Extensive genome evolution distinguishes maize within a stable tribe of grasses

Journal article

Michelle C. Stitzer, Arun S. Seetharam, Armin Scheben, Sheng-Kai Hsu, Aimee J. Schulz, Taylor M. Aubuchon-Elder, Mohamed El-Walid, Taylor H. Ferebee, Charles O. Hale, Thuy La, Zong-Yan Liu, Sarah J. McMorrow, P. Minx, Alyssa R. Phillips, Michael L. Syring, Travis Wrightsman, Jingjing Zhai, Rémy Pasquet, C. McAllister, S. Malcomber, P. Traiperm, D. Layton, Jinshun Zhong, D. Costich, R. Dawe, K. Fengler, Charlotte Harris, Zach Irelan, V. Llaca, P. Parakkal, Gina Zastrow-Hayes, M. Woodhouse, Ethalinda K. S. Cannon, J. Portwood, Carson M. Andorf, Patrice S. Albert, J. Birchler, Adam Siepel, J. Ross-Ibarra, M. Romay, Elizabeth A. Kellogg, E. Buckler, M. Hufford
bioRxiv, 2025

Semantic Scholar DOI PubMedCentral PubMed

Cite

APA Click to copy
Stitzer, M. C., Seetharam, A. S., Scheben, A., Hsu, S.-K., Schulz, A. J., Aubuchon-Elder, T. M., … Hufford, M. (2025). Extensive genome evolution distinguishes maize within a stable tribe of grasses. BioRxiv.

Chicago/Turabian Click to copy
Stitzer, Michelle C., Arun S. Seetharam, Armin Scheben, Sheng-Kai Hsu, Aimee J. Schulz, Taylor M. Aubuchon-Elder, Mohamed El-Walid, et al. “Extensive Genome Evolution Distinguishes Maize within a Stable Tribe of Grasses.” bioRxiv (2025).

MLA Click to copy
Stitzer, Michelle C., et al. “Extensive Genome Evolution Distinguishes Maize within a Stable Tribe of Grasses.” BioRxiv, 2025.

BibTeX Click to copy

@article{michelle2025a,
  title = {Extensive genome evolution distinguishes maize within a stable tribe of grasses},
  year = {2025},
  journal = {bioRxiv},
  author = {Stitzer, Michelle C. and Seetharam, Arun S. and Scheben, Armin and Hsu, Sheng-Kai and Schulz, Aimee J. and Aubuchon-Elder, Taylor M. and El-Walid, Mohamed and Ferebee, Taylor H. and Hale, Charles O. and La, Thuy and Liu, Zong-Yan and McMorrow, Sarah J. and Minx, P. and Phillips, Alyssa R. and Syring, Michael L. and Wrightsman, Travis and Zhai, Jingjing and Pasquet, Rémy and McAllister, C. and Malcomber, S. and Traiperm, P. and Layton, D. and Zhong, Jinshun and Costich, D. and Dawe, R. and Fengler, K. and Harris, Charlotte and Irelan, Zach and Llaca, V. and Parakkal, P. and Zastrow-Hayes, Gina and Woodhouse, M. and Cannon, Ethalinda K. S. and Portwood, J. and Andorf, Carson M. and Albert, Patrice S. and Birchler, J. and Siepel, Adam and Ross-Ibarra, J. and Romay, M. and Kellogg, Elizabeth A. and Buckler, E. and Hufford, M.}
}

Abstract

Over the last 20 million years, the Andropogoneae tribe of grasses has evolved to dominate 17% of global land area. Domestication of these grasses in the last 10,000 years has yielded our most productive crops, including maize, sugarcane, and sorghum. The majority of Andropogoneae species, including maize, show a history of polyploidy – a condition that, while offering the evolutionary advantage of multiple gene copies, poses challenges to basic cellular processes, gene expression, and epigenetic regulation. Genomic studies of polyploidy have been limited by sparse sampling of taxa in groups with multiple polyploidy events. Here, we present 33 genome assemblies from 27 species, including chromosome-scale assemblies of maize relatives Zea and Tripsacum. In maize, the after-effects of polyploidy have been widely studied, showing reduced chromosome number, biased fractionation of duplicate genes, and transposable element (TE) expansions. While we observe these patterns within the genus Zea, 12 other polyploidy events deviate significantly. Those tetraploids and hexaploids retain elevated chromosome number, maintain nearly complete complements of duplicate genes, and have only stochastic TE amplifications. These genomes reveal variable outcomes of polyploidy, challenging simple predictions and providing a foundation for understanding its evolutionary implications in an ecologically and economically important clade.