A recently collectedXanthomonas translucensisolate encodes TAL effectors distinct from older, less virulent isolates DOI Creative Commons
Diego E. Gutierrez-Castillo, Emma Barrett, R. H. Roberts

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: Sept. 16, 2023

ABSTRACT Xanthomonas translucens, the causal agent of bacterial leaf streak disease (BLS) in cereals, is a re-emerging pathogen that becoming increasingly destructive across world. While BLS has caused yield losses past, there anecdotal evidence newer isolates may be more virulent. We observed two translucens collected from sites Colorado are aggressive on current wheat and barley varieties compared to older isolates, we hypothesize genetic changes between recent contribute differences isolate aggressiveness. To test this, phenotyped genetically characterized X. 2018, which designated CO236 (from barley) CO237 wheat). Using pathovar-specific phenotyping PCR primers, determined belongs pathovar undulosa. sequenced full genomes using Oxford Nanopore long-read sequencing, their whole against published genomes. This analysis confirmed our designations for Xtt Xtu CO237, showed that, at whole-genome level, were no obvious genomic structural other respective Focusing undulosa (Xtu CO237), then putative Type III effectors among all available found they highly conserved. However, striking presence sequence various transcription activator-like (TALE) genomes, correlate with virulence. Here, explore potential implications these virulence factors, provide possible explanations increased recently-emerged isolates. Data Summary A list accessions used this study can Supplemental Table S1. sequences deposited GenBank (Accession: PRJNA1017868 PRJNA1017870, respectively). Software packages custom Conda environment S4. The dataset MinION reads Dryad, https://doi.org/10.5061/dryad.d51c5b06q . Custom bash Python scripts effector ( https://github.com/robertslabcsu/xanthanalysis.git ). Impact statement destructive, cereal crops known resistance or methods chemical control. Recent have emphasizes need understand how evolves, interacts its host, find new ways manage disease. identify factors aggressiveness recently impacts understanding host range evolution.

Language: Английский

Bioinformatics Applications in Identifying Plant Disease Resistance Genes for Crop Yield Enhancement DOI
Raghunath Satpathy

Published: Jan. 1, 2025

Language: Английский

Citations

0
Comparative genomics of the Liberibacter genus reveals widespread diversity in genomic content and positive selection history DOI Creative Commons
Tiffany N. Batarseh, Sarah N. Batarseh, Abraham Morales‐Cruz

et al.

Frontiers in Microbiology, Journal Year: 2023, Volume and Issue: 14

Published: June 26, 2023

‘ Candidatus Liberibacter’ is a group of bacterial species that are obligate intracellular plant pathogens and cause Huanglongbing disease citrus trees Zebra Chip in potatoes. Here, we examined the extent intra- interspecific genetic diversity across genus using comparative genomics. Our approach wide set Liberibacter genome sequences including five pathogenic one not known to disease. By performing genomics analyses, sought understand evolutionary history this identify genes or regions may affect pathogenicity. With 52 genomes, performed genomics, measured rearrangement, completed statistical tests positive selection. We explored markers genus, such as average nucleotide identity whole genome. These analyses revealed highest intraspecific amongst Ca. solanacearum’ species, which also has largest host range. identified sets core accessory within each ratio nonsynonymous synonymous mutations (dN/dS) genes. ten with evidence selection Tad complex, have been previously implicated being highly divergent L. capsica’ based on high values dN.

Language: Английский

Citations

4
Population Genomics Reveals an Emerging Lineage of Xanthomonas perforans on Pepper DOI
Aastha Subedi,

Laura Belen Tapia de la Barrera,

Melanie L. Lewis Ivey

et al.

Phytopathology, Journal Year: 2023, Volume and Issue: 114(1), P. 241 - 250

Published: July 11, 2023

Xanthomonas perforans—the dominant causal agent of bacterial leaf spot tomato—is an emerging pathogen pepper, indicative a potential host expansion across the southeastern United States. However, studies genetic diversity and evolution X. perforans from pepper remain limited. In this study, whole-genome sequences 35 strains isolated four fields two transplant facilities southwest Florida between 2019 2021 were used to compare genomic divergence, evolution, variation in type III secreted effectors. Phylogenetic analysis based on core genes revealed that all formed one cluster with tomato Alabama Turkey closely related Indiana, Mexico, Louisiana. The planta population growth Louisiana, mesophyll was par euvesicatoria strains. Molecular clock dated their emergence approximately 2017. While varied copper tolerance, sequenced harbored avrHah1 transcription activation-like effector located conjugative plasmid, not previously reported Florida. Our findings suggest there is geographically distributed lineage has background cause disease pepper. Moreover, study clarifies adaptive variants could help forecast such enable immediate or preemptive intervention.

Language: Английский

Citations

4
Isolation, molecular identification, and genomic analysis of Mangrovibacter phragmitis strain ASIOC01 from activated sludge harboring the bioremediation prowess of glycerol and organic pollutants in high-salinity DOI Creative Commons
Hong Soon Chin,

Narendrakumar Ravi Varadharajulu,

Zhi-Han Lin

et al.

