TY - JOUR
T1 - A happy accident
T2 - a novel turfgrass reference genome
AU - Phillips, Alyssa R.
AU - Seetharam, Arun S.
AU - Albert, Patrice S.
AU - AuBuchon-Elder, Taylor
AU - Birchler, James A.
AU - Buckler, Edward S.
AU - Gillespie, Lynn J.
AU - Hufford, Matthew B.
AU - Llaca, Victor
AU - Romay, Maria Cinta
AU - Soreng, Robert J.
AU - Kellogg, Elizabeth A.
AU - Ross-Ibarra, Jeffrey
N1 - Funding Information:
Thank you to Dr. Chrissy McAllister and Bess Bookout for sharing samples collected with permission from Nature Conservancy Canada properties and Lynn Riedel for collection of samples with permission from the City of Boulder Open Space and Mountain Parks. The Texas Advanced Computing Center (TACC) at The University of Texas at Austin and HPC@ISU equipment at Iowa State University (partially funded by NSF under MRI grant number 1726447) provided HPC resources that have contributed to the research results reported within this paper. We thank Dr. Kevin Fengler (for providing assembly instructions) and Dr. Gina Zastrow-Hayes (for establishing sequencing contracts) of Corteva Agriscience for their help in this project. ARP would like to thank Andrew L. Murray for his support throughout the duration of this project. Additionally, the authors would like to thank our A. gerardi reference plant for being contaminated with Poa and Felix Andrews for his alleged role in the happy accident that led to this work. Finally, thank you to Bob Ross for inspiring a generation of scientists to persevere.
Funding Information:
This project was funded by the National Science Foundation (NSF) grant number 1822330. HPC resources at TACC were partially funded by NSF under MRI grant number 1726447.
Funding Information:
Thank you to Dr. Chrissy McAllister and Bess Bookout for sharing samples collected with permission from Nature Conservancy Canada properties and Lynn Riedel for collection of samples with permission from the City of Boulder Open Space and Mountain Parks. The Texas Advanced Computing Center (TACC) at The University of Texas at Austin and HPC@ISU equipment at Iowa State University (partially funded by NSF under MRI grant number 1726447) provided HPC resources that have contributed to the research results reported within this paper. We thank Dr. Kevin Fengler (for providing assembly instructions) and Dr. Gina Zastrow-Hayes (for establishing sequencing contracts) of Corteva Agriscience for their help in this project. ARP would like to thank Andrew L. Murray for his support throughout the duration of this project. Additionally, the authors would like to thank our A. gerardi reference plant for being contaminated with Poa and Felix Andrews for his alleged role in the happy accident that led to this work. Finally, thank you to Bob Ross for inspiring a generation of scientists to persevere. This project was funded by the National Science Foundation (NSF) grant number 1822330. HPC resources at TACC were partially funded by NSF under MRI grant number 1726447.
Publisher Copyright:
© The Author(s) 2023. Published by Oxford University Press on behalf of The Genetics Society of America.
PY - 2023/6
Y1 - 2023/6
N2 - Poa pratensis, commonly known as Kentucky bluegrass, is a popular cool-season grass species used as turf in lawns and recreation areas globally. Despite its substantial economic value, a reference genome had not previously been assembled due to the genome’s relatively large size and biological complexity that includes apomixis, polyploidy, and interspecific hybridization. We report here a fortuitous de novo assembly and annotation of a P. pratensis genome. Instead of sequencing the genome of a C4 grass, we accidentally sampled and sequenced tissue from a weedy P. pratensis whose stolon was intertwined with that of the C4 grass. The draft assembly consists of 6.09 Gbp with an N50 scaffold length of 65.1 Mbp, and a total of 118 scaffolds, generated using PacBio long reads and Bionano optical map technology. We annotated 256K gene models and found 58% of the genome to be composed of transposable elements. To demonstrate the applicability of the reference genome, we evaluated population structure and estimated genetic diversity in P. pratensis collected from three North American prairies, two in Manitoba, Canada and one in Colorado, USA. Our results support previous studies that found high genetic diversity and population structure within the species. The reference genome and annotation will be an important resource for turfgrass breeding and study of bluegrasses.
AB - Poa pratensis, commonly known as Kentucky bluegrass, is a popular cool-season grass species used as turf in lawns and recreation areas globally. Despite its substantial economic value, a reference genome had not previously been assembled due to the genome’s relatively large size and biological complexity that includes apomixis, polyploidy, and interspecific hybridization. We report here a fortuitous de novo assembly and annotation of a P. pratensis genome. Instead of sequencing the genome of a C4 grass, we accidentally sampled and sequenced tissue from a weedy P. pratensis whose stolon was intertwined with that of the C4 grass. The draft assembly consists of 6.09 Gbp with an N50 scaffold length of 65.1 Mbp, and a total of 118 scaffolds, generated using PacBio long reads and Bionano optical map technology. We annotated 256K gene models and found 58% of the genome to be composed of transposable elements. To demonstrate the applicability of the reference genome, we evaluated population structure and estimated genetic diversity in P. pratensis collected from three North American prairies, two in Manitoba, Canada and one in Colorado, USA. Our results support previous studies that found high genetic diversity and population structure within the species. The reference genome and annotation will be an important resource for turfgrass breeding and study of bluegrasses.
KW - Kentucky bluegrass
KW - Poaceae
KW - aneuploidy
KW - genetic diversity
KW - genome assembly
KW - polyploidy
KW - population structure
KW - turfgrass
UR - http://www.scopus.com/inward/record.url?scp=85160968848&partnerID=8YFLogxK
U2 - 10.1093/g3journal/jkad073
DO - 10.1093/g3journal/jkad073
M3 - Article
C2 - 37002915
AN - SCOPUS:85160968848
SN - 2160-1836
VL - 13
JO - G3: Genes, Genomes, Genetics
JF - G3: Genes, Genomes, Genetics
IS - 6
M1 - jkad073
ER -