Genome assembly and annotation of Timothy

NAISS 2024/5-230


NAISS Medium Compute

Principal Investigator:

Pär Ingvarsson


Sveriges lantbruksuniversitet

Start Date:


End Date:


Primary Classification:

10609: Genetics (medical to be 30107 and agricultural to be 40402)

Secondary Classification:

10610: Bioinformatics and Systems Biology (methods development to be 10203)

Tertiary Classification:

40402: Genetics and Breeding in Agricultural Sciences



Timothy (genus Phleum, L.) are cool-season perennial grasses that are fast growing, winter hardy and highly palatable forage species. They are well adapted to cool, cold and humid climates and is widely grown in the temperate regions of Europe, North America and Asia. In the Nordic countries, timothy is the most important forage grass species. Its adaptation to the wider climate ranges and high quality fodder make timothy one of the most popular and globally important forage grasses for livestock production. This project aims at assembling the genomes of the two parental species of main cultivated Timothy species, Phleum pratense. The two species are Phleum nodosum (2n = 2x = 14, haploid genome size, 1C ~1.4 GB) and the tetraploid P. alpinum (2n = 4x = 28, haploid genome size, 1C ~2.8 Gb). We have sequenced these two species on the PacBio Sequel II System for HiFi long-reads sequences at the SciLifeLab in Uppsala. Furthermore, the transcriptome sequencing of the two parental species will be soon ready using the same PacBio platform for Iso-Seq datasets. The HiFi and Iso-Seq sequencing datasets will be used to develop phased de novo genome and transcriptome references for the two parental species, and thereby serve as key resources towards unlocking of the genome and transcriptome of the hexaploid timothy grass. This project aims to assemble and annotate the two genomes using this data.