Assembling highly repetitive Xanthomonas TALomes using Oxford Nanopore sequencing

verfasst von

Annett Erkes, René P. Grove, Milena Žarković, Sebastian Krautwurst, Ralf Koebnik, Richard D. Morgan, Geoffrey G. Wilson, Martin Hölzer, Manja Marz, Jens Boch, Jan Grau

Abstract

Background: 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. Results: 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 reads and longer PacBio reads are insufficient to fully resolve the genome. While ONT reads are perfectly suited to yield highly contiguous genomes, they suffer from a specific error profile within homopolymers. To still yield complete and correct TALomes from ONT assemblies, we present a computational correction pipeline specifically tailored to TALE genes, which yields at least comparable accuracy as Illumina-based polishing. We further systematically assess the ONT-based pipeline for its multiplexing capacity and find that, combined with computational correction, the complete TALome of Xoo PXO35 could have been reconstructed from less than 20,000 ONT reads. Conclusions: Our results indicate that multiplexed ONT sequencing combined with a computational correction of TALE genes constitutes a highly capable tool for characterizing the TALomes of huge collections of Xanthomonas strains in the future.

Organisationseinheit(en)

Abteilung Pflanzenbiotechnologie

Externe Organisation(en)

Martin-Luther-Universität Halle-Wittenberg
Friedrich-Schiller-Universität Jena
Université Montpellier
New England Biolabs
Robert Koch-Institut (RKI)

Typ

Artikel

Journal

BMC GENOMICS

Band

24

ISSN

1471-2164

Publikationsdatum

12.2023

Publikationsstatus

Veröffentlicht

Peer-reviewed

Ja

ASJC Scopus Sachgebiete

Biotechnologie, Genetik

Elektronische Version(en)

https://doi.org/10.1186/s12864-023-09228-1 (Zugang: Offen)