The perennial ryegrass GenomeZipper: targeted use of genome resources for comparative grass genomics

Abstract

Whole-genome sequences established for model and major crop species constitute a key resource for advanced genomic research. For outbreeding forage and turf grass species like ryegrasses (Lolium spp.), such resources have yet to be developed. Here, we present a model of the perennial ryegrass (Lolium perenne) genome on the basis of conserved synteny to barley (Hordeum vulgare) and the model grass genome Brachypodium (Brachypodium distachyon) as well as rice (Oryza sativa) and sorghum (Sorghum bicolor). A transcriptome-based genetic linkage map of perennial ryegrass served as a scaffold to establish the chromosomal arrangement of syntenic genes from model grass species. This scaffold revealed a high degree of synteny and macrocollinearity and was then utilized to anchor a collection of perennial ryegrass genes in silico to their predicted genome positions. This resulted in the unambiguous assignment of 3,315 out of 8,876 previously unmapped genes to the respective chromosomes. In total, the GenomeZipper incorporates 4,035 conserved grass gene loci, which were used for the first genome-wide sequence divergence analysis between perennial ryegrass, barley, Brachypodium, rice, and sorghum. The perennial ryegrass GenomeZipper is an ordered, information-rich genome scaffold, facilitating map-based cloning and genome assembly in perennial ryegrass and closely related Poaceae species. It also represents a milestone in describing synteny between perennial ryegrass and fully sequenced model grass genomes, thereby increasing our understanding of genome organization and evolution in the most important temperate forage and turf grass species.

Figure 1.

Heat maps illustrate the degree of macrosynteny between perennial ryegrass and barley. For each of the seven perennial ryegrass LGs, the EST sequences of mapped DNA markers were compared against fl-cDNA sequences of barley that were arranged in the virtual barley genome (Mayer et al., 2011) using sequence homology analysis. Connections indicate the positions of the perennial ryegrass DNA marker and its associated barley fl-cDNA. The syntenic regions of each perennial ryegrass LG are indicated by the increased height of the heat maps.

Figure 2.

Syntenic relationships between perennial ryegrass and Brachypodium (Bd; A), rice (Os; B), and sorghum (Sb; C). Heat maps represent entire syntenic chromosomes of Brachypodium, rice, and sorghum. Colored bars visualize that part of the chromosome that was defined as syntenic to perennial ryegrass via the barley bridge. Chromosomes are assigned according to the color key. The color of the heat maps illustrates the density of perennial ryegrass marker sequences matching the Brachypodium, rice, and sorghum genomes.

Figure 3.

Venn diagrams of the perennial ryegrass GenomeZipper. Each diagram represents the number of Brachypodium (Bd), rice (Os), and sorghum (Sb) genes anchored in the GenomeZipper for each individual perennial ryegrass chromosome (L1–L7) as well as for the combined zipped-up genome. Intersections between circles indicate the number of genes that were anchored at a single unambiguous locus in all species. [See online article for color version of this figure.]

Figure 4.

Analysis of sequence divergence between perennial ryegrass, barley, Brachypodium, rice, and sorghum based on K_s. A, Frequency distribution of K_s rates based on protein alignments of perennial ryegrass genes to 3,301 orthologous barley, 3,789 Brachypodium, 3,434 rice, and 3,528 sorghum genes. B, Based on mean K_s rates against barley (0.31), Brachypodium (0.33), rice (0.53), and sorghum (0.59), the divergence times of perennial ryegrass from barley and Brachypodium, rice, and sorghum was estimated to 22 to 30, 23 to 32, 37 to 52, and 42 to 58 Mya, respectively.

Figure 5.

Microsynteny between perennial ryegrass and barley. Conserved blocks between the seven chromosomes of perennial ryegrass (horizontal axis; L1–L7) and barley (vertical axis; 1H–7H) are shown by comparison of common anchored Brachypodium genes. Each dot represents a Brachypodium gene (colored according to its chromosomal origin) that was anchored in both the perennial ryegrass and the barley GenomeZipper. The x and y axes are scaled according to the anchoring loci in the perennial ryegrass and barley GenomeZipper, respectively. Gray rectangles indicate loci of the barley GenomeZipper that are located in the genetic centromere region of the corresponding chromosome.