The 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. To 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 upregulate 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 upregulation of these genes. Previous 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.

/pdf/rapid-transcriptional-plasticity-of-duplicated-gene-clusters-25y2phiguc.pdf

Rapid transcriptional plasticity of duplicated gene clusters enables a clonally reproducing aphid to colonise diverse plant species

Mitochondrial genome (mitogenome) plays important roles in evolutionary and ecological studies. It becomes routine to utilize multiple genes on mitogenome or the entire mitogenomes to investigate phylogeny and biodiversity of focal groups with the onset of High Throughput Sequencing (HTS) technologies. We developed a mitogenome toolkit MitoZ, consisting of independent modules of de novo assembly, findMitoScaf (find Mitochondrial Scaffolds), annotation and visualization, that can generate mitogenome assembly together with annotation and visualization results from HTS raw reads. We evaluated its performance using a total of 50 samples of which mitogenomes are publicly available. The results showed that MitoZ can recover more full-length mitogenomes with higher accuracy compared to the other available mitogenome assemblers. Overall, MitoZ provides a one-click solution to construct the annotated mitogenome from HTS raw data and will facilitate large scale ecological and evolutionary studies. MitoZ is free open source software distributed under GPLv3 license and available at https://github.com/linzhi2013/MitoZ.

/pdf/mitoz-a-toolkit-for-animal-mitochondrial-genome-assembly-1c16x98mdy.pdf

MitoZ: a toolkit for animal mitochondrial genome assembly, annotation and visualization.

WormBase ParaSite - a comprehensive resource for helminth genomics.

Parasitic nematodes (roundworms) and platyhelminths (flatworms) cause debilitating chronic infections of humans and animals, decimate crop production and are a major impediment to socioeconomic development. Here we report the broadest comparative study to date of the genomes of parasitic and non-parasitic worms, involving 81. We have identified gene family births and hundreds of expanded gene families at key nodes in the phylogeny that are relevant to parasitism. Examples include gene families that modulate host immune responses, enable parasite migration though host tissues or allow the parasite to feed. We reveal extensive lineage-specific differences in core metabolism and protein families historically targeted for drug development. From an in silico screen, we have identified and prioritised new potential drug targets and compounds for testing. This comparative genomics resource provides a much needed boost for the research community to understand and combat parasitic worms.

/pdf/comparative-genomics-of-the-major-parasitic-worms-4kdqf5ty69.pdf

Comparative genomics of the major parasitic worms

The majority of the 30-100 million people infected with Strongyloides stercoralis, a soil transmitted intestinal nematode, have subclinical (or asymptomatic) infections. These infections are commonly chronic and longstanding because of the autoinfective process associated with its unique life cycle. A change in immune status can increase parasite numbers, leading to hyperinfection syndrome, dissemination, and death if unrecognized. Corticosteroid use and HTLV-1 infection are most commonly associated with the hyperinfection syndrome. Strongyloides adult parasites reside in the small intestine and induce immune responses both local and systemic that remain poorly characterized. Definitive diagnosis of S. stercoralis infection is based on stool examinations for larvae, but newer diagnostics - including new immunoassays and molecular tests - will assume primacy in the next few years. Although good treatment options exist for infection and control of this infection might be possible, S. stercoralis remains largely neglected.

/pdf/human-infection-with-strongyloides-stercoralis-and-other-1cj8dh079e.pdf

Human infection with Strongyloides stercoralis and other related Strongyloides species.

Taisei Kikuchi, Mark Viney, Matthew Berriman and colleagues report the genome sequences of six species of nematodes from the Strongyloides clade of nematodes, including human and animal pathogens, facultative parasites and a free-living species. They find that expansions of the astacin and SCP/TAPS gene families are associated with parasitism in these species.

/pdf/the-genomic-basis-of-parasitism-in-the-strongyloides-clade-1ooa81njf9.pdf

Haruhiko Murayama

Papers

The genomic basis of parasitism in the Strongyloides clade of nematodes