Assembling highly repetitive Xanthomonas TALomes using Oxford Nanopore sequencing DOI Creative Commons
Annett Erkes, René Grove, Milena Žarković

и другие.

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2022, Номер unknown

Опубликована: Авг. 18, 2022

Abstract 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 up to 29 TALE a strain is also referred TALome. DNA-binding domain TALEs comprised highly conserved repeats often occur in gene clusters, precludes the assembly TALE-carrying genomes based on standard sequencing approaches. Here, we report successful 5 Mbp five strains from Oxford Nanopore Technologies (ONT) data. For one these strains, oryzae pv. ( Xoo ) PXO35, illustrate why Illumina short reads longer PacBio are insufficient fully resolve genome. While ONT perfectly suited yield contiguous genomes, they suffer specific error profile within homopolymers. To still complete correct TALomes assemblies, present computational correction pipeline specifically tailored yields at least comparable accuracy Illumina-based polishing. We further systematically assess ONT-based for its multiplexing capacity find that, combined with correction, TALome PXO35 could have been reconstructed less than 20,000 reads. Our results indicate that multiplexed constitutes capable tool characterizing huge collections future.

Язык: Английский

Overexpression of ORP1C gene increases the rice resistance to Xanthomonas oryzae pv. oryzae through negatively regulating transcription activator-like effectors translocation DOI Creative Commons
Hongtao Ji,

Lan Zhou,

Ruibin Yang

и другие.

Plant Signaling & Behavior, Год журнала: 2024, Номер 20(1)

Опубликована: Дек. 24, 2024

Bacterial leaf blight (BLB) caused by Xanthomonas oryzae pv. (Xoo) has shown a high incidence rate in rice fields recent years. Rice resistance breeding is considered as the most effective method for achieving economical and sustainable management of BLB disease. The essential basis rooted exploration genes clarification molecular mechanisms that underlie Xoo resistance. In our previous research, we showed outer protein XopZ oxysterol-binding related ORP1C collaboratively regulate compatible interaction between strain PXO99 Nipponbare rice, but deeper regulatory remain unknown. this study, successfully constructed overexpression using plant binary expression vector pCAMBIA1301. Through series virulence effector translocation detections Xoo-rice interactions, revealed gene largely increases to multiple strains from different countries regions. Mechanistically, plays resistant role through negatively regulating transcription activator-like effectors (TALEs) translocation, become potential candidate resource disease-resistant rice. Further studies also indicated PXO99-Nipponbare modulating TALEs translocation.

Язык: Английский

Процитировано

0
Genome Resource for the Highly Virulent Xanthomonas oryzae pv. oryzae Strain HN2011 from China DOI Creative Commons
Pu Zhao, Quanlin Li,

Han Yin

и другие.

PhytoFrontiers™, Год журнала: 2023, Номер 3(4), С. 855 - 858

Опубликована: Май 2, 2023

Xanthomonas oryzae pv. ( Xoo) is the causal bacterium of rice bacterial blight (BB), which one most destructive diseases worldwide. Although more than 40 BB resistance genes Xa genes) have been identified, only a few conferring broad (e.g., Xa4 and Xa21) widely used for breeding in Asia. The narrow genetic basis cultivars has resulted emergence new pathogenic strains that can overcome commonly grown derived from programs. For example, Xoo strain HN2011, was isolated Hainan (China), mediated by multiple genes, including Xa21. We herein present complete genome sequence HN2011 generated Nanopore sequencing. genomic data will be useful elucidating variations contribute to clarifying interaction between rice. [Formula: see text] Copyright © 2023 Author(s). This an open access article distributed under CC BY-NC-ND 4.0 International license .

Язык: Английский

Процитировано

0
High genomic plasticity and unique features ofXanthomonas translucenspv.graminisrevealed through comparative analysis of complete genome sequences DOI Creative Commons
Florian Goettelmann, Ralf Koebnik, Verónica Román-Reyna

и другие.

