A draft Diabrotica virgifera virgifera genome: insights into control and host plant adaption by a major maize pest insect.

BACKGROUND: Adaptations by arthropod pests to host plant defenses of crops determine their impacts on agricultural production. The larval host range of western corn rootworm, Diabrotica virgifera virgifera (Coleoptera: Chrysomelidae), is restricted to maize and a few grasses. Resistance of D. v. virgifera to crop rotation practices and multiple insecticides contributes to its status as the most damaging pest of cultivated maize in North America and Europe. The extent to which adaptations by this pest contributes to host plant specialization remains unknown. RESULTS: A 2.42 Gb draft D. v. virgifera genome, Dvir_v2.0, was assembled from short shotgun reads and scaffolded using long-insert mate-pair, transcriptome and linked read data. K-mer analysis predicted a repeat content of ≥ 61.5%. Ortholog assignments for Dvir_2.0 RefSeq models predict a greater number of species-specific gene duplications, including expansions in ATP binding cassette transporter and chemosensory gene families, than in other Coleoptera. A majority of annotated D. v. virgifera cytochrome P450s belong to CYP4, 6, and 9 clades. A total of 5,404 transcripts were differentially-expressed between D. v. virgifera larvae fed maize roots compared to alternative host (Miscanthus), a marginal host (Panicum virgatum), a poor host (Sorghum bicolor) and starvation treatments; Among differentially-expressed transcripts, 1,908 were shared across treatments and the least number were between Miscanthus compared to maize. Differentially-expressed transcripts were enriched for putative spliceosome, proteosome, and intracellular transport functions. General stress pathway functions were unique and enriched among up-regulated transcripts in marginal host, poor host, and starvation responses compared to responses on primary (maize) and alternate hosts. CONCLUSIONS: Manual annotation of D. v. virgifera Dvir_2.0 RefSeq models predicted expansion of paralogs with gene families putatively involved in insecticide resistance and chemosensory perception. Our study also suggests that adaptations of D. v. virgifera larvae to feeding on an alternate host plant invoke fewer transcriptional changes compared to marginal or poor hosts. The shared up-regulation of stress response pathways between marginal host and poor host, and starvation treatments may reflect nutrient deprivation. This study provides insight into transcriptomic responses of larval feeding on different host plants and resources for genomic research on this economically significant pest of maize.

Comparative transcriptomics of ice-crawlers demonstrates cold specialization constrains niche evolution in a relict lineage.

Key changes in ecological niche space are often critical to understanding how lineages diversify during adaptive radiations. However, the converse, or understanding why some lineages are depauperate and relictual, is more challenging, as many factors may constrain niche evolution. In the case of the insect order Grylloblattodea, highly conserved thermal breadth is assumed to be closely tied to their relictual status, but has not been formerly tested. Here, we investigate whether evolutionary constraints in the physiological tolerance of temperature can help explain relictualism in this lineage. Using a comparative transcriptomics approach, we investigate gene expression following acute heat and cold stress across members of Grylloblattodea and their sister group, Mantophasmatodea. We additionally examine patterns of protein evolution, to identify candidate genes of positive selection. We demonstrate that cold specialization in Grylloblattodea has been accompanied by the loss of the inducible heat shock response under both acute heat and cold stress. Additionally, there is widespread evidence of selection on protein-coding genes consistent with evolutionary constraints due to cold specialization. This includes positive selection on genes involved in trehalose transport, metabolic function, mitochondrial function, oxygen reduction, oxidative stress, and protein synthesis. These patterns of molecular adaptation suggest that Grylloblattodea have undergone evolutionary trade-offs to survive in cold habitats and should be considered highly vulnerable to climate change. Finally, our transcriptomic data provide a robust backbone phylogeny for generic relationships within Grylloblattodea and Mantophasmatodea. Major phylogenetic splits in each group relate to arid conditions driving biogeographical patterns, with support for a sister-group relationship between North American Grylloblatta and Altai-Sayan Grylloblattella, and a range disjunction in Namibia splitting major clades within Mantophasmatodea.

