Soft rot disease of Belamcanda chinensis caused by Dickeya fangzhongdai in China

Yang, Yawen; Chen, Qiaohuan; Zhou, Jia; Xu, Jiawei; Li, Jinxin; Zhao, Tingting; Luo, Mi; Huang, Bisheng; Miao, Yuhuan; Liu, Dahui

doi:10.1016/j.pmpp.2023.101974

Cited by 4 publications

(2 citation statements)

References 29 publications

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“…As compared to corechromosomes, mini-chromosomes in M. oryzae are more repetitive, containing more transposable elements and fewer genes. The repeat-rich characteristic provides ample intrachromosomal homology for DNA duplication, loss, and rearrangements, creating conducive environments to accelerate genome evolution (Peng et al, 2019;Huang et al, 2023). Indeed, mini-chromosomes are highly variable among M. oryzae strains (Peng et al, 2019;Langner et al, 2021;Liu et al, 2022).…”

Section: Introductionmentioning

confidence: 99%

Using recurrent neural networks to detect supernumerary chromosomes in fungal strains causing blast diseases

Gyawali,

Hao,

Lin

et al. 2023

Preprint

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The genomes of the fungus Magnaporthe oryzae that causes blast diseases on diverse grass species, including major crop plants, have indispensable core-chromosomes and may contain one or more additional supernumerary chromosomes, also known as mini-chromosomes. The mini-chromosome is speculated to play a role in fungal biology, provide effector gene mobility, and may transfer between strains. To understand and study the biological function of mini-chromosomes, it is crucial to be able to identify whether a given strain of M. oryzae possesses a mini-chromosome. In this study, we applied recurrent neural network models, more specifically, Bidirectional Long Short-Term Models (Bi-LSTM), for classifying DNA sequences as core- or mini-chromosomes. The models were trained with sequences from multiple available core- and mini-chromosome assemblies. The trained model was then used to predict the presence of the mini-chromosome in a global collection of M. oryzae isolates using short-read DNA sequences. The model predicted that the mini-chromosome was prevalent in M. oryzae isolates, including those isolated from rice, wheat, Lolium and many other grass species. Interestingly, 23 recent wheat strains collected since 2005 all carried the mini-chromosome, but none of nine early strains collected before 1991 had the mini-chromosome, indicating the preferential selection for strains carrying the mini-chromosome in recent years. Based on the limited sample size, we found the presence of the mini-chromosome in isolates of pathotype Eleusine was not as high as isolates of other pathotypes. The deep learning model was also used to identify assembled sequence contigs that were derived from the mini-chromosome and partial regions on core-chromosomes potentially translocated from a mini-chromosome. In summary, our study has developed a reliable method for categorizing DNA sequences and showcases an application of recurrent neural networks in the field of predictive genomics.

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Section: Introductionmentioning

confidence: 99%

Using recurrent neural networks to detect supernumerary chromosomes in fungal strains causing blast diseases

Gyawali,

Hao,

Lin

et al. 2023

Preprint

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show abstract

“…Compared with core chromosomes, supernumerary mini-chromosomes in M. oryzae have a lower gene density and higher levels of repetitive sequences. The repeat-rich mini-chromosome provides abundant intrachromosomal homology for DNA duplication, loss, and rearrangements, which can serve as a reservoir to accelerate fungal genome evolution (Peng et al, 2019;Huang et al, 2023). Indeed, sequence comparisons among mini-chromosomes from different M. oryzae strains showed that they are highly variable (Peng et al, 2019;Langner et al, 2021).…”

Section: Introductionmentioning

confidence: 99%

Rapid mini‐chromosome divergence among fungal isolates causing wheat blast outbreaks in Bangladesh and Zambia

Liu,

Lin,

Ramachandran

et al. 2023

New Phytologist

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Summary The fungal pathogen, Magnaporthe oryzae Triticum pathotype, causing wheat blast disease was first identified in South America and recently spread across continents to South Asia and Africa. Here, we studied the genetic relationship among isolates found on the three continents. Magnaporthe oryzae strains closely related to a South American field isolate B71 were found to have caused the wheat blast outbreaks in South Asia and Africa. Genomic variation among isolates from the three continents was examined using an improved B71 reference genome and whole‐genome sequences. We found strong evidence to support that the outbreaks in Bangladesh and Zambia were caused by the introductions of genetically separated isolates, although they were all close to B71 and, therefore, collectively referred to as the B71 branch. In addition, B71 branch strains carried at least one supernumerary mini‐chromosome. Genome assembly of a Zambian strain revealed that its mini‐chromosome was similar to the B71 mini‐chromosome but with a high level of structural variation. Our findings show that while core genomes of the multiple introductions are highly similar, the mini‐chromosomes have undergone marked diversification. The maintenance of the mini‐chromosome and rapid genomic changes suggest the mini‐chromosomes may serve important virulence or niche adaptation roles under diverse environmental conditions.

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First report of Alternaria longipes causing kiwifruit leaf spot in China and screening of potentially fungicidal active substances

Chen,

Chen

et al. 2024

J Plant Dis Prot

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Soft rot disease of Belamcanda chinensis caused by Dickeya fangzhongdai in China

Cited by 4 publications

References 29 publications

Using recurrent neural networks to detect supernumerary chromosomes in fungal strains causing blast diseases

Using recurrent neural networks to detect supernumerary chromosomes in fungal strains causing blast diseases

Rapid mini‐chromosome divergence among fungal isolates causing wheat blast outbreaks in Bangladesh and Zambia

First report of Alternaria longipes causing kiwifruit leaf spot in China and screening of potentially fungicidal active substances

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