Determination of Significantly Differentially Expressed Candidate Effectors of Striga at Stages 3 and 4.1 of Infection in the Host and their Functions
Anyolo, Ahija Laban
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Striga (witchweed) is a successful parasitic plant whose interaction with the host is poorly understood, making it difficult to control. Plants become visibly stunted in 2-4 days of attachment by the parasitic plant and hence any control strategy has to act before or immediately after attachment in the host. Like other plant pathogens, the parasitic plant may be producing effectors that helps it in overcoming the host immunity. Firstly, the study screened for candidate effectors on transcriptome data of Striga asiatica and Striga hermonthica using bioinformatics tools namely; SignalPV4.1b, TmhmmV2.0c and TargetP and obtained sequences that have a signal peptide, a cleavage site within the first 40 amino acids, with no transmembrane domain after the cleaved region and not targeted to the mitochondria. Secondly, the study obtained expression levels of Striga asiatica and Striga hermonthica transcriptomes at stages 3 and 4.1 of infection in the host using cufflinks and performed differential gene expression analysis using DESeq2 package in R to obtain genes that are significantly differentially expressed at stages 3 and 4.1 using a threshold of p-value ≤ 0.05. The study then identified virulence genes that are significantly differentially expressed at stages 3 and 4.1 of infection in the host. Lastly, the study identified functions of this virulence genes using bioinformatics tool Blast2GO/OmicsBox and amplified key effectors using PCR. In Striga asiatica, the study identified 80 significantly differentially expressed effector genes at stage 3, 59 at stage 4.1 and 38 at both stage 3 and stage 4.1 of infection in the host. In Striga hermonthica, the study identified 156 significantly differentially expressed effector genes at stage 3, 148 at stage 4.1 and 60 at both stage 3 and stage 4.1 of infection in the host. Functions of candidate effectors majorly comprised of cell wall degrading enzymes that are very important in penetration of the parasite in the host, catalytic enzymes that may obtain nutrients or subdue host immunity by targeting proteins and sugars and enzymes that may inhibit immune response or neutralize the environment. The study amplified 5 virulence genes which are cell wall degrading enzymes namely; pectate lyase, pectinesterase 53, pectate lyase 4, xyloglucan endotransglucosylase and another xyloglucan endotransglucosylase. This study is very important in understanding the molecular basis of virulence in Striga and will aid in expanding the genetic basis of Striga resistance in the host so that resistance is broadspectrum and durable.