With an objective of identifying candidate genes for these diseases, Illumina 1G sequencing was used on the transcriptomes of FW-challenged root tissues and SMD-challenged leaf tissues of five each resistant (ICPL 87119, ICPB 2049, ICPL 20096, BSMR 736 and ICPL 7035) and susceptible genotypes (ICPL 87091, ICPL 99050, TAT 10, ICPL 332 and TTB 7).
It is worth noting that these steps only need to be run once for one population beforehand, and after sig-mers are selected and their connections with transcripts are established, the result can be repeatedly used on quantifying the transcriptome of many samples.
The running median expression values are not normally distributed, and the non-parametric Spearman correlation test was used on the ranks of the paired transcriptome maps.
IL8 (CXCL8 in human) was not DE in our experimental conditions at the transcript level at both T4 and T24, whereas nucleotide probes specific for this gene are available on the microarrays used for the transcriptome analyses.
This transformation has been shown to be well approximated by the square root (Wagner et al. 2013), which is the transformation used on all transcriptomes in this article.
As Arabidopsis is the most thoroughly annotated plant, sequence homology to Arabidopsis was also used to characterize the transcriptome based on Gene Ontology (GO) information.
Because the transcriptome of LG was not available in this data set, we used the transcriptome of the salivary glands as a representative secretory gland.
We used the transcriptome sequencing results of upland cotton genetic standard line TM-1 and carried out expression pattern analysis on 169 GhRabs.
This approach takes advantage of the large amount of annotation of the transcriptome and can be used on other arrays with genome-wide coverage.
The presence of the identified proteins in the asexual erythrocytic stages was also checked using the published data on the transcriptome and proteome of this stage of development of P. falciparum (www.PlasmoDB.org; [31]).
