Daniel Mapleson | bioRxiv Science

bioRxiv2016

A clonally reproducing generalist aphid pest colonises diverse host plants by rapid transcriptional plasticity of duplicated gene clusters

BackgroundThe prevailing paradigm of host-parasite evolution is that arms races lead to increasing specialisation via genetic adaptation. Insect herbivores are no exception, and the majority have evolved to colonise a small number of closely related host species. Remarkably, the green peach aphid, Myzus persicae, colonises plant species across 40 families and single M. persicae clonal lineages can colonise distantly related plants. This remarkable ability makes M. persicae a highly destructive pest of many important crop species.\n\nResultsTo investigate the exceptional phenotypic plasticity of M. persicae, we sequenced the M. persicae genome and assessed how one clonal lineage responds to host plant species of different families. We show that genetically identical individuals are able to colonise distantly related host species through the differential regulation of genes belonging to aphid-expanded gene families. Multigene clusters collectively up-regulate in single aphids within two days upon host switch. Furthermore, we demonstrate the functional significance of this rapid transcriptional change using RNA interference (RNAi)-mediated knock-down of genes belonging to the cathepsin B gene family. Knock-down of cathepsin B genes reduced aphid fitness, but only on the host that induced up-regulation of these genes.\n\nConclusionsPrevious research has focused on the role of genetic adaptation of parasites to their hosts. Here we show that the generalist aphid pest M. persicae is able to colonise diverse host plant species in the absence of genetic specialisation. This is achieved through rapid transcriptional plasticity of genes that have duplicated during aphid evolution.

Genomics↗

bioRxiv2016

KAT: A K-mer Analysis Toolkit to quality control NGS datasets and genome assemblies

MotivationDe novo assembly of whole genome shotgun (WGS) next-generation sequencing (NGS) data bene[fi]ts from high-quality input with high coverage. However, in practice, determining the quality and quantity of useful reads quickly and in a reference-free manner is not trivial. Gaining a better understanding of the WGS data, and how that data is utilised by assemblers, provides useful insights that can inform the assembly process and result in better assemblies.\n\nResultsWe present the K-mer Analysis Toolkit (KAT): a multi-purpose software toolkit for reference-free quality control (QC) of WGS reads and de novo genome assemblies, primarily via their k-mer frequencies and GC composition. KAT enables users to assess levels of errors, bias and contamination at various stages of the assembly process. In this paper we highlight KATs ability to provide valuable insights into assembly composition and quality of genome assemblies through pairwise comparison of k-mers present in both input reads and the assemblies.\n\nAvailabilityKAT is available under the GPLv3 license at: https://github.com/TGAC/KAT.\n\nContactbernardo.clavijo@earlham.ac.uk\n\nSupplementary InformationSupplementary Information (SI) is available at Bioinformatics online. In addition, the software documentation is available online at: http://kat.readthedocs.io/en/latest/.

Bioinformatics↗