“…Transcription activator-like effectors (TALEs) constitute the largest effector family in X. oryzae with up to 19 ( Xoo ) and 29 ( Xoc ) different TALEs within one strain [ 3 – 5 ]. TALEs function inside the plant nucleus as transcription factors to induce transcription of specific target genes [ 6 , 7 ]. The outstanding feature of TALEs is their modular DNA-binding domain, consisting of a variable number of 34 amino acid-repeats with each repeat facilitating binding to one DNA base in a sequential fashion [ 8 , 9 ].…”
Section: Introductionmentioning
confidence: 99%
“…TALEs interact with subunits of the transcription initiation factor IIA [ 12 ] and initiate transcription via a C-terminal acidic activation domain in a somewhat defined distance downstream of the TALE binding site [ 13 , 14 ]. Accordingly, bioinformatic prediction of TALE target sites in plant promoters in combination with gene expression analysis of host plant genes after Xanthomonas infection is the standard procedure to identify potential virulence targets of TALEs [ 4 , 7 , 15 , 16 ]. Fig.…”
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.
“…Transcription activator-like effectors (TALEs) constitute the largest effector family in X. oryzae with up to 19 ( Xoo ) and 29 ( Xoc ) different TALEs within one strain [ 3 – 5 ]. TALEs function inside the plant nucleus as transcription factors to induce transcription of specific target genes [ 6 , 7 ]. The outstanding feature of TALEs is their modular DNA-binding domain, consisting of a variable number of 34 amino acid-repeats with each repeat facilitating binding to one DNA base in a sequential fashion [ 8 , 9 ].…”
Section: Introductionmentioning
confidence: 99%
“…TALEs interact with subunits of the transcription initiation factor IIA [ 12 ] and initiate transcription via a C-terminal acidic activation domain in a somewhat defined distance downstream of the TALE binding site [ 13 , 14 ]. Accordingly, bioinformatic prediction of TALE target sites in plant promoters in combination with gene expression analysis of host plant genes after Xanthomonas infection is the standard procedure to identify potential virulence targets of TALEs [ 4 , 7 , 15 , 16 ]. Fig.…”
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.
“…The zf-BED domains of XA1, XA2, and XA14 interact with themselves and also one another, which indicates homodimers and heterodimers may be formed in the resistance process ( Figure 2D ; Zhang et al, 2020 ). It has been reported that many transcription activator-like effectors (TALEs) are crucial for Xa1 -mediated resistance, but the physical interaction between them is still uncovered yet (Zhao et al, 2016 ; Zhang et al, 2022 ).…”
Section: Atypical Nlrs Confer Resistance In Diverse Mannersmentioning
Pathogens are important threats to many plants throughout their lifetimes. Plants have developed different strategies to overcome them. In the plant immunity system, nucleotide-binding domain and leucine-rich repeat-containing proteins (NLRs) are the most common components. And recent studies have greatly expanded our understanding of how NLRs function in plants. In this review, we summarize the studies on the mechanism of NLRs in the processes of effector recognition, resistosome formation, and defense activation. Typical NLRs are divided into three groups according to the different domains at their N termini and function in interrelated ways in immunity. Atypical NLRs contain additional integrated domains (IDs), some of which directly interact with pathogen effectors. Plant NLRs evolve with pathogen effectors and exhibit specific recognition. Meanwhile, some NLRs have been successfully engineered to confer resistance to new pathogens based on accumulated studies. In summary, some pioneering processes have been obtained in NLR researches, though more questions arise as a result of the huge number of NLRs. However, with a broadened understanding of the mechanism, NLRs will be important components for engineering in plant resistance improvement.
“…TALEs interact with subunits of the transcription initiation factor IIA (12) and initiate transcription via a C-terminal acidic activation domain in a somewhat defined distance downstream of the TALE binding site (13,14). Accordingly, bioinformatic prediction of TALE target sites in plant promoters in combination with gene expression analysis of host plant genes after Xanthomonas infection is the standard procedure to identify potential virulence targets of TALEs (4,7,15,16). Different strains of Xoo, Xoc and other Xanthomonads carry individual repertoires of TALEs which evolve by base substitution in RVD codons, recombination between TALEs and deletion of repeats within a TALE (17)(18)(19)(20).…”
Section: Introductionmentioning
confidence: 99%
“…Transcription activator-like effectors (TALEs) constitute the largest effector family in X. oryzae with up to 19 ( Xoo ) and 29 ( Xoc ) different TALEs within one strain (3–5). TALEs function inside the plant nucleus as transcription factors to induce transcription of specific target genes (6, 7). The outstanding feature of TALEs is their modular DNA-binding domain, consisting of a variable number of 34 amino acid-repeats with each repeat facilitating binding to one DNA base in a sequential fashion (8, 9).…”
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. 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. 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.
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