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1.  A supergene determines highly divergent male reproductive morphs in the ruff 
Nature genetics  2015;48(1):79-83.
Three strikingly different alternative male mating morphs (aggressive “Independents”, semi-cooperative “Satellites” and female mimic “Faeders”) coexist as a balanced polymorphism in the ruff, Philomachus pugnax, a lek-breeding wading bird1,2,3. Major differences in body size, ornamentation, and aggressive and mating behaviour are inherited as an autosomal polymorphism4,5. We show that development into Satellites and Faeders is determined by a supergene6,7,8 consisting of divergent alternative, dominant, non-recombining haplotypes of an inversion on chromosome 11, which contains 125 predicted genes. Independents are homozygous for the ancestral sequence. One breakpoint of the inversion disrupts the essential Centromere protein N (CENP-N) gene, and pedigree analysis confirms lethality of inversion homozygotes. We describe novel behavioural, testes size, and steroid metabolic differences among morphs, and identify polymorphic genes within the inversion that are likely to contribute to the differences among morphs in reproductive traits.
doi:10.1038/ng.3443
PMCID: PMC5218575  PMID: 26569125
2.  Para‐allopatry in hybridizing fire‐bellied toads (Bombina bombina and B. variegata): Inference from transcriptome‐wide coalescence analyses 
Ancient origins, profound ecological divergence, and extensive hybridization make the fire‐bellied toads Bombina bombina and B. variegata (Anura: Bombinatoridae) an intriguing test case of ecological speciation. Previous modeling has proposed that the narrow Bombina hybrid zones represent strong barriers to neutral introgression. We test this prediction by inferring the rate of gene exchange between pure populations on either side of the intensively studied Kraków transect. We developed a method to extract high confidence sets of orthologous genes from de novo transcriptome assemblies, fitted a range of divergence models to these data and assessed their relative support with analytic likelihood calculations. There was clear evidence for postdivergence gene flow, but, as expected, no perceptible signal of recent introgression via the nearby hybrid zone. The analysis of two additional Bombina taxa (B. v. scabra and B. orientalis) validated our parameter estimates against a larger set of prior expectations. Despite substantial cumulative introgression over millions of years, adaptive divergence of the hybridizing taxa is essentially unaffected by their lack of reproductive isolation. Extended distribution ranges also buffer them against small‐scale environmental perturbations that have been shown to reverse the speciation process in other, more recent ecotypes.
doi:10.1111/evo.12978
PMCID: PMC5129456  PMID: 27282112
Ecological speciation; genome‐wide coalescence; hybrid zone; introgression; RNA‐seq
3.  Imagining Sisyphus happy: DNA barcoding and the unnamed majority 
The vast majority of life on the Earth is physically small, and is classifiable as micro- or meiobiota. These organisms are numerically dominant and it is likely that they are also abundantly speciose. By contrast, the vast majority of taxonomic effort has been expended on ‘charismatic megabionts’: larger organisms where a wealth of morphology has facilitated Linnaean species definition. The hugely successful Linnaean project is unlikely to be extensible to the totality of approximately 10 million species in a reasonable time frame and thus alternative toolkits and methodologies need to be developed. One such toolkit is DNA barcoding, particularly in its metabarcoding or metagenetics mode, where organisms are identified purely by the presence of a diagnostic DNA sequence in samples that are not processed for morphological identification. Building on secure Linnaean foundations, classification of unknown (and unseen) organisms to molecular operational taxonomic units (MOTUs) and deployment of these MOTUs in biodiversity science promises a rewarding resolution to the Sisyphean task of naming all the world's species.
This article is part of the themed issue ‘From DNA barcodes to biomes’.
doi:10.1098/rstb.2015.0329
PMCID: PMC4971181  PMID: 27481781
metabarcoding; Sisyphus; meiofauna
4.  A metagenetic approach to determine the diversity and distribution of cyst nematodes at the level of the country, the field and the individual 
Molecular Ecology  2015;24(23):5842-5851.
Abstract
Distinct populations of the potato cyst nematode (PCN) Globodera pallida exist in the UK that differ in their ability to overcome various sources of resistance. An efficient method for distinguishing between populations would enable pathogen‐informed cultivar choice in the field. Science and Advice for Scottish Agriculture (SASA) annually undertake national DNA diagnostic tests to determine the presence of PCN in potato seed and ware land by extracting DNA from soil floats. These DNA samples provide a unique resource for monitoring the distribution of PCN and further interrogation of the diversity within species.
