Pan-Genome Analysis of Effectors in Korean Strains of the Soybean Pathogen Xanthomonas citri pv. glycines

Xanthomonas citri pv. glycines is a major pathogen of soybean in Korea. Here, we analyzed pathogenicity genes based on a comparative genome analysis of five Korean strains and one strain from the United States, 8ra. Whereas all six strains had nearly identical profiles of carbohydrate-active enzymes, they varied in diversity and number of candidate type III secretion system effector (T3SE) genes. The five Korean strains were similar in their effectors, but differed from the 8ra strain. Across the six strains, transcription activator-like effectors (TALEs) showed diverse repeat sizes and at least six forms of the repeat variable di-residue (RVD) sequences, with differences not correlated with the origin of the strains. However, a phylogenetic tree based on the alignment of RVD sequences showed two distinct clusters with 17.5 repeats, suggesting that two distinct 17.5 RVD clusters have evolved, potentially to adapt Xcg to growth on distinct soybean cultivars. The predicted effector binding elements of the TALEs fell into six groups and were strongly overlapping in sequence, suggesting evolving target specificity of the binding domains in soybean cultivars. Our findings reveal the variability and adaptability of T3SEs in the Xcg strains and enhance our understanding of Xcg pathogenicity in soybean.

Download Full-text

Identification of virulence tal gene in the cotton pathogen, Xanthomonas citri pv. malvacearum strain Xss-V2-18

10.21203/rs.2.20197/v1 ◽

2020 ◽

Author(s):

Fazal Haq ◽

Syed Mashab Ali Shah ◽

Shiwang Xie ◽

Kunxuan Huang ◽

Wenxiu Ma ◽

...

Keyword(s):

Virulent Strain ◽

Evolutionary Relationship ◽

The United States ◽

In Planta ◽

Dna Encoding ◽

Transcription Activator ◽

Xanthomonas Citri ◽

Suicide Vector ◽

In Trans ◽

Highly Virulent

Abstract Background Bacterial blight of cotton (BBC), which is incited by Xanthomonas citri pv. malvacearum ( Xcm ), is a destructive disease in cotton. Transcription activator-like effectors (TALEs), encoded by tal -genes, play critical roles in the pathogenesis of xanthomonads. Characterized strains of cotton pathogenic Xcm harbor 6-13 different tal genes and only one of them is functionally decoded. Further identification of novel tal genes in Xcm strains with virulence contributions are prerequisite to decipher the Xcm -cotton interactionsResults In this study, we identified six tal genes in Xss-V 2 -18, a highly-virulent strain of Xcm from China, and assessed their role in BBC. RFLP-based Southern hybridization assays indicated that Xss-V 2 -18 harbors the six tal genes on a plasmid. The plasmid-encoded tal genes were isolated by cloning Bam HI fragments and screening clones by colony hybridization. The tal genes were sequenced by inserting a Tn 5 transposon in the DNA encoding the central repeat region (CRR) of each tal gene. Xcm TALome evolutionary relationship based on TALEs CRR revealed relatedness of Xss-V 2 -18 to MSCT1 and MS14003 from the United States. However, Tal2 of Xss-V 2 -18 differs at two repeat variable diresidues (RVDs) from Tal6 and Tal26 in MSCT1 and MS14003, respectively, inferred functional dissimilarity. The suicide vector pKMS1 was then used to construct tal deletion mutants in Xcm Xss-V 2 -18. The mutants were evaluated for pathogenicity in cotton based on symptomology and growth in planta . Four mutants showed attenuated virulence and all contained mutations in tal2 . One tal2 mutant designated M2 was further investigated in complementation assays. When tal2 was introduced into Xcm M2 and expressed in trans , the mutant was complemented for both symptoms and growth in planta , thus indicating that tal2 functions as a virulence factor in Xcm Xss-V 2 -18.Conclusions Overall, the results demonstrated that Tal2 is a major pathogenicity factor in Xcm strain Xss-V 2 -18 that contributes significantly in BBC. This study provides a foundation for future efforts aimed at identifying susceptibility genes in cotton that are targeted by Tal2.

Download Full-text

Genomics-enabled analysis of the emergent disease cotton bacterial blight

10.1101/127670 ◽

2017 ◽

Author(s):

Anne Z. Phillips ◽

Jeffrey C. Berry ◽

Mark C. Wilson ◽

Anupama Vijayaraghavan ◽

Jillian Burke ◽

...

