About

Matthew Hudson is a professor in the Department of Bioengineering at the University of Illinois Urbana-Champaign, where he has been serving since 2014. His academic background includes a Ph.D. in Biology from the University of Leicester, an M.A. and B.A. in Natural Sciences from the University of Cambridge. His research focuses on bioinformatics, genomics, and molecular biology, with contributions to understanding gene evolution, transcriptional responses, and genetic variation in various organisms including bees, soybeans, and other plants. Hudson has held positions as an associate and assistant professor at the University of Illinois and has worked as a bioinformatics scientist and specialist in the biotech industry. His work involves investigating gene expression, transposable elements, and genomic signatures related to evolutionary transitions and complex traits in plants and insects.

Research topics

• Biology
• Genetics
• Computer Science
• Agronomy
• Botany
• Evolutionary biology
• Ecology
• Psychology
• Social psychology
• Biotechnology
• Computational biology
• Zoology

Selected publications

• Retroelement expansions underlie genome evolution in stingless bees

  BMC Genomics · 2026-01-08 · 1 citations

  articleOpen access

  Stingless bees serve as crucial pollinators and are increasingly recognized as models for investigating behavioral and genomic evolution in insects. In the genus Melipona, a major difference in heterochromatin organization defines two groups: Group I species (e.g., M. quadrifasciata) with < 50% of pericentromeric heterochromatin and Group II species (e.g., M. scutellaris) containing > 50% heterochromatin across their chromosomes. These differences are believed to correlate with genome size and transposable element (TE) content, offering a unique opportunity to explore how heterochromatin variation, TE dynamics, and chromosomal evolution interact in a phylogenetic context. We present pseudo-chromosome-level genome assemblies for M. quadrifasciata and M. scutellaris obtained through long-read sequencing and 3D chromosome conformation scaffolding. Comparative analyses reveal conserved synteny but marked divergence in structural variants and TE types. M. scutellaris exhibits an expansion of retrotransposons, particularly Gypsy/DIRS1 elements, concentrated in TE hotspots linked to chromosomal rearrangements and structural variants. This coincides with distinct methylation entropy patterns across the genome and an expansion of histone deacetylase orthologs. The increased proportion of retrotransposons in M. scutellaris is counterbalanced by more DNA transposons in M. quadrifasciata, resulting in genomes of similar overall sizes but with distinct heterochromatin distributions. Advancing our understanding of genome evolution in eusocial insects, we provide high-resolution genomic resources for two Melipona species that differ in heterochromatin content. Our results highlight the complex role of TEs in shaping genomes and underscore their influence on chromosomal and epigenetic innovation, providing compelling evidence that TE dynamics underlie the pronounced heterochromatic differences observed in Melipona.

  PublisherDOI

• Genetic diversity analysis of North Dakota public soybean breeding program cultivars

  Scientific Reports · 2026-01-22

  articleOpen access

  Soybean [Glycine max (L.) Merr.] is a critical crop globally, valued for its protein and oil content. However, historical bottlenecks have constrained genetic diversity in soybean, particularly in high-latitude regions such as North Dakota, where environmental conditions necessitate maturity group (MG) 00 and 0 cultivars. This genetic diversity study examines the North Dakota State University (NDSU) soybean breeding program using pedigree, coefficient of parentage (CP), and SNP-based analyses. Pedigree tracing of 40 NDSU cultivars revealed a genetic base derived from 49 founders. CP analysis confirmed these findings, emphasizing dependence on limited germplasm, with the top ten founders accounting for over 70% of the genetic background and Mandarin (Ottawa) alone contributing 24%. SNP-based dendrograms and genetic relationship structures demonstrate the relationships among cultivars and founders. Notably, the specialty food grade natto cultivars formed a distinct cluster unrelated to commodity soybean. Population structure analyses emphasized the reliance on specific ancestral germplasm for breeding. This study underscores the need to diversify breeding materials to prevent genetic gain plateaus in MG 00 and 0 soybeans, thereby enhancing yield potential and adaptability in high-latitude regions.