Frontiers in Microbiology, Journal Year: 2024, Volume and Issue: 15

Published: June 25, 2024

The physiological and genotypic characteristics of Mangrovibacter (MGB) remain largely unexplored, including their distribution abundance within ecosystems. M. phragmitis (MPH) ASIOC01 was successfully isolated from activated sludge (AS), which pre-enriched by adding 1,3-dichloro-2-propanol 3-chloro-1,2-propanediol as carbon sources. new isolate, MPH ASIOC01, exhibited resilience in a medium containing sodium chloride concentration up to 11% (with optimal growth observed at 3%) effectively utilizing glycerol sole source. However, species delimitation MGBs remains challenging due high 16S rRNA sequence similarity (greater than 99% ANI) among different MGBs. In contrast, the housekeeping gene discrepancies, tryptophan synthase beta chain can serve robust marker for fast Furthermore, complete genome fully sequenced circlized single contig using PacBio HiFi sequencing method. Comparative genomics revealed genes potentially associated with various phenotypic features MGBs, such nitrogen-fixing, phosphate-solubilizing, cellulose-digesting, Cr-reducing, salt tolerance. Computational analysis suggested that may have undergone horizontal transfer events, possibly contributing unique traits antibiotic resistance. Finally, our findings also disclosed introduction into AS assist remediation wastewater chemical oxygen demand, evaluated gas chromatograph-mass spectrometry. To best knowledge, this study offers most comprehensive understanding date.

Language: Английский

Citations

1
Unlocking the Mycobacteroides abscessus pan-genome using computational tools: insights into evolutionary dynamics and lifestyle DOI

Mistu Karmakar,

Saubashya Sur

Antonie van Leeuwenhoek, Journal Year: 2024, Volume and Issue: 118(1)

Published: Nov. 23, 2024

Language: Английский

Citations

1
A recently collected Xanthomonas translucens isolate encodes TAL effectors distinct from older, less virulent isolates DOI Creative Commons
Diego E. Gutierrez-Castillo, Emma Barrett, R. H. Roberts

et al.

Microbial Genomics, Journal Year: 2024, Volume and Issue: 10(1)

Published: Jan. 8, 2024

Xanthomonas translucens, the causal agent of bacterial leaf streak disease (BLS) in cereals, is a re-emerging pathogen that becoming increasingly destructive across world. While BLS has caused yield losses past, there anecdotal evidence newer isolates may be more virulent. We observed two X. translucens collected from sites Colorado, USA, are aggressive on current wheat and barley varieties compared to older isolates, we hypothesize genetic changes between recent contribute differences isolate aggressiveness. To test this, phenotyped genetically characterized Colorado 2018, which designated CO236 (from barley) CO237 wheat). Using pathovar-specific phenotyping PCR primers, determined belongs pathovar (Xtt) undulosa (Xtu). sequenced full genomes using Oxford Nanopore long-read sequencing, their whole against published genomes. This analysis confirmed our designations for Xtt Xtu CO237, showed that, at whole-genome level, were no obvious genomic structural other respective Focusing (Xtu CO237), then putative type III effectors among all available found they highly conserved. However, striking presence sequence various transcription activator-like genomes, correlate with virulence. Here, explore potential implications these virulence factors, provide possible explanations increased recently emerged isolates.

Language: Английский

Citations

0
Exploring the pangenome landscape of Mycobacterium avium complex: insights into phylogeny and lifestyle DOI
Anindita Banerjee, Saubashya Sur

Biologia, Journal Year: 2024, Volume and Issue: 79(12), P. 3663 - 3676

Published: Oct. 14, 2024

Language: Английский

Citations

0
A recently collectedXanthomonas translucensisolate encodes TAL effectors distinct from older, less virulent isolates DOI Creative Commons
Diego E. Gutierrez-Castillo, Emma Barrett, R. H. Roberts

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: Sept. 16, 2023

ABSTRACT Xanthomonas translucens, the causal agent of bacterial leaf streak disease (BLS) in cereals, is a re-emerging pathogen that becoming increasingly destructive across world. While BLS has caused yield losses past, there anecdotal evidence newer isolates may be more virulent. We observed two translucens collected from sites Colorado are aggressive on current wheat and barley varieties compared to older isolates, we hypothesize genetic changes between recent contribute differences isolate aggressiveness. To test this, phenotyped genetically characterized X. 2018, which designated CO236 (from barley) CO237 wheat). Using pathovar-specific phenotyping PCR primers, determined belongs pathovar undulosa. sequenced full genomes using Oxford Nanopore long-read sequencing, their whole against published genomes. This analysis confirmed our designations for Xtt Xtu CO237, showed that, at whole-genome level, were no obvious genomic structural other respective Focusing undulosa (Xtu CO237), then putative Type III effectors among all available found they highly conserved. However, striking presence sequence various transcription activator-like (TALE) genomes, correlate with virulence. Here, explore potential implications these virulence factors, provide possible explanations increased recently-emerged isolates. Data Summary A list accessions used this study can Supplemental Table S1. sequences deposited GenBank (Accession: PRJNA1017868 PRJNA1017870, respectively). Software packages custom Conda environment S4. The dataset MinION reads Dryad, https://doi.org/10.5061/dryad.d51c5b06q . Custom bash Python scripts effector ( https://github.com/robertslabcsu/xanthanalysis.git ). Impact statement destructive, cereal crops known resistance or methods chemical control. Recent have emphasizes need understand how evolves, interacts its host, find new ways manage disease. identify factors aggressiveness recently impacts understanding host range evolution.

Language: Английский

Citations

0