The evolutionary dynamics of variant antigen genes in Babesia reveal a history of genomic innovation underlying host-parasite interaction.

Babesia spp. are tick-borne, intraerythrocytic hemoparasites that use antigenic variation to resist host immunity, through sequential modification of the parasite-derived variant erythrocyte surface antigen (VESA) expressed on the infected red blood cell surface. We identified the genomic processes driving antigenic diversity in genes encoding VESA (ves1) through comparative analysis within and between three Babesia species, (B. bigemina, B. divergens and B. bovis). Ves1 structure diverges rapidly after speciation, notably through the evolution of shortened forms (ves2) from 5' ends of canonical ves1 genes. Phylogenetic analyses show that ves1 genes are transposed between loci routinely, whereas ves2 genes are not. Similarly, analysis of sequence mosaicism shows that recombination drives variation in ves1 sequences, but less so for ves2, indicating the adoption of different mechanisms for variation of the two families. Proteomic analysis of the B. bigemina PR isolate shows that two dominant VESA1 proteins are expressed in the population, whereas numerous VESA2 proteins are co-expressed, consistent with differential transcriptional regulation of each family. Hence, VESA2 proteins are abundant and previously unrecognized elements of Babesia biology, with evolutionary dynamics consistently different to those of VESA1, suggesting that their functions are distinct.

Antigen cocktails: valid hypothesis or unsubstantiated hope?

After more than three decades of research into the development of vaccines against parasites, a substantial number of antigens have been identified that, as purified native proteins or recombinant proteins, induce some protection against the target parasite. Very few achieve a degree of efficacy likely to make them candidates for single-antigen vaccines. Therefore, multi-antigen or 'cocktail' vaccines are proposed based on the assumption that such cocktails will show enhanced efficacy. This assumption, although often poorly acknowledged, has become central to much vaccine research. The experimental evidence for it, however, is extremely scarce and contradictory. The efficacy of multicomponent vaccines deserves greater experimental attention than it has received.

Acaricide rotation strategy for managing resistance in the tick Rhipicephalus (Boophilus) microplus (Acarina: Ixodidae): laboratory experiment with a field strain from Costa Rica.

During the past two decades, resistance to pyrethroids within the cattle tick genus Boophilus has caused tick control problems in various tropical countries, mainly in Latin America, southern Africa, Australia, and New Caledonia. A Rhipicephalus (Boophilus) microplus (Canestrini) strain from Costa Rica, exhibiting resistance to the pyrethroid deltamethrin but only a very low resistance to organophosphates (OP) was kept under selection pressure for 9 to 11 generations by using deltamethrin or coumaphos (OP), either exclusively or in rotation. The objective of this acaricide rotation was to examine the possibility of delaying or reducing the full emergence of pyrethroid resistance. In the substrain selected with deltamethrin at the LD50 concentration, resistance to deltamethrin was measured after five generations (resistance factor [RF] = 9.2) and very high resistance after 11 generations (RF = 756), compared with the starting field strain from Costa Rica. In the substrain selected with deltamethrin then coumaphos in rotation, resistance to deltamethrin was variable from one generation to the next (RF = 1-4.2), but no high, stable resistance developed. After 10 generations of rotation, the deltamethrin RF was 1.6. In the substrains selected continuously with coumaphos or coumaphos and deltamethrin in rotation, no consistent change in resistance to coumaphos was observed. Rotation of deltamethrin with coumaphos seems to delay the development of strong resistance to deltamethrin in a population that had initially a low level of deltamethrin resistance.

A ten-year review of commercial vaccine performance for control of tick infestations on cattle.