  PublisherOA PDFDOI

• A sorghum pangenome reference improves global crop trait discovery

  Nature · 2026-03-11 · 6 citations

  articleOpen access

  Although the green revolution adapted a handful of crops to homogeneous and high-input industrialized agriculture, much of the global population still relies on the local production of variable crop cultivars by low-input smallholder farms. This diversity of unhomogenized crops1, like that of the grain and bioenergy crop sorghum2–5, offers raw materials for genetic gain and cultivar improvement. However, breeding efforts can be constrained by highly specialized traits and breeding targets6. Here, to bridge this diversity, we constructed a 33-member pangenome reference and a diversity panel across 1,984 cultivars and landraces. We leveraged these resources to explore the complex interplay among historical contingency, ongoing adaptation and previously uncharacterized structural diversity. Specifically, our analyses conclusively demonstrated multiple nested and deeply diverged structural variants in the domestication gene SHATTERING1, which distinguish the previously established multicentric origin of sorghum. We then applied landscape genomics to reveal how gene flow and secondary contact created the complex genetic mosaic in contemporary breeding networks. As proof of concept for pangenome-accelerated trait discovery, we connected biosynthetic gene cluster structural variation to phenotypic leaf concentration of the cyanogenic glucoside dhurrin. Combined, these approaches will accelerate breeding and trait discovery and provide a framework for similar applications in other crops. A pangenome reference for the phenotypically diverse crop sorghum aims to help accelerate future efforts to breed crops that are better adapted to changing environments.

  PublisherDOI

• Pangenome analysis of nine soybean cyst nematode genomes reveals hidden variation contributing to diversity and adaptation

  BMC Genomics · 2026-01-15

  articleOpen accessSenior authorCorresponding

  BACKGROUND: The soybean cyst nematode (SCN) is a persistent threat to soybean production. SCN populations continually overcome resistant cultivars, causing significant yield losses. Studies conducted with a single reference genome restrict our understanding of intraspecific diversity, masking significant mechanisms of virulence evolution and host adaptation. Here we report a pangenome constructed of nine SCN populations of different pathotypes, including eight newly generated high-fidelity genome assemblies. RESULTS: We detected over 19,000 orthologous gene families and more than 12,000 putative secreted proteins in SCN. Combined, these data indicate substantial diversity across populations. Gene content analysis showed that 35% of gene families were the conserved core, 15% were soft-core, and 48% were accessory. Evidence of rapid evolution was identified in a high portion (40%) of core single-copy genes, most notably inside the protein domains responsible for host recognition and immune modulation. Analysis of gene-family expansion revealed extensive duplication and loss across lineages, suggesting ongoing paralog turnover within SCN populations. Finally, a graph-based pangenome enabled the identification of numerous structural variants within regions under selection. CONCLUSIONS: Our study highlights substantial genetic variation in SCN that is not captured by single-reference analyses. By integrating multiple high-quality assemblies, we show that the SCN genome is highly dynamic, with extensive gene duplication and loss as well as structural variation shaping the differences among nematode populations. Collectively, the SCN pangenome provides a robust resource for studying virulence and adaptation mechanisms in SCN and establishes a genomic foundation for the development of more precise management strategies.

  PublisherDOI

• Pangenome analysis of nine Soybean Cyst Nematode genomes reveal hidden variation contributing to diversity and adaptation

  Research Square · 2025-10-16

  preprintOpen accessSenior author
  PublisherOA PDFDOI

• Vascular Trainees’ Peripheral Operative Experience in the Endovascular Era

  Journal of Vascular Surgery · 2025-09-16

  articleOpen access
  PublisherOA PDFDOI

• Enhancing lipid production in plant cells through automated high-throughput genome engineering and phenotyping

  The Plant Cell · 2025-02-01 · 10 citations

  articleOpen accessSenior author

  Plant bioengineering is a time-consuming and labor-intensive process with no guarantee of achieving desired traits. Here, we present a fast, automated, scalable, high-throughput pipeline for plant bioengineering (FAST-PB) in maize (Zea mays) and Nicotiana benthamiana. FAST-PB enables genome editing and product characterization by integrating automated biofoundry engineering of callus and protoplast cells with single-cell matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). We first demonstrated that FAST-PB could streamline Golden Gate cloning, with the capacity to construct 96 vectors in parallel. Using FAST-PB in protoplasts, we found that PEG2050 increased transfection efficiency by over 45%. For proof-of-concept, we established a reporter-gene-free method for CRISPR editing and phenotyping via mutation of high chlorophyll fluorescence 136. We show that diverse lipids were enhanced up to 6-fold using CRISPR activation of lipid controlling genes. In callus cells, an automated transformation platform was employed to regenerate plants with enhanced lipid traits through introducing multigene cassettes. Lastly, FAST-PB enabled high-throughput single-cell lipid profiling by integrating MALDI-MS with the biofoundry, protoplast, and callus cells, differentiating engineered and unengineered cells using single-cell lipidomics. These innovations massively increase the throughput of synthetic biology, genome editing, and metabolic engineering and change what is possible using single-cell metabolomics in plants.

