Figure 1.
Strategy to obtain extended representation of the expressed Ae. sharonensis leaf gene space.
Overview showing the sequence input (far left), assembly program (Newbler or CAP3; top), and parameters (default, strict or relaxed; see Methods), for each assembly, and extraction of a non-redundant sequence set.
Figure 2.
The overlap of Ae. sharonensis best reciprocal BLAST hits against four grass proteomes.
(A) Contigs of the Newbler default assembly. The core set of 7,740 common orthologs of Ae. sharonensis among all grasses represents 35.6% of all four grass orthologs for this assembly. (B) Isotigs of the Newbler default assembly. The core set of 7,719 common orthologs represents 63.3% of all the four grass orthologs for this assembly. (C) Contigs of the ‘CAP3 relaxed’ assembly. The core set of 6,038 common orthologs represents 56.1% of all the four grass orthologs for this assembly.
Figure 3.
GO molecular function categories hits.
Frequencies of contig/isotig hits in the top 20 GO term categories from two Ae. sharonensis transcriptome assemblies (contigs and isotigs from the Newbler default assembly and contigs from the CAP3 relaxed assembly). (A) Molecular Function categories. (B) Biological Processes categories.
Figure 4.
Analysis of the prediction approaches for members of the NB-LRR gene family.
(A) Flowcharts of the two NB-LRR prediction approaches; HMM based left, BLAST and GO terms right. (B) Venn diagrams depicting overlaps between the two approaches.
Figure 5.
Analysis of heterozygosity in Ae sharonensis accessions 1644 and 2232.
Histograms of the ratio between the most and least frequently observed alleles of individual SNP with read coverage of ≥20 between accessions (A) 1644 and (B) 2232 using the ‘Combined Newbler Default Isotigs’. Heterozygous SNP-bearing Unigenes were identified using a ratio threshold of 3.0 (most versus least frequently observed allele within a genotype) and mapped using best reciprocal BLAST hits to genes in the barley consensus genetic map (C). Dot size reflects number of SNPs in a genetic bin (see legend).