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2023, Номер unknown

Опубликована: Июнь 30, 2023

Abstract Background Xanthomonas translucens pv. graminis ( Xtg ) is a major bacterial pathogen of economically important forage grasses, causing severe yield losses. So far, genomic resources for this pathovar consisted mostly draft genome sequences, and only one complete sequence was available, preventing comprehensive comparative analyses. Such analyses are essential in understanding the mechanisms involved virulence pathogens to identify factors pathogenicity. Results In study, we produced high-quality, sequences four strains , complementing recently obtained pathotype strain. These allowed analysis, which revealed high plasticity with many chromosomal rearrangements, although were highly related, 99.9 100% average nucleotide identity. A number transposases exclusively found corresponded 413 457 insertion/excision transposable elements per mobile genetic likely be observed may play an role adaptation . The lack type IV secretion system, it possessed smallest set III effectors species. However, three XopE XopX family found, while other pathovars species two or less present. Additional genes that specific identified, including unique minor pilins pilus, 17 TonB-dependent receptors (TBDRs), 11 degradative enzymes. Conclusion results suggest adaptability conferred by abundance elements, have led loss features. Conserved features further investigation will help determine pathogenicity host

Язык: Английский

Процитировано

0
High genomic plasticity and unique features of Xanthomonas translucens pv. graminis revealed through comparative analysis of complete genome sequences DOI Creative Commons
Florian Goettelmann, Ralf Koebnik, Verónica Román-Reyna

и другие.

BMC Genomics, Год журнала: 2023, Номер 24(1)

Опубликована: Дек. 5, 2023

Abstract Background Xanthomonas translucens pv. graminis ( Xtg ) is a major bacterial pathogen of economically important forage grasses, causing severe yield losses. So far, genomic resources for this pathovar consisted mostly draft genome sequences, and only one complete sequence was available, preventing comprehensive comparative analyses. Such analyses are essential in understanding the mechanisms involved virulence pathogens to identify factors pathogenicity. Results In study, we produced high-quality, sequences four strains , complementing recently obtained pathotype strain. These allowed analysis, which revealed high plasticity with many chromosomal rearrangements, although were highly related. A number transposases exclusively found corresponded 413 457 insertion/excision transposable elements per mobile genetic likely be observed may play an role adaptation . The lack type IV secretion system, it possessed smallest set III effectors species. However, three XopE XopX family found, while other pathovars species two or less present. Additional genes that specific identified, including unique minor pilins pilus, 17 TonB-dependent receptors (TBDRs), 11 plant cell wall degradative enzymes. Conclusion results suggest adaptability conferred by abundance elements, could crucial adaptation. large amount such compared could, at least partially, explain its broad host range. Conserved features further investigation will help determine pathogenicity

Язык: Английский

Процитировано

0
Assembling highly repetitive Xanthomonas TALomes using Oxford Nanopore sequencing DOI Creative Commons
Annett Erkes, René Grove, Milena Žarković

и другие.

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2022, Номер unknown

Опубликована: Авг. 18, 2022

Abstract 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 up to 29 TALE a strain is also referred TALome. DNA-binding domain TALEs comprised highly conserved repeats often occur in gene clusters, precludes the assembly TALE-carrying genomes based on standard sequencing approaches. Here, we report successful 5 Mbp five strains from Oxford Nanopore Technologies (ONT) data. For one these strains, oryzae pv. ( Xoo ) PXO35, illustrate why Illumina short reads longer PacBio are insufficient fully resolve genome. While ONT perfectly suited yield contiguous genomes, they suffer specific error profile within homopolymers. To still complete correct TALomes assemblies, present computational correction pipeline specifically tailored yields at least comparable accuracy Illumina-based polishing. We further systematically assess ONT-based for its multiplexing capacity find that, combined with correction, TALome PXO35 could have been reconstructed less than 20,000 reads. Our results indicate that multiplexed constitutes capable tool characterizing huge collections future.

Язык: Английский

Процитировано

0