Fig. 1.
Fig. 1.

Classification of intraspecific and interspecific single-nucleotide polymorphisms (SNPs). Selection criteria are indicated in italics. (A) De novo assembly and Orthology Guided Assembly generate a reference transcriptome for each of the three species. Intraspecific SNPs (INTRA) are identified by mapping all RNA-seq data from Festuca pratensis, Lolium multiflorum, and L. perenne onto a single reference transcriptome. This analysis is performed in parallel for each reference transcriptome. (B) Interspecific SNPs are identified between two species (INTER-2W) or by comparing all three species (INTER-3W). (C) Filtering scheme for the selection of high-quality reference transcripts in pairwise genotype comparisons (INTER-PW).

 


Fig. 2.
Fig. 2.

Venn diagram of the overlap in the number of transcripts in three different reference transcriptomes (Festuca pratensis, Lolium multiflorum, and L. perenne). The number of near full-length transcripts is given in parentheses.

 


Fig. 3.
Fig. 3.

SNPhylo phylogenetic tree based on 33,725 single-nucleotide polymorphisms shared among 26 genotypes of Lolium perenne, L. multiflorum, and Festuca pratensis. Asterisk (*) indicates overlapping positions in the phylogenetic tree of the three replicates for Fp52, Fp53, Lm51, and Lm52.

 


Fig. 4.
Fig. 4.

Selection of single-nucleotide polymorphisms (SNPs) suitable for discrimination between parental genome-specific alleles in progeny derived from a cross between Festuca pratensis genotype Fp52 and Lolium multiflorum genotype Lm51. Comparison of selected genes sets carrying such SNPs using various filtering criteria. FL, filtered for near full-length transcript length; RD, filtered for average read depth per transcript; HQ (high quality), filtered for number of SNPs per transcript. The numbers of transcripts that pass the filtering criteria are given in parentheses. Only transcripts with at least one SNP per gene in both transcript references are shown.

 


Fig. 5.
Fig. 5.

Circular map of the seven Lolium perenne genetic linkage groups. From outer to inner circle: orthologous blocks of Brachypodium distachyon chromosomes with Lolium perenne (each color represents one B. distachyon chromosome: Bd1 blue, Bd2 yellow, Bd3 orange, Bd4 gray, and Bd5 green); distribution of all L. multiflorum transcripts; distribution of 6475 near full-length (FL) transcripts assembled in all three species; the number of intraspecific SNPs per gene INTRAFp (yellow), INTRALm (green), INTRALp (orange) with maximum 400 SNPs per gene; the number of interspecific SNPs per gene in pairwise comparisons (violet) with a maximum of 150 SNPs per gene (INTER-PWFp52-Lm51 and INTER-PWFp54-Lm51). Note that the circular maps show linear order of genes but not physical distances between them.