Expression profiles of Falster and Veyo transcripts involved in fructan biosynthesis.

<p>Falster transcripts are depicted in blue, Veyo transcripts in red. The <i>x</i> axis presents the sample collection time points: I =  autumn conditions, before the start of vernalization; II = 2 days of vernalization; III = 4 weeks of vernalization; IV = 9 weeks of vernalization; V = 7 days of long day conditions. The <i>y</i> axis corresponds to the variance stabilized data from DESeq. The blue background illustrates vernalization treatment, the pink background illustrates long day conditions. Figure adapted from the Plant Metabolic Pathways database (<a href="http://www.plantcyc.org/" target="_blank">http://www.plantcyc.org/</a>).</p

Expression profiles of differentially expressed predicted signaling peptides.

<p>The X-axis is the six tissues and the Y-axis is the median centered log2 expression. (A) 314 transcripts show high expression in root tissue. (B) 7 transcripts show high expression in meristem tissue. (C) 44 transcripts show high expression in both inflorescence tissue, (D) 24 transcripts show high expression in inflorescence, mature leaf, and stem tissue.</p

<i>De Novo</i> Assembly of the Perennial Ryegrass Transcriptome Using an RNA-Seq Strategy

<div><p>Background</p><p>Perennial ryegrass is a highly heterozygous outbreeding grass species used for turf and forage production. Heterozygosity can affect de-Bruijn graph assembly making <i>de novo</i> transcriptome assembly of species such as perennial ryegrass challenging. Creating a reference transcriptome from a homozygous perennial ryegrass genotype can circumvent the challenge of heterozygosity. The goals of this study were to perform RNA-sequencing on multiple tissues from a highly inbred genotype to develop a reference transcriptome. This was complemented with RNA-sequencing of a highly heterozygous genotype for SNP calling.</p><p>Result</p><p><i>De novo</i> transcriptome assembly of the inbred genotype created 185,833 transcripts with an average length of 830 base pairs. Within the inbred reference transcriptome 78,560 predicted open reading frames were found of which 24,434 were predicted as complete. Functional annotation found 50,890 transcripts with a BLASTp hit from the Swiss-Prot non-redundant database, 58,941 transcripts with a Pfam protein domain and 1,151 transcripts encoding putative secreted peptides. To evaluate the reference transcriptome we targeted the high-affinity K⁺ transporter gene family and found multiple orthologs. Using the longest unique open reading frames as the reference sequence, 64,242 single nucleotide polymorphisms were found. One thousand sixty one open reading frames from the inbred genotype contained heterozygous sites, confirming the high degree of homozygosity.</p><p>Conclusion</p><p>Our study has developed an annotated, comprehensive transcriptome reference for perennial ryegrass that can aid in determining genetic variation, expression analysis, genome annotation, and gene mapping.</p></div

Trasncriptome assembly results.

<p>Trasncriptome assembly results.</p

Plant GO-Slim terms associated with inbred perennial ryegrass reference transcriptome.

<p>Horizontal bar chart of the distribution of plant GO slim terms associated with the inbred genotype P226/135/16 transcripts represented in biological process, cellular component and molecular function categories. X axis is a logarithmic scale.</p

Expression profiles of Falster and Veyo transcripts involved in trehalose-6-phosphate synthesis and degradation.

<p>Falster transcripts are depicted in blue, Veyo transcripts in red. The <i>x</i> axis presents the sample collection time points: I =  autumn conditions, before the start of vernalization; II = 2 days of vernalization; III = 4 weeks of vernalization; IV = 9 weeks of vernalization; V = 7 days of long day conditions. The <i>y</i> axis corresponds to the variance stabilized data from DESeq. The blue background illustrates vernalization treatment, the pink background illustrates long day conditions. Figure adapted from the Plant Metabolic Pathways database (<a href="http://www.plantcyc.org/" target="_blank">http://www.plantcyc.org/</a>).</p

Multidimensional scaling plots of the Falster and Veyo transcriptome assemblies.

<p>The first dimension illustrates grouping based on sample type. The second dimension illustrates grouping based on the sample collection time points (stage of induction). The numbers illustrate the samples as follows: 1 =  leaf samples collected before the start of vernalization; 2 =  leaf samples collected after two days of vernalization; 3 =  leaf samples collected after four weeks of vernalization; 4 =  leaf samples collected after nine weeks of vernalization; 5 =  leaf samples collected after seven long days; 6 =  enriched meristem samples collected after nine weeks of vernalization; 7 =  enriched meristem samples collected after one long day; 8 =  enriched meristem samples collected after seven long days.</p

K-means clustering analysis of transcripts differentially expressed in Falster enriched meristem samples.

<p>K = 25 clusters. The <i>x</i> axis presents the sample collection time points: I = 9 weeks of vernalization; II = 1 long day; III = 7 days of long day conditions. The <i>y</i> axis corresponds to the variance stabilized data from DESeq. The blue background illustrates vernalization treatment, the pink background illustrates long day conditions.</p

Expression profiles of Falster and Veyo transcripts involved in fructan degradation.

<p>Falster transcripts are depicted in blue, Veyo transcripts in red. The <i>x</i> axis presents the sample collection time points: I =  autumn conditions, before the start of vernalization; II = 2 days of vernalization; III = 4 weeks of vernalization; IV = 9 weeks of vernalization; V = 7 days of long day conditions. The <i>y</i> axis corresponds to the variance stabilized data from DESeq. The blue background illustrates vernalization treatment, the pink background illustrates long day conditions. Figure adapted from the Plant Metabolic Pathways database (<a href="http://www.plantcyc.org/" target="_blank">http://www.plantcyc.org/</a>).</p

Summary of SNP discovery data.

<p>Summary of SNP discovery data.</p