  PublisherOA PDFDOI

• Genomic analysis and predictive modeling in the Northern Uniform Soybean Tests

  Crop Science · 2025-08-29 · 1 citations

  articleOpen access

  Abstract The Northern Uniform Soybean Tests (NUST) are a regional field trial network coordinated by the United States Department of Agriculture to evaluate experimental soybean ( Glycine max L.) strains developed by public institutions. Historical data from the NUST compiled, curated, and reported herein comprise a valuable multi‐environment trial dataset including relevant elite soybean germplasm from maturity groups 00 to IV evaluated over 28 years in 199 locations, totaling 1652 environments. Our aim was to characterize the genetic structure of the NUST experimental strains, perform genome‐wide association studies using historical phenotypic data, and assess the usefulness of these historical data for genomic prediction model training. Molecular marker information was collected on 2544 unique NUST experimental strains using the BARCSoySNP6K assay. High fixation index values between early and later maturity groups were observed in a region on chromosome 10 near the known soybean maturity gene E2 . We failed to find strong genetic divergence between strains from different breeding programs, reflecting the germplasm sharing common among public programs. Genome‐wide association analyses on important agronomic traits identified marker‐trait associations, many of which overlap with quantitative trait loci previously reported in the literature. Genomic prediction models trained using the historical NUST data produced moderate to high predictive abilities in most cases, suggesting these data could make useful contributions to training sets. We have made these data publicly available as a data resource for others to study genotype–phenotype relationships within elite public soybean germplasm and develop predictive models for advancement and implementation of genomics‐assisted breeding.

  PublisherOA PDFDOI

• Synthetic feed-forward loop circuit boosts transgene expression in sugarcane

  Plant Cell Reports · 2025-07-08

  articleOpen accessSenior author

  KEY MESSAGE: A new GAL4-based feed-forward loop circuit enhances β-glucuronidase (GUS) reporter gene expression in leaves and stems of stably transformed sugarcane plants.

  PublisherOA PDFDOI

• Retroelement expansions underlie genome evolution in stingless bees

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-04-16 · 2 citations

  preprintOpen access

  ABSTRACT Stingless bees are essential pollinators and emerging models for studying behavioral and genomic evolution. In the genus Melipona , a major difference in heterochromatin organization defines two groups: Group I species (e.g., M. quadrifasciata ) with &lt;50% of pericentromeric heterochromatin and Group II species (e.g., M. scutellaris ) containing &gt;50% heterochromatin across their chromosomes. These differences are thought to correlate with genome size and transposable element (TE) content, offering a unique opportunity to explore how heterochromatin variation, TE dynamics, and chromosomal evolution interact in a phylogenetic context. We present pseudo-chromosome-level genome assemblies for M. quadrifasciata and M. scutellaris obtained by long-read sequencing and Hi-C scaffolding. Comparative analyses reveal conserved synteny but marked divergence in structural variants and TEs. M. scutellaris shows an expansion of retrotransposons, particularly Gypsy/DIRS1 elements, concentrated in TE hotspots linked to chromosomal rearrangements and structural variants. This coincides with distinct methylation entropy and an expansion of histone deacetylase orthologs, potentially affecting heterochromatin organization. The increased ratio of retrotransposons in M. scutellaris is counterbalanced by more DNA transposons in M. quadrifasciata , resulting in genomes of similar overall sizes but of distinct heterochromatin distribution. Advancing our understanding of genome evolution in eusocial insects, we provide high-resolution genomic resources for two Melipona species that differ in heterochromatin content. Our results highlight the complex role of TEs in shaping genomes and underscore their influence on chromosomal and epigenetic innovation, providing strong evidence that TE dynamics underly the striking heterochromatic differences observed in Melipona .

  PublisherOA PDFDOI

Recent grants

• Exploring the Role of Noncoding RNAs in Heterosis

  NSF · $500k · 2009–2014

Frequent coauthors

• Peter H. Quail

  Agricultural Research Service

  31 shared

• Liudmila S. Mainzer

  University of Wyoming

  31 shared

• Mary A. Schuler

  University of Illinois Urbana-Champaign

  28 shared

• Stephen P. Moose

  University of Illinois Urbana-Champaign

  28 shared

• Todd P. Michael

  Salk Institute for Biological Studies

  27 shared

• Tong Zhu

  Nanjing Agricultural University

  26 shared

• Jacob R. Heldenbrand

  National Center for Supercomputing Applications

  25 shared

• Yinghong Pan

  25 shared

Labs

• Matt Hudson LabPI

Education

• PhD

  University of Leicester

  1997

• MA

  University of Cambridge

  1994