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Genomics and Transcriptomics of 3ANX (NX-2) and NX (NX-3) producing isolates of Fusarium graminearum

ABSTRACT: In this study, we used an -omics approach coupled with high resolution mass spectrometry to characterize twenty F. graminearum isolates collected from five distinct regions across Manitoba, containing both 3-acetyl deoxynivalenol (3ADON) and 15-acetyl deoxynivalenol (15ADON) chemotypes. These data identified regional F. graminearum populations within Manitoba that demonstrate distinct genomic variation and patterns of gene expression, particularly within pathogenicity associated processes. Further, we identified genetic variation and differential expression between isolates showing high and low levels of pathogenicity, allowing for the identification of previously characterized and novel putative pathogenicity factors, as well as regions of genetic diversity between these groups. Lastly, we detected production of 3ANX and/or NX mycotoxins within the majority of our twenty characterized F. graminearum isolates, suggesting the 3ANX chemotype may be more prevalent than previously expected in Canada. These findings highlight the diversity of F. graminearum across Manitoba, and more importantly uncover specific genomic regions and candidate pathogenicity factors influenced by this diversity. These data can ultimately help researchers develop improved disease management strategies against FHB and the dynamic populations of F. graminearum.

ORGANISM(S): Fusarium graminearum

PROVIDER: GSE292521 | GEO | 2025/03/25

REPOSITORIES: GEO

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Project description:Background. The Beijing family of Mycobacterium tuberculosis is dominant in countries in East Asia. Genomic polymorphisms are a source of diversity within the M.tuberculosis genome and may account for the variation of virulence among M.tuberculosis isolates. To date there are no studies that have examined the genomic composition of M.tuberculosis isolates from the high TB-burden country, Myanmar. Methodology/Principle findings. Twenty-two M.tuberculosis isolates from Myanmar were screened on whole-genome arrays containing genes from M.tuberculosis H37Rv, M.tuberculosis CDC1551 and M.bovis AF22197. Screening identified 198 deletions or extra regions in the clinical isolates compared to H37Rv. Twenty-two regions differentiated between Beijing and non-Beijing isolates and were verified by PCR on an additional 40 isolates. Six regions (Rv0071-0074 [RD105], Rv1572-1576c [RD149], Rv1585c-1587c[RD149], MT1798-Rv1755c [RD152], Rv1761c [RD152] and Rv0279c) were deleted in Beijing isolates, of which 4 (Rv1572-1576c, Rv1585c-1587c, MT1798-Rv1755c and Rv1761c) were variably deleted among ST42 isolates, indicating a closer relationship between the Beijing and ST42 lineages. The TbD1 region, Mb1582-Mb1583 was deleted in Beijing and ST42 isolates. One M.bovis gene of unknown function, Mb3184c was present in all isolates, except 11 of 13 ST42 isolates. The CDC1551 gene, MT1360 coding for a putative adenylate cyclase, was present in all Beijing and ST42 isolates (except 1). The pks15/1 gene, coding for a putative virulence factor, was intact in all Beijing and non-Beijing isolates, except in ST42 and ST53 isolates. Conclusion. This study describes previously unreported deletions/extra regions in Beijing and non-Beijing M.tuberculosis isolates. The modern and highly frequent ST42 lineage showed a closer relationship to the hypervirulent Beijing lineage than to the ancient non-Beijing lineages. The pks15/1 gene was disrupted only in modern non-Beijing isolates. This is the first report of an in-depth analysis on the genomic diversity of M.tuberculosis isolates from Myanmar. Data is also available from http://bugs.sgul.ac.uk/E-BUGS-66

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Genomics and Transcriptomics of 3ANX (NX-2) and NX (NX-3) producing isolates of Fusarium graminearum

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