomonas strain is also referred to as TALome. The DNA-binding domain of TALEs is comprised of highly conserved repeats and TALE genes often occur in gene clusters, which precludes the assembly of TALE-carrying Xanthomonas genomes based on standard sequencing approaches.<h4>Results</h4>Here, we report the successful assembly of the 5 Mbp genomes of five Xanthomonas strains from Oxford Nanopore Technologies (ONT) sequencing data. For one of these strains, Xanthomonas oryzae pv. oryzae (Xoo) PXO35, we illustrate why Illumina short rea2023-01-01T00:00:00Z2023 Mar2026-05-29T03:14:24.343Z2025-02-19T02:38:25.101ZS-EPMC100459453697364310.1186/s12864-023-09228-1