Homoeologous evolution of the allotetraploid genome of Poa annua L.

Authors: BENSON, CHRISTOPHER - Pennsylvania State University; SHELTRA, MATTHEW - Pennsylvania State University; MAUGHAN, PETER - Brigham Young University; JELLEN, ERIC - Brigham Young University; Robbins, Matthew; Bushman, Shaun; PATTERSON, ERIC - Michigan State University; HALL, NATHAN - Michigan State University; HUFF, DAVID - Pennsylvania State University

Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/15/2023
Publication Date: 6/26/2023
Citation: Benson, C.W., Sheltra, M.R., Maughan, P.J., Jellen, E.N., Robbins, M.D., Bushman, B.S., Patterson, E.L., Hall, N.D., Huff, D.R. 2023. Homoeologous evolution of the allotetraploid genome of Poa annua L. BMC Genomics. 24. Article 350. https://doi.org/10.1186/s12864-023-09456-5.
DOI: https://doi.org/10.1186/s12864-023-09456-5

Interpretive Summary: Poa annua (annual bluegrass) is one of the most widely dispersed plant species on earth and has a complex genome that comes from two progenitor species, Poa infima and Poa supina. In order to understand the genome of P. annua and how it evolved, we sequenced and assembled the genomes of the two progenitor species. Sequence data suggests that P. infirma and P. supina diverged from their common ancestor 5.5 - 6.3 million years ago and hybridized to form P. annua =50,000 years ago. We find that the diploid genomes are similar in chromosome structure but mostly differ in their transposable elements (TEs) which led to expansion of the genome from P. infirma to be 1.7 times larger than the genome from P. supina. We show that P. annua’s smaller subgenome from P. supina is accumulating genes and, overall, had slightly higher gene expression than the genome from P. infirma. Whole-genome resequencing of several additional P. annua ecotypes revealed large-scale chromosomal rearrangements with a reduction in transposable elements, which supports the Genome Balance Hypothesis, where subgenomes of different sizes will eventually become more similar. The findings and genomic resources presented here will aid turfgrass breeders and weed scientists.

Technical Abstract: Poa annua (annual bluegrass) is an allotetraploid grass and one of the most widely dispersed plant species on earth. Here, we report the chromosome-scale genome assemblies of P. annua’s diploid progenitors, Poa infima and Poa supina. We suggest that the diploids diverged from their common ancestor 5.5 - 6.3 million years ago and hybridized to form P. annua =50,000 years ago. We find that the diploid genomes are similar in chromosome structure and most notably distinguished by the divergent evolutionary histories of their transposable elements (TEs), leading to a 1.7' difference in genome size. We show that P. annua’s smaller (supina) subgenome is preferentially accumulating genes and that its genes are marginally more highly expressed. Whole-genome resequencing of several additional P. annua ecotypes revealed large-scale chromosomal rearrangements characterized by extensive TE-downsizing and evidence to support the Genome Balance Hypothesis. The findings and genomic resources presented here will aid turfgrass breeders and weed scientists.