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Comparative gene expression analysis reveals mechanism of Pinus contorta response to the fungal pathogen Dothistroma septosporum
Lu, Mengmeng; Feau, Nicolas; Obreht Vidakovic, Dragana; Ukrainetz, Nicholas; Wong, Barbara; Aitken, Sally; Hamelin, Richard; Yeaman, Sam — 2020-11-17 <p>Many conifers have distributions that span wide ranges in both biotic and abiotic conditions, but the basis of response to biotic stress has received much less attention than response to abiotic stress. In this study,<span style="background-color:#ffffff;"> w</span>e investigated the gene expression response of lodgepole pine (<i>Pinus contorta</i>) to attack by the fungal pathogen <i>Dothistroma septosporum</i>, which causes <i>Dothistroma </i>needle blight (DNB), a disease that has caused severe climate-related outbreaks in northwestern British Columbia. We inoculated tolerant and susceptible pines with two <i>D. septosporum</i> isolates and analyzed the differentially expressed genes, differential exon usage, and co-expressed gene modules using RNA-seq data. We found a rapid and strong transcriptomic response in tolerant lodgepole pine samples inoculated with one <i>D. septosporum</i> isolate, and a late and weak response in susceptible samples inoculated with another isolate. We mapped 43 of the DEG- or gene-module-identified genes to the reference plant-pathogen interaction pathway deposited in KEGG database. These genes are present in PAMP-triggered and effector-triggered immunity pathways, including genes encoding mitogen-activated protein kinase and disease resistance protein. Genes comprising pathways and gene modules had signatures of strong selective constraint, while the highly expressed genes in tolerant samples appear to have been favored by selection to counterattack the pathogen. We identified candidate resistance genes that may respond to <i>D. septosporum</i> effectors. Taken together, our results show that gene expression response to <i>D. septosporum</i> infection in lodgepole pine varies both among tree genotypes and pathogen strains, and involves both known candidate genes and a number of genes with previously unknown functions.</p>
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Genome-scale phylogeography resolves the native population structure of the Asian longhorned beetle, Anoplophora glabripennis (Motschulsky)
Cui, Mingming; Wu, Yunke; Javal, Marion; Giguère, Isabelle; Roux, Géraldine; Andres, Jose; Keena, Melody; Shi, Juan; Wang, Baode; Braswell, Evan; Pfister, Scott; Hamelin, Richard; Roe, Amanda; Porth, Ilga — 2022-04-28 <p><span lang="EN-US">Human assisted movement has allowed the Asian longhorned beetle (ALB, <em>Anoplophora glabripennis</em> (Motschulsky)) to spread beyond its native range and become a globally regulated invasive pest. Within its native range of China and the Korean peninsula, human-mediated dispersal has also caused cryptic translocation of insects, resulting in population structure complexity. Previous studies used genetic methods to detangle this complexity but were unable to clearly delimit native populations which is needed to develop downstream biosurveillance tools. We used genome-wide markers to define historical population structure in native ALB populations and contemporary movement between regions. We used genotyping-by-sequencing to generate 6,102 single nucleotide polymorphisms (SNPs) and amplicon sequencing to genotype 53 microsatellites. In total, we genotyped</span> <span lang="EN-US">712 individuals from</span> <span lang="EN-US">ALB’s native distribution. We observed six distinct population clusters among native ALB populations, with a clear delineation between northern and southern groups. Most of the individuals from South Korea were distinct from populations in China. Our results also indicate historical divergence among populations and suggest limited large-scale admixture, but we did identify a restricted number of cases of contemporary movement between regions. We identified SNPs under selection and describe a clinal allele frequency pattern in a missense variant associated with glycerol kinase, an important enzyme in the utilization of an insect cryoprotectant. We further demonstrate that small numbers of SNPs can assign individuals to geographic regions with high probability, paving the way for novel ALB biosurveillance tools.</span></p>

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(Author: Hamelin, Richard)

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