The paper analyzes genomic changes in mini-chromosomes of wheat blast fungal pathogens over time, showing their dynamic presence, sequence alterations, and role in pathogen adaptation.

bioRxiv · Jun 3, 2026 · PreprintEvolutionary Biology

Distinct modes of sequence evolution and epigenetic modifications underpin the origins of Starship-mediated variation in Pyricularia fungal plant pathogens

Samuel O’Donnell, Aidan McVey, Barbara S. Valent, Sanzhen Liu, Emile Gluck‐Thaler, David E. Cook

The paper identifies two distinct Starship families in Pyricularia oryzae, showing differences in sequence evolution, epigenetic modifications, and impacts on genome variation and plant-fungal interactions.

bioRxiv · Jan 29, 2026 · PreprintGenomics

Highly dynamic supernumerary mini-chromosomes in a Magnaporthe oryzae strain

Guifang Lin, Huakun Zheng, Dal‐Hoe Koo, Zonghua Wang, David E. Cook, Barbara S. Valent, Sanzhen Liu

The paper investigates genomic plasticity in Magnaporthe oryzae by analyzing supernumerary mini-chromosomes and their structural variations.

Fungal Genetics and Biology · Sep 1, 2025Peer-reviewedGenomics

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

Nikesh Gyawali, Yangfan Hao, Guifang Lin, Jun T. Huang, Ravi Bika, Lidia Calderón, Huakun Zheng, Giovana Cruppe, Doina Caragea, David E. Cook, Barbara S. Valent, Sanzhen Liu

This study uses Bi-LSTM models to detect mini-chromosomes in M. oryzae strains, finding their prevalence increased in recent wheat strains.

NAR Genomics and Bioinformatics · Jul 2, 2024Peer-reviewedGenomics

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

Sanzhen Liu, Guifang Lin, Sowmya R. Ramachandran, Lidia Calderón, Giovana Cruppe, Batiseba Tembo, Pawan Kumar Singh, David E. Cook, Kerry F. Pedley, Barbara S. Valent

The paper investigates genetic relationships among Magnaporthe oryzae isolates causing wheat blast outbreaks in Bangladesh and Zambia, finding that outbreaks were caused by genetically distinct isolates with divergent mini-chromosomes.

New Phytologist · Nov 20, 2023Peer-reviewedGenomics

Estimating Assembly Base Errors Using K-mer Abundance Difference (KAD) Between Short Reads and Genome Assembled Sequences

Cheng He, Guifang Lin, Hairong Wei, Haibao Tang, Frank F. White, Barbara S. Valent, Sanzhen Liu

This study introduces KAD, a method to estimate base errors and assess genome assembly quality by comparing k-mer abundance from short reads and assembled sequences.

NAR Genomics and Bioinformatics · Sep 1, 2020Peer-reviewedBioinformatics

Effector Gene Reshuffling Involves Dispensable Mini-chromosomes in the Wheat Blast Fungus

Peng Zhao, Ely Oliveira Garcia, Guifang Lin, Ying Hu, Melinda Dalby, Pierre Migeon, Haibao Tang, MARK L. FARMAN, David E. Cook, Frank F. White, Barbara S. Valent, Sanzhen Liu

The paper reports the genome of a wheat blast fungus, revealing dispensable mini-chromosomes containing effector genes that evolve rapidly and contribute to pathogen adaptation.

PLoS Genetics · Sep 12, 2019Peer-reviewedGenomics

Cellular Dynamics and Genomic Identity of Centromeres in the Cereal Blast Fungus

Vikas Yadav, Fan Yang, Md Hashim Reza, Sanzhen Liu, Barbara S. Valent, Kaustuv Sanyal, Naweed I. Naqvi

This study identifies unusual centromere dynamics and maps centromere DNA sequences in the rice blast fungus Magnaporthe oryzae, revealing epigenetic specification of centromere function.

mBio · Jul 29, 2019Peer-reviewedGenetics