Keyword(s):

Rna Sequencing ◽

Resistance Genes ◽

Bacterial Blight ◽

Durable Resistance ◽

Gene List ◽

Susceptibility Gene ◽

The United States ◽

Transcription Activator ◽

Xanthomonas Citri ◽

Putative Gene

AbstractCotton bacterial blight (CBB), an important disease of (Gossypium hirsutum) in the early 20th century, had been controlled by resistant germplasm for over half a century. Recently, CBB re-emerged as an agronomic problem in the United States. Here, we report analysis of cotton variety planting statistics that indicate a steady increase in the percentage of susceptible cotton varieties grown each year since 2009. Phylogenetic analysis revealed that strains from the current outbreak cluster with race 18 Xanthomonas citri pv. malvacearum (Xcm) strains.Illumina based draft genomes were generated for thirteen Xcm isolates and analyzed along with 4 previously published Xcm genomes. These genomes encode 24 conserved and nine variable type three effectors. Strains in the race 18 clade contain 3 to 5 more effectors than other Xcm strains. SMRT sequencing of two geographically and temporally diverse strains of Xcm yielded circular chromosomes and accompanying plasmids. These genomes encode eight and thirteen distinct transcription activator-like effector genes. RNA-sequencing revealed 52 genes induced within two cotton cultivars by both tested Xcm strains. This gene list includes a homeologous pair of genes, with homology to the known susceptibility gene, MLO. In contrast, the two strains of Xcm induce different clade III SWEET sugar transporters. Subsequent genome wide analysis revealed patterns in the overall expression of homeologous gene pairs in cotton after inoculation by Xcm. These data reveal host-pathogen specificity at the genetic level and strategies for future development of resistant cultivars.Author SummaryCotton bacterial blight (CBB), caused by Xanthomonas citri pv. malvacearum (Xcm), significantly limited cotton yields in the early 20th century but has been controlled by classical resistance genes for more than 50 years. In 2011, the pathogen re-emerged with a vengeance. In this study, we compare diverse pathogen isolates and cotton varieties to further understand the virulence mechanisms employed by Xcm and to identify promising resistance strategies. We generate fully contiguous genome assemblies for two diverse Xcm strains and identify pathogen proteins used to modulate host transcription and promote susceptibility. RNA-Sequencing of infected cotton reveals novel putative gene targets for the development of durable Xcm resistance. Together, the data presented reveal contributing factors for CBB re-emergence in the U.S. and highlight several promising routes towards the development of durable resistance including classical resistance genes and potential manipulation of susceptibility targets.

Download Full-text

Tal2 is a major virulence factor in the cotton pathogen, Xanthomonas citri pv. malvacearum Xss-V2-18

10.21203/rs.2.14271/v1 ◽

2019 ◽

Author(s):

Fazal Haq ◽

Syed Mashab Ali Shah ◽

Shiwang Xie ◽

Huangkun Xuan ◽

Wenxiu Ma ◽

...

Keyword(s):

Virulence Factor ◽

Virulent Strain ◽

The United States ◽

In Planta ◽

Dna Encoding ◽

Transcription Activator ◽

Xanthomonas Citri ◽

Tal Effectors ◽

Tn5 Transposon ◽

Suicide Vector

Abstract Background Bacterial blight of cotton (BBC), which is incited by Xanthomonas citri pv. malvacearum (Xcm), is a destructive disease in cotton. Transcription activator-like (tal) effectors (TALEs) play critical roles in the pathogenesis of xanthomonads; however, TALEs have not been well-investigated in the Xcm – cotton interaction.Results In this study, we identified six tal genes in Xcm Xss-V2-18, a highly-virulent strain from China, and assessed their roles in BBC. RFLP-based Southern hybridization assays indicated that Xss-V2-18 harbors the six tal genes on a plasmid. The plasmid-encoded tal genes were isolated by cloning BamHI fragments and screening clones by colony hybridization. The tal genes were sequenced by inserting a Tn5 transposon in the DNA encoding the central repeat region of each tal gene. Phylogenetically the TALEs in Xss-V2-18 show close similarity to the TALEs in Xcm strains MSCT1 and MS14003 from the United States. Tal2 in Xss-V2-18 differs from Tal6 and Tal26 in MSCT1 and MS14003, respectively, at two repeat variable diresidues (RVDs) indicates that they are functionally different. The suicide vector pKMS1 was then used to construct tal deletion mutants in Xcm Xss-V2-18. The mutants were evaluated for pathogenicity in cotton based on symptomology and growth in planta. Four mutants showed attenuated virulence and all contained mutations in tal2. One tal2 mutant designated M2 was further investigated in complementation assays. When tal2 was introduced into Xcm M2 and expressed in trans, the mutant was complemented for both symptoms and growth in planta, thus indicating that tal2 functions as a virulence factor in Xcm Xss-V2-18.Conclusions Overall, the results demonstrated that Tal2 is a major pathogenicity factor in Xcm Xss-V2-18 that contributes significantly in BBC. This study provides a foundation for future efforts aimed at identifying susceptibility genes in cotton that are targeted by Tal2.