Ticks are important ectoparasites of domestic and wild animals, and tick infestations economically impact cattle production worldwide. Control of cattle tick infestations has been primarily by application of acaricides which has resulted in selection of resistant ticks and environmental pollution. Herein we discuss data from tick vaccine application in Australia, Cuba, Mexico and other Latin American countries. Commercial tick vaccines for cattle based on the Boophilus microplus Bm86 gut antigen have proven to be a feasible tick control method that offers a cost-effective, environmentally friendly alternative to the use of acaricides. Commercial tick vaccines reduced tick infestations on cattle and the intensity of acaricide usage, as well as increasing animal production and reducing transmission of some tick-borne pathogens. Although commercialization of tick vaccines has been difficult owing to previous constraints of antigen discovery, the expense of testing vaccines in cattle, and company restructuring, the success of these vaccines over the past decade has clearly demonstrated their potential as an improved method of tick control for cattle. Development of improved vaccines in the future will be greatly enhanced by new and efficient molecular technologies for antigen discovery and the urgent need for a tick control method to reduce or replace the use of acaricides, especially in regions where extensive tick resistance has occurred.

Advances in the genomics of ticks and tick-borne pathogens.

Ticks and the diseases for which they are vectors engage in complex interactions with their mammalian hosts. These interactions involve the developmental processes of tick and pathogen, and interplay between the defensive responses and counter responses of host, tick and pathogen. Understanding these interactions has long been an intractable problem, but progress is now being made thanks to the flood of genomic information on host, tick and pathogen, and the attendant, novel experimental tools that have been generated. Each advance reveals new levels of complexity, but there are encouraging signs that genomics is leading to novel means of parasite control.

Sequencing a new target genome: the Boophilus microplus (Acari: Ixodidae) genome project.

The southern cattle tick, Boophilus microplus (Canestrini), causes annual economic losses in the hundreds of millions of dollars to cattle producers throughout the world, and ranks as the most economically important tick from a global perspective. Control failures attributable to the development of pesticide resistance have become commonplace, and novel control technologies are needed. The availability of the genome sequence will facilitate the development of these new technologies, and we are proposing sequencing to a 4-6X draft coverage. Many existing biological resources are available to facilitate a genome sequencing project, including several inbred laboratory tick strains, a database of approximately 45,000 expressed sequence tags compiled into a B. microplus Gene Index, a bacterial artificial chromosome (BAC) library, an established B. microplus cell line, and genomic DNA suitable for library synthesis. Collaborative projects are underway to map BACs and cDNAs to specific chromosomes and to sequence selected BAC clones. When completed, the genome sequences from the cow, B. microplus, and the B. microplus-borne pathogens Babesia bovis and Anaplasma marginale will enhance studies of host-vector-pathogen systems. Genes involved in the regeneration of amputated tick limbs and transitions through developmental stages are largely unknown. Studies of these and other interesting biological questions will be advanced by tick genome sequence data. Comparative genomics offers the prospect of new insight into many, perhaps all, aspects of the biology of ticks and the pathogens they transmit to farm animals and people. The B. microplus genome sequence will fill a major gap in comparative genomics: a sequence from the Metastriata lineage of ticks. The purpose of the article is to synergize interest in and provide rationales for sequencing the genome of B. microplus and for publicizing currently available genomic resources for this tick.

Tick control: thoughts on a research agenda.

Tick control is critical to the control of tick borne disease, while the direct impact of ticks on livestock productivity is also well known. For livestock, tick control today rests overwhelmingly on the twin approaches of genetics and chemical acaricides, although the disadvantages and limitations of both are recognized. The achievement of the full potential of vaccination, the application of biocontrol agents and the coordinated management of the existing technologies all pose challenging research problems. Progress in many areas has been steady over the last decade, while the acquisition of molecular information has now reached a revolutionary stage. This is likely to have immediate impact on the identification of potential antigens for improved vaccines and novel targets for acaricide action. In many circumstances, the rate limiting step in making scientific progress will remain unchanged, namely the resource constraint on evaluating these appropriately in large animals. For other approaches, such as the use of biocontrol agents, the limitation is likely to be less in the identification of suitable agents than in their delivery in an efficient and cost effective way. Our scientific understanding of the molecular basis for the tick vector-tick borne disease interaction is in its infancy but the area is both challenging and, in the long term, likely to be of great practical importance. What is arguably the most difficult problem of all remains: the translation of laboratory research into the extremely diverse parasite control requirements of farming systems in a way that is practically useful.

