Owain R. Edwards

Uncovering the novel characteristics of Asian honey bee, Apis cerana , by whole genome sequencing

BackgroundThe honey bee is an important model system for increasing understanding of molecular and neural mechanisms underlying social behaviors relevant to the agricultural industry and basic science. The western honey bee, Apis mellifera, has served as a model species, and its genome sequence has been published. In contrast, the genome of the Asian honey bee, Apis cerana, has not yet been sequenced. A. cerana has been raised in Asian countries for thousands of years and has brought considerable economic benefits to the apicultural industry. A cerana has divergent biological traits compared to A. mellifera and it has played a key role in maintaining biodiversity in eastern and southern Asia. Here we report the first whole genome sequence of A. cerana.ResultsUsing de novo assembly methods, we produced a 238 Mbp draft of the A. cerana genome and generated 10,651 genes. A.cerana-specific genes were analyzed to better understand the novel characteristics of this honey bee species. Seventy-two percent of the A. cerana-specific genes had more than one GO term, and 1,696 enzymes were categorized into 125 pathways. Genes involved in chemoreception and immunity were carefully identified and compared to those from other sequenced insect models. These included 10 gustatory receptors, 119 odorant receptors, 10 ionotropic receptors, and 160 immune-related genes.ConclusionsThis first report of the whole genome sequence of A. cerana provides resources for comparative sociogenomics, especially in the field of social insect communication. These important tools will contribute to a better understanding of the complex behaviors and natural biology of the Asian honey bee and to anticipate its future evolutionary trajectory.

Aphid resistance in Medicago truncatula involves antixenosis and phloem-specific, inducible antibiosis, and maps to a single locus flanked by NBS-LRR resistance gene analogs

Aphids and related insects feed from a single cell type in plants: the phloem sieve element. Genetic resistance to Acyrthosiphon kondoi Shinji (bluegreen aphid or blue alfalfa aphid) has been identified in Medicago truncatula Gaert. (barrel medic) and backcrossed into susceptible cultivars. The status of M. truncatula as a model legume allows an in-depth study of defense against this aphid at physiological, biochemical, and molecular levels. In this study, two closely related resistant and susceptible genotypes were used to characterize the aphid-resistance phenotype. Resistance conditions antixenosis since migratory aphids were deterred from settling on resistant plants within 6 h of release, preferring to settle on susceptible plants. Analysis of feeding behavior revealed the trait affects A. kondoi at the level of the phloem sieve element. Aphid reproduction on excised shoots demonstrated that resistance requires an intact plant. Antibiosis against A. kondoi is enhanced by prior infestation, indicating induction of this phloem-specific defense. Resistance segregates as a single dominant gene, AKR (Acyrthosiphon kondoi resistance), in two mapping populations, which have been used to map the locus to a region flanked by resistance gene analogs predicted to encode the CC-NBS-LRR subfamily of resistance proteins. This work provides the basis for future molecular analysis of defense against phloem parasitism in a plant model system.

Predicted effector molecules in the salivary secretome of the pea aphid (Acyrthosiphon pisum): a dual transcriptomic/proteomic approach.

The relationship between aphids and their host plants is thought to be functionally analogous to plant-pathogen interactions. Although virulence effector proteins that mediate plant defenses are well-characterized for pathogens such as bacteria, oomycetes, and nematodes, equivalent molecules in aphids and other phloem-feeders are poorly understood. A dual transcriptomic-proteomic approach was adopted to generate a catalog of candidate effector proteins from the salivary glands of the pea aphid, Acyrthosiphon pisum. Of the 1557 transcript supported and 925 mass spectrometry identified proteins, over 300 proteins were identified with secretion signals, including proteins that had previously been identified directly from the secreted saliva. Almost half of the identified proteins have no homologue outside aphids and are of unknown function. Many of the genes encoding the putative effector proteins appear to be evolving at a faster rate than homologues in other insects, and there is strong evidence that genes with multiple copies in the genome are under positive selection. Many of the candidate aphid effector proteins were previously characterized in typical phytopathogenic organisms (e.g., nematodes and fungi) and our results highlight remarkable similarities in the saliva from plant-feeding nematodes and aphids that may indicate the evolution of common solutions to the plant-parasitic lifestyle.

The i5K Initiative: Advancing Arthropod Genomics for Knowledge, Human Health, Agriculture, and the Environment

Insects and their arthropod relatives including mites, spiders, and crustaceans play major roles in the worlds terrestrial, aquatic, and marine ecosystems. Arthropods compete with humans for food and transmit devastating diseases. They also comprise the most diverse and successful branch of metazoan evolution, with millions of extant species. Here, we describe an international effort to guide arthropod genomic efforts, from species prioritization to methodology and informatics. The 5000 arthropod genomes initiative (i5K) community met formally in 2012 to discuss a roadmap for sequencing and analyzing 5000 high-priority arthropods and is continuing this effort via pilot projects, the development of standard operating procedures, and training of students and career scientists. With university, governmental, and industry support, the i5K Consortium aspires to deliver sequences and analytical tools for each of the arthropod branches and each of the species having beneficial and negative effects on humankind.