Download Full-text

Identification of a virulence tal gene in the cotton pathogen, Xanthomonas citri pv. malvacearum strain Xss-V2-18

10.21203/rs.2.20197/v2 ◽

2020 ◽

Author(s):

Fazal Haq ◽

Shiwang Xie ◽

Kunxuan Huang ◽

Syed Mashab Ali Shah ◽

Wenxiu Ma ◽

...

Keyword(s):

Virulent Strain ◽

Evolutionary Relationship ◽

The United States ◽

In Planta ◽

Dna Encoding ◽

Transcription Activator ◽

Xanthomonas Citri ◽

Tn5 Transposon ◽

Suicide Vector ◽

In Trans

Abstract Background: Bacterial blight of cotton (BBC), which is caused by the bacterium Xanthomonas citri pv. malvacearum (Xcm), is a destructive disease in cotton. Transcription activator-like effectors (TALEs), encoded by tal-genes, play critical roles in the pathogenesis of xanthomonads. Characterized strains of cotton pathogenic Xcm harbor 8-12 different tal genes and only one of them is functionally decoded. Further identification of novel tal genes in Xcm strains with virulence contributions are prerequisite to decipher the Xcm-cotton interactions. Results: In this study, we identified six tal genes in Xss-V2-18, a highly-virulent strain of Xcm from China, and assessed their role in BBC. RFLP-based Southern hybridization assays indicated that Xss-V2-18 harbors the six tal genes on a plasmid. The plasmid-encoded tal genes were isolated by cloning BamHI fragments and screening clones by colony hybridization. The tal genes were sequenced by inserting a Tn5 transposon in the DNA encoding the central repeat region (CRR) of each tal gene. Xcm TALome evolutionary relationship based on TALEs CRR revealed relatedness of Xss-V2-18 to MSCT1 and MS14003 from the United States. However, Tal2 of Xss-V2-18 differs at two repeat variable diresidues (RVDs) from Tal6 and Tal26 in MSCT1 and MS14003, respectively, inferred functional dissimilarity. The suicide vector pKMS1 was then used to construct tal deletion mutants in Xcm Xss-V2-18. The mutants were evaluated for pathogenicity in cotton based on symptomology and growth in planta. Four mutants showed attenuated virulence and all contained mutations in tal2. One tal2 mutant designated M2 was further investigated in complementation assays. When tal2 was introduced into Xcm M2 and expressed in trans, the mutant was complemented for both symptoms and growth in planta, thus indicating that tal2 functions as a virulence factor in Xcm Xss-V2-18. Conclusions: Overall, the results demonstrated that Tal2 is a major pathogenicity factor in Xcm strain Xss-V2-18 that contributes significantly in BBC. This study provides a foundation for future efforts aimed at identifying susceptibility genes in cotton that are targeted by Tal2.

Download Full-text

Comparative genome analysis of Corynebacterium species: The underestimated pathogens with high virulence potential

Infection Genetics and Evolution ◽

10.1016/j.meegid.2021.104928 ◽

2021 ◽

pp. 104928

Author(s):

Fouzia Nasim ◽

Arijit Dey ◽

Insaf Ahmed Qureshi

Keyword(s):

Genome Analysis ◽

Comparative Genome Analysis ◽

Comparative Genome ◽

Virulence Potential ◽

Corynebacterium Species ◽

High Virulence

Download Full-text

Synteny Conservation and Chromosome Rearrangements During Mammalian Evolution

Genetics ◽

10.1093/genetics/147.1.289 ◽

1997 ◽

Vol 147 (1) ◽

pp. 289-296 ◽

Cited By ~ 2

Author(s):

Jason Ehrlich ◽

David Sankoff ◽

Joseph H Nadeau

Keyword(s):

Genome Analysis ◽

Systematic Errors ◽

Chromosome Rearrangements ◽

Mammalian Evolution ◽

Comparative Genome Analysis ◽

Reciprocal Translocations ◽

Comparative Genome ◽

Strong Selection ◽

Synteny Conservation

Abstract An important problem in comparative genome analysis has been defining reliable measures of synteny conservation. The published analytical measures of synteny conservation have limitations. Nonindependence of comparisons, conserved and disrupted syntenies that are as yet unidentified, and redundant rearrangements lead to systematic errors that tend to overestimate the degree of conservation. We recently derived methods to estimate the total number of conserved syntenies within the genome, counting both those that have already been described and those that remain to be discovered. With this method, we show that ~65% of the conserved syntenies have already been identified for humans and mice, that rates of synteny disruption vary ~25-fold among mammalian lineages, and that despite strong selection against reciprocal translocations, inter-chromosome rearrangements occurred approximately fourfold more often than inversions and other intra-chromosome rearrangements, at least for lineages leading to humans and mice.

Download Full-text