Chromosome-scale genome assembly and annotation of allotetraploid annual bluegrass (Poa annua L.)

Authors: Robbins, Matthew; Bushman, Shaun; HUFF, DAVID - Pennsylvania State University; BENSON, CHRISTOPHER - Pennsylvania State University; WARNKE, SCOTT - US Department Of Agriculture (USDA); MAUGHAN, CHASE - Brigham Young University; JELLEN, ERIC - Brigham Young University; JOHNSON, PAUL - Utah State University; MAUGHAN, P - Brigham Young University

Submitted to: Genome Biology and Evolution
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/10/2022
Publication Date: 12/28/2022
Citation: Robbins, M.D., Bushman, B.S., Huff, D.R., Benson, C.W., Warnke, S.E., Maughan, C.A., Jellen, E.N., Johnson, P.G., Maughan, P.J. 2022. Chromosome-scale genome assembly and annotation of allotetraploid annual bluegrass (Poa annua L.). Genome Biology and Evolution. 15(1). Article evac180. https://doi.org/10.1093/gbe/evac180.
DOI: https://doi.org/10.1093/gbe/evac180

Interpretive Summary: Annual bluegrass (Poa annua L.) is an economically and horticulturally important grass species that is found throughout the world. Poa annua is used as a turfgrass but is also a common weed where other turfgrass is grown such as golf courses. Poa annua has two sets of 14 pairs of chromosomes with one set each from its progenitor species Poa infirma (Knuth) and Poa supina (Schrad). Due to its broad adaptability, wide range of physical characteristics, and evolutionary history, this species is an intriguing subject of genetic and evolutionary studies. The lack of genomic resources and tools have hampered genetic studies to date. To overcome this limitation, a reference genome was assembled and annotated that represents the sequence of 14 chromosomes, one from each pair. The assembly metrics of 1.78 Gb total length, N50 of 112 Mb and 96.7% BUSCO scores indicate the assembly is high quality. Seventy percent of the genome sequence was repetitive DNA sequences, while 13.3% was from 76,420 predicted genes. The 14 chromosomes were divided into the 7 that originated from Poa infirma and the 7 from Poa supina. Although the 7 chromosomes from Poa infirma were generally longer than those from Poa supina, they were similar in sequence and organization with more repetitive DNA sequences contributing to their longer length.

Technical Abstract: Poa annua L. is a globally distributed plant species with economic and horticultural significance as a weed and as a turfgrass. This dual significance, due to its phenotypic plasticity and ecological adaptation, has made P. annua an intriguing plant for genetic and evolutionary studies. The lack of genomic resources and the allotetraploid (2n = 4x = 28) nature of this species have hampered genetic studies. A reference genome sequence would be a valuable asset to understand the genetics and polyploid origin of Poa annua. Here we report a genome assembly with scaffolds representing the 14 haploid chromosomes that are 1.78 Gb in length with an N50 of 112 Mb and 96.7% of BUSCO orthologs. Seventy percent of the genome was identified as repetitive elements, 91.0% of which were Copia- or Gypsy-like long-terminal repeats. The genome was annotated with 76,420 genes spanning 13.3% of the 14 chromosomes. The two subgenomes originating from Poa infirma (Knuth) and Poa supina (Schrad) were sufficiently divergent to be distinguishable, but syntenic in sequence and annotation with repetitive elements contributing to the expansion of the P. infirma subgenome.