RNA-Seq and Genome Sequencing of Lolium tenmulentum, a Relative of Perennial Ryegrass

The genus Lolium consists of two important forage grasses, Italian ryegrass and perennial ryegrass, and a self-fertile species L. temulentum that is used as a model species for genomic studies of cool-season forage grass. Here, we report the results of RNA-Seq and genomic sequencing of L. temulentum.

A total of 108 Gbp RNA-Seq reads from four tissues (seedling leaf and root, young inflorescence and stem) of an L. temulentumstrain (PI170516 from Turkey) were generated. Transcriptome assembly using these RNA-Seq data yielded 61,759 contigs/supercontigs with an average length of 1.1 kb. Differential expression analysis showed that the vast majority of contigs (54,321/61,738) exhibit differential expression among tissues at a 5% false discovery rate. In addition, among the six pairwise comparisons, on average 36% of contigs exhibited differential expression between any two tissues. No evidence was obtained for differential expression of 7,252 genes.

 Genomic sequences (121 Gbp) from same genotype (PI170516) were generated through a paired-end library (1X shotgun with 350bp insert size) and several mate-pair libraries (1 x 4kb and 2 x 2kb). These genomic reads were combined with three additional Hi-Seq lanes of WGS sequencing data. All of the genomic sequencing data described above formed 614,472 scaffold sequences (671,234,248bp) with minimum,maximum,and average lengths of 300 bp, 115,728 bp, and 1,092 bp, respectively. 60% (37,285/61,738) of the transcriptomic contigs/supercontigs from the RNA-Seq experiment could be mapped to the genomic scaffold sequences when using a cut-off of at least 95% identity and at least 50% coverage.