Veterinary parasitic vaccines: pitfalls and future directions.

Most available antiparasitic drugs are safe, cheap and highly effective against a broad spectrum of parasites. However, the alarming increase in the number of parasite species that are resistant to these drugs, the issue of residues in the food chain and the lack of new drugs stimulate development of alternative control methods in which vaccines would have a central role. Parasite vaccines are still rare, but there are encouraging signs that their number will increase in the next decade. The modern paradigm is that an understanding of parasite genes will lead to the identification of useful antigens, which can then be produced in recombinant systems developed as a result of the huge investment in biotechnology. However, we should also continue to devote efforts to basic research on the host-parasite interface.

A novel antigen from Anaplasma marginale: characterization, expression and preliminary evaluation of the recombinant protein.

Through a process of protein fractionation and vaccination we previously identified four native antigens that confer a degree of protection against challenge with Anaplasma marginale. One of these, Ana 29 has been successfully cloned and sequenced using degenerate primers designed to N-terminal and internal peptide sequences. The full-length gene codes for a protein with a theoretical molecular weight of 27 kDa and pI 8.6. The sequence is highly conserved, showing 99% identity between two Australian and an American isolate of A. marginale. The gene sequences from these isolates also share 99% identity with the strain of Anaplasma centrale used in the commercial Australian vaccine. Protein prediction algorithms suggest the native protein is an integral membrane protein. This protein has been over-expressed and purified from Escherichia coli and used in vaccination trials in cattle using two adjuvants. The initial results from the trial show a significant level of protection was obtained with one adjuvant; in comparison, the second adjuvant slightly aggravated the disease. Preliminary data suggests a good correlation between the induction of an IgG2 response and protection.

Identification of novel protective antigens from Anaplasma marginale.

A successful recombinant vaccine against Anaplasma marginale remains elusive, despite intensive study of the protective, though variable major surface antigens. As an alternative approach to the discovery of additional antigens, crude parasite material was subjected to conventional protein fractionation, coupled with vaccination and parasite challenge trials, without making assumptions as to the nature or location of these antigens. This has lead to the identification of four novel antigens that, in microgram amounts, have significant protective effects in vaccination trials. The antigens have molecular weights in the range 17-43 kDa and isoelectric points above 7.8. Limited N-terminal and internal sequencing of these antigens has established that they are parasite proteins previously unreported in the literature, although one of the four is identifiable with a recently reported open reading frame of unknown function.

The purine salvage enzyme hypoxanthine guanine xanthine phosphoribosyl transferase is a major target antigen for cell-mediated immunity to malaria.

Although there is good evidence that immunity to the blood stages of malaria parasites can be mediated by different effector components of the adaptive immune system, target antigens for a principal component, effector CD4(+) T cells, have never been defined. We generated CD4(+) T cell lines to fractions of native antigens from the blood stages of the rodent parasite, Plasmodium yoelii, and identified fraction-specific T cells that had a Th1 phenotype (producing IL-2, IFN-gamma, and tumor necrosis factor-alpha, but not IL-4, after antigenic stimulation). These T cells could inhibit parasite growth in recipient severe combined immunodeficient mice. N-terminal sequencing of the fraction showed identity with hypoxanthine guanine xanthine phosphoribosyl transferase (HGXPRT). Recombinant HGXPRT from the human malaria parasite, Plasmodium falciparum, activated the T cells in vitro, and immunization of normal mice with recombinant HGXPRT reduced parasite growth rates in all mice after challenge.