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

Trait Association and Prediction Through Integrative K-mer Analysis

Cheng He, Jacob D. Washburn, Nathaniel Schleif, Yangfan Hao, Heidi F. Kaeppler, Shawn M. Kaeppler, Zhiwu Zhang, Jinliang Yang, Sanzhen Liu

This study uses k-mer GWAS to identify genetic associations with maize traits and shows comparable prediction accuracy to SNP-based methods.

The Plant Journal · Sep 11, 2024Peer-reviewedGenetics

Origin and evolution of the bread wheat D genome

Emile Cavalet-Giorsa, Andrea González-Muñoz, Naveenkumar Athiyannan, Samuel Holden, Adil Salhi, Catherine H. Gardener, Jesús Quiroz-Chávez, Samira Mahammadrahim Rustamova, Ahmed F. Elkot, Mehran Patpour, Awais Rasheed, Long Mao, Evans S. Lagudah, Sambasivam K. Periyannan, Amir Sharon, , Simon G. Krattinger

The paper analyzes the genetic composition and history of the bread wheat D genome using a pangenome of its donor species, revealing contributions from discrete subpopulations of Aegilops tauschii.

Nature · Aug 14, 2024Peer-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

A historically balanced locus under recent directional selection in responding to changed nitrogen conditions during modern maize breeding

Gen Xu, Jing Lyu, Toshihiro Obata, Sanzhen Liu, Yufeng Ge, James C. Schnable, Jinliang Yang

The paper identifies a historically balanced locus under recent directional selection in maize linked to nitrogen response traits, revealing genetic changes associated with modern breeding practices.

bioRxiv · Feb 9, 2022 · PreprintGenomics

Chromosome-level Genome Assembly of a Regenerable Maize Inbred Line A188

Guifang Lin, Cheng He, Jun Zheng, Dal‐Hoe Koo, Ha Le, Huakun Zheng, Tej Man Tamang, Jinguang Lin, Yàn Liú, Mingxia Zhao, Yangfan Hao, Frank McFraland, Bo Wang, Yang Qin, Haibao Tang, , Sanzhen Liu

This paper presents a chromosome-level genome assembly of maize inbred line A188 and identifies structural variations and gene expression differences compared to the reference line B73.

Genome biology · Jun 9, 2021Peer-reviewedGenomics

HB-PLS: An algorithm for identifying biological process or pathway regulators by integrating Huber loss and Berhu penalty with Partial Least Square

Wenping Deng, Kui Zhang, Cheng He, Sanzhen Liu, Hairong Wei

HB-PLS identifies pathway regulators by integrating Huber loss and Berhu penalty with PLS, outperforming existing methods in efficiency and distinct regulator identification.

Forestry Research · Jan 1, 2021Peer-reviewedBioinformatics

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

Temporal Small RNA Expression Profiling Under Drought Reveals a Potential Regulatory Role of snoRNAs in Drought Responses of Maize

Jun Zheng, Erliang Zeng, Yicong Du, Cheng He, Ying Hu, Zhenzhen Jiao, Kai Wang, Wenxue Li, Maria Ludens, Junjie Fu, Haiyan Wang, Frank F. White, Guoying Wang, Sanzhen Liu

The paper profiles temporal small RNA expression in maize under drought stress and identifies snoRNAs as potential regulators of drought responses.

The Plant Genome · Feb 14, 2019Peer-reviewedGenomics

Tunable Genotyping-By-Sequencing (tGBS(R)) Enables Reliable Genotyping of Heterozygous Loci

Alina Ott, Sanzhen Liu, James C. Schnable, Cheng‐Ting Yeh, Kai-Sin Wang, Patrick S. Schnable

This paper introduces tGBS(R), a genome reduction method that improves SNP calling accuracy and reduces missing data for heterozygous loci compared to conventional GBS.

Nucleic Acids Research · Sep 13, 2017Peer-reviewedGenomics

Unbiased K-mer Analysis Reveals Changes in Copy Number of Highly Repetitive Sequences During Maize Domestication and Improvement

Sanzhen Liu, Jun Zheng, Pierre Migeon, Jie Ren, Ying Hu, Cheng He, Hongjun Liu, Junjie Fu, Frank F. White, Christopher Toomajian, Guoying Wang

The paper uses k-mer analysis of maize genomes to identify changes in repetitive sequence copy numbers during domestication and improvement.

Scientific Reports · Feb 10, 2017Peer-reviewedGenomics