Genome annotations for: Multi-omics approaches define novel aphid effector candidates associated with virulence and avirulence phenotypes

<div> <p><span><span>Peter Thorpe</span></span><span><span>1</span></span><span><span>, Simone Altmann</span></span><span><span>1</span></span><span><span>, Rosa Lopez-Cobollo</span></span><span><span>2</span></span><span><span>, Nadine Douglas</span></span><span><span>3</span></span><span><span>, Javaid Iqbal</span></span><span><span>2</span></span><span><span>, Sadia Kanvil</span></span><span><span>2</span></span><span><span>, </span><span>Jean-Christophe Simon</span></span><span><span>4</span></span><span><span>, </span><span>James </span><span>C. </span><span>Carolan</span></span><span><span>3</span></span><span><span>, Jorunn Bos</span></span><span><span>1</span><span>*</span></span><span><span>, Colin Turnbull</span></span><span><span>2</span><span>*</span></span><span>&nbsp;</span></p> </div> <div> <p><span><span>1</span></span><span><span>School of Life Sciences, University of Dundee, UK;</span> </span><span><span>2</span></span><span><span>Department of Life Sciences, Imperial College London, UK; </span></span><span><span>3</span></span><span><span>Department of Biology, Maynooth University, </span><span>Republic of Ireland</span><span>; </span></span><span><span>4</span></span>&nbsp;<span><span>INRAE , France</span><span>. *Authors for correspondenc</span><span>e: </span></span><a href="mailto:j.bos@dundee.ac.uk" target="_blank" rel="noreferrer noopener"><span><span>j.bos@dundee.ac.uk</span></span></a><span><span>, </span></span><a href="mailto:c.turnbull@imperial.ac.uk" target="_blank" rel="noreferrer noopener"><span><span>c.turnbull@imperial.ac.uk</span></span></a><span><span>.&nbsp;</span></span><span>&nbsp;</span></p> <p>&nbsp;</p> <p><span>This is a repository for the version3 gene predictions and annotation for the pea aphid used for the publication:</span></p> <p>&nbsp;</p> <p><strong><span><span><span>Multi-omics approaches define novel aphid effector candidates associated with </span><span>virulence and </span><span>avirulence</span> <span>phenotypes</span></span><span>&nbsp;</span></span></strong></p> <p>&nbsp;</p> <div> <p><span><span>ABSTRACT</span></span></p> </div> <div> <p><span><span>Background</span></span><span><span>. Compatibility between aphids and plant hosts is genetically </span><span>determined</span><span> by both interacting organisms. For example, plants may carry resistance (R) genes or deploy chemical defences. Aphid saliva </span><span>contains</span><span> many proteins that are secreted into host tissues. </span><span>S</span><span>ubset</span><span>s</span><span> of these proteins are predicted to act as effectors, either subverting or triggering host immunity. However, associating </span><span>particular effectors</span><span> with virulence or </span><span>avirulence</span><span> outcomes presents challenges due to the combinatorial complexity. Here we use defined aphid and host genetics to test for co-segregation of expressed aphid transcripts and proteins with virulent or avirulent phenotypes.</span></span><span>&nbsp;</span></p> </div> <div> <p><span><span>Results</span><span>. </span></span><span><span>We compared virulent and avirulent pea aphid parental genotypes, and their bulk segregant F</span></span><span><span>1</span></span><span><span> progeny on </span></span><span><span>Medicago </span><span>truncatula</span> </span><span><span>genotypes</span></span> <span><span>carrying or lacking the </span></span><span><span>RAP1 </span></span><span><span>resistance </span><span>quantitative trait locus</span><span>. </span><span>D</span><span>ifferential expression </span><span>analysis based on </span><span>RNA sequencing </span><span>of whole bod</span><span>y and head samples, </span><span>in combination with proteomics of saliva and salivary glands</span><span>,</span> <span>enabled us </span><span>to pinpoint proteins </span><span>associated</span><span> with virulence/</span><span>avirulence</span><span> phenotypes. </span></span><span><span><span>There was relatively </span><span>little impact</span><span> of </span></span></span><span><span><span>host genotype, </span></span></span><span><span><span>whereas</span><span> l</span></span></span><span><span>arge numbers of transcripts and proteins were differentially expressed between parental aphids, </span><span>likely a</span><span> reflection of their classification as divergent biotypes within the pea aphid species complex. Many fewer </span><span>transcripts</span> <span>intersected with the equivalent differential expression patterns in the bulked F</span></span><span><span>1</span></span><span><span> progeny, providing an effective filter for removing </span><span>genomic </span><span>background effects</span></span><span><span>. </span><span>Overall, t</span><span>here were more upregulated genes detected in the </span><span>F</span></span><span><span>1</span></span><span> <span>avirulent </span><span>dataset </span><span>compared with the virulent one. </span><span>Some of the</span><span> differentially expressed transcripts </span><span>were also found in the differentially expressed proteomes</span><span>, with a</span><span>minopeptidase N prot</span><span>eins </span><span>being </span><span>t</span><span>he most frequent</span><span> differentially expressed</span><span> family</span></span><span><span>. </span><span>In addition</span><span>, a </span><span>substantial</span> <span>proportion </span><span>(26%) </span><span>of salivary proteins lack annotations, suggesting that </span><span>many </span><span>novel functions </span><span>remain</span><span> to be discovered.&nbsp;</span></span><span>&nbsp;</span></p> </div> <div> <p><span><span>Conclusions.</span></span><span><span> Especially when combined with tightly controlled genetics of both insect and host, multi-</span><span>omic</span><span> approaches are powerful tools for revealing and filtering candidate lists down to plausible genes for further functional analysis as putative </span><span>aphid </span><span>effectors.</span></span><span>&nbsp;</span></p> </div> </div>