Involvement of the octadecanoid pathway in bluegreen aphid resistance in Medicago truncatula

Aphids are major insect pests of plants that feed directly from the phloem. We used the model legume Medicago truncatula Gaert. (barrel medic) to elucidate host resistance to aphids and identified a single dominant gene which confers resistance to Acyrthosiphon kondoi Shinji (bluegreen aphid). To understand how this gene conditions resistance to bluegreen aphid, transcription profiling of 23 defense-related genes representing various signaling pathways was undertaken using a pair of near-isogenic lines that are susceptible or resistant to bluegreen aphid. All salicylic acid- and ethylene-responsive genes tested were induced by bluegreen aphid in resistant and susceptible plants, although there were some differences in the magnitude and kinetics of the induction. In contrast, 10 of 13 genes associated with the octadecanoid pathway were induced exclusively in the resistant plants following bluegreen aphid infestation. These results are in contrast to plant-pathogen interactions where similar sets of defense genes typically are induced in compatible interactions, but to a lesser degree and later than in incompatible interactions. Treatment of susceptible plants with methyl jasmonate reduced bluegreen aphid infestation but not to the same levels as the resistant line. Together, these results strongly suggest that the octadecanoid pathway is important for this naturally derived aphid resistance trait.

A functional DNA methylation system in the pea aphid, Acyrthosiphon pisum.

Methylation of cytosine is one of the main epigenetic mechanisms involved in controlling gene expression. Here we show that the pea aphid (Acyrthosiphon pisum) genome possesses homologues to all the DNA methyltransferases found in vertebrates, and that 0.69% (±0.25%) of all cytosines are methylated. Identified methylation sites are predominantly restricted to the coding sequence of genes at CpG sites. We identify twelve methylated genes, including genes that interact with juvenile hormone, a key endocrine signal in insects. Bioinformatic prediction using CpG ratios for all predicted genes suggest that a large proportion of genes are methylated within the pea aphid.

Characterization of Pea Aphid Resistance in Medicago truncatula

To achieve a thorough understanding of plant-aphid interactions, it is necessary to investigate in detail both the plant and insect side of the interaction. The pea aphid (PA; Acyrthosiphon pisum) has been selected by an international consortium as the model species for genetics and genomics studies, and the model legume Medicago truncatula is a host of this aphid. In this study, we identified resistance to PA in a M. truncatula line, ‘Jester’, with well-characterized resistance to a closely related aphid, the bluegreen aphid (BGA; Acyrthosiphon kondoi). The biology of resistance to the two aphid species shared similarity, with resistance in both cases occurring at the level of the phloem, requiring an intact plant and involving a combination of antixenosis, antibiosis, and plant tolerance. In addition, PA resistance cosegregated in ‘Jester’ with a single dominant gene for BGA resistance. These results raised the possibility that both resistances may be mediated by the same mechanism. This was not supported by the results of gene induction studies, and resistance induced by BGA had no effect on PA feeding. Moreover, different genetic backgrounds containing a BGA resistance gene from the same resistance donor differ in resistance to PA. These results suggest that distinct mechanisms are involved in resistance to these two aphid species. Resistance to PA and BGA in the same genetic background in M. truncatula makes this plant an attractive model for the study of both plant and aphid components of resistant and susceptible plant-aphid interactions.

Opinion: Is CRISPR-based gene drive a biocontrol silver bullet or global conservation threat?

Scientists have recognized the potential for applying gene drive technologies to the control of invasive species for several years (1, 2), yet debate about the application of gene drive has been primarily restricted to mosquitoes (3). Recent developments in clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 technology have restarted discussions of using gene drive for invasive species control (4).

Safeguarding gene drive experiments in the laboratory

Multiple stringent confinement strategies should be used whenever possible Gene drive systems promote the spread of genetic elements through populations by assuring they are inherited more often than Mendelian segregation would predict (see the figure). Natural examples of gene drive from Drosophila include sex-ratio meiotic drive, segregation distortion, and replicative transposition. Synthetic drive systems based on selective embryonic lethality or homing endonucleases have been described previously in Drosophila melanogaster (1–3), but they are difficult to build or are limited to transgenic populations. In contrast, RNAguided gene drives based on the CRISPR/Cas9 nuclease can, in principle, be constructed by any laboratory capable of making transgenic organisms (4). They have tremendous potential to address global problems in health, agriculture, and conservation, but their capacity to alter wild populations outside the laboratory demands caution (4–7). Just as researchers working with self-propagating pathogens must ensure that these agents do not escape to the outside world, scientists working in the laboratory with gene drive constructs are responsible for keeping them confined (4, 6, 7).

Resistance to insect pests: What do legumes have to offer?

SummaryInsect pests are major problems for all crops, worldwide. In this review we will focus on legumes, which are attacked by a range of insect pests including pod/seed feeders, defoliators and sap feeders. We review the history of breeding for resistance to insect pests in legumes, which has had mixed success, and discuss further opportunities in this area. We also review the extraordinary array of direct and indirect mechanisms contributing to insect defence in legumes, the understanding and exploitation of which offer opportunities for both legume and non-legume crops. There is also good potential to improve insect resistance in legume crops through a detailed understanding of the signaling pathways that regulate induced responses to insect feeding, and recent progress in this area, primarily obtained from non-legume systems, is reviewed. The importance legumes play in farming systems, their wide range of novel chemistry and the emergence of model systems suitable for genomic approaches present opportunities for research in this area strongly linked to breeding programs to help develop legume crops with enhanced insect resistance.