Determination of Significantly Differentially Expressed Candidate Effectors of Striga at Stages 3 and 4.1 of Infection in the Host and their Functions
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Date
2021
Authors
Anyolo, Ahija Laban
Journal Title
Journal ISSN
Volume Title
Publisher
Kenyatta University
Abstract
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.
Description
A Thesis Submitted in Partial Fulfillment of the Requirements for the Award of the Degree of Masters of Science (Biotechnology) in the School of Pure and Applied Science of Kenyatta University, September, 2021
Keywords
Determination, Significantly Differentially, Expressed Candidate Effectors, Striga, Stages 3 and 4.1, Infection in the Host, Functions