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The effects of different TopHap alignment parameters on the proportion of RNA-seq reads misaligned to single copy homoeologous genes in the wheat genome. To reduce false variant calling rate in the highly duplicated genomic regions, a maximum read coverage depth for each variable site was set to be two times the mean coverage depth for entire genome. Table S3. Schafer J, Strimmer K. In other words, it seems that very different systematic changes caused by each isolate treatment can produce very similar results with regard to these SA-responsive genes. Nat Protoc.
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Comparison of Pgt -wheat gene co-expression networks. To investigate whether the degree of GO sub-network conservation is related to the sequence level conservation of effector candidates between the isolates, we compared the proportion conserved edges within each sub-network with the degree of DNA sequence conservation as described in Fig.
Genome Biol Evol. In light of what is known about the genes in the GO sub-networks it is perhaps unsurprising that these same five SA-responsive genes are modulated in a similar manner by two different Pgt isolates.
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Between the two isolate-specific networks, edges linking wheat nodes to other wheat nodes were The results of the permutations revealed that many of the GO sub-networks within the experimental dataset show a significantly higher degree of edge conservation than is expected between randomly generated networks of equal size and degree of connectedness.
Additional file 6: File contain the results of k-means clustering and GO term enrichment analyses. Here, we have performed the comparative analyses of genomic and transcriptomic data for two North American Pgt isolates showing distinct virulence profiles on the panel of wheat lines carrying known stem rust resistance genes [ 40 ].
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To assure that RNA-seq reads are mapped to the correct copies of genes within the polyploid genome, the parameters of the Tophat aligner [ 37 ] were optimized using a subset of reads mapping to a homoeologous set of genes present in single copy in each of the wheat genomes. Obligate biotrophy features unraveled by the genomic analysis of rust fungi. As rapid urbanization and growth in the 19th century pushed families westward, men and women often found themselves sharing in domestic and work-related activities.