We identify a region of mitochondrial DNA descriptive of three main groups of G. pallida present in the UK and adopt a metagenetic approach to the sequencing and analysis of all SASA samples simultaneously. Using this approach, we describe the distribution of G. pallida mitotypes across Scotland with field‐scale resolution. Most fields contain a single mitotype, one‐fifth contain a mix of mitotypes, and less than 3% contain all three mitotypes. Within mixed fields, we were able to quantify the relative abundance of each mitotype across an order of magnitude. Local areas within mixed fields are dominated by certain mitotypes and indicate towards a complex underlying ‘pathoscape’. Finally, we assess mitotype distribution at the level of the individual cyst and provide evidence of ‘hybrids’. This study provides a method for accurate, quantitative and high‐throughput typing of up to one thousand fields simultaneously, while revealing novel insights into the national genetic variability of an economically important plant parasite.
doi:10.1111/mec.13434
PMCID: PMC4981918  PMID: 26607216
distribution; diversity; metagenetics; mitotype; potato cyst nematode
5.  The genome of the emerging barley pathogen Ramularia collo-cygni 
BMC Genomics  2016;17:584.
Background
Ramularia collo-cygni is a newly important, foliar fungal pathogen of barley that causes the disease Ramularia leaf spot. The fungus exhibits a prolonged endophytic growth stage before switching life habit to become an aggressive, necrotrophic pathogen that causes significant losses to green leaf area and hence grain yield and quality.
Results
The R. collo-cygni genome was sequenced using a combination of Illumina and Roche 454 technologies. The draft assembly of 30.3 Mb contained 11,617 predicted gene models. Our phylogenomic analysis confirmed the classification of this ascomycete fungus within the family Mycosphaerellaceae, order Capnodiales of the class Dothideomycetes. A predicted secretome comprising 1053 proteins included redox-related enzymes and carbohydrate-modifying enzymes and proteases. The relative paucity of plant cell wall degrading enzyme genes may be associated with the stealth pathogenesis characteristic of plant pathogens from the Mycosphaerellaceae. A large number of genes associated with secondary metabolite production, including homologs of toxin biosynthesis genes found in other Dothideomycete plant pathogens, were identified.
Conclusions
The genome sequence of R. collo-cygni provides a framework for understanding the genetic basis of pathogenesis in this important emerging pathogen. The reduced complement of carbohydrate-degrading enzyme genes is likely to reflect a strategy to avoid detection by host defences during its prolonged asymptomatic growth. Of particular interest will be the analysis of R. collo-cygni gene expression during interactions with the host barley, to understand what triggers this fungus to switch from being a benign endophyte to an aggressive necrotroph.
Electronic supplementary material
The online version of this article (doi:10.1186/s12864-016-2928-3) contains supplementary material, which is available to authorized users.
doi:10.1186/s12864-016-2928-3
PMCID: PMC4979122  PMID: 27506390
Ramularia leaf spot; Dothideomycetes; Rubellin toxin; Endophyte; Necrotroph; Whole genome sequencing
6.  A molecular palaeobiological exploration of arthropod terrestrialization 
Understanding animal terrestrialization, the process through which animals colonized the land, is crucial to clarify extant biodiversity and biological adaptation. Arthropoda (insects, spiders, centipedes and their allies) represent the largest majority of terrestrial biodiversity. Here we implemented a molecular palaeobiological approach, merging molecular and fossil evidence, to elucidate the deepest history of the terrestrial arthropods. We focused on the three independent, Palaeozoic arthropod terrestrialization events (those of Myriapoda, Hexapoda and Arachnida) and showed that a marine route to the colonization of land is the most likely scenario. Molecular clock analyses confirmed an origin for the three terrestrial lineages bracketed between the Cambrian and the Silurian. While molecular divergence times for Arachnida are consistent with the fossil record, Myriapoda are inferred to have colonized land earlier, substantially predating trace or body fossil evidence. An estimated origin of myriapods by the Early Cambrian precedes the appearance of embryophytes and perhaps even terrestrial fungi, raising the possibility that terrestrialization had independent origins in crown-group myriapod lineages, consistent with morphological arguments for convergence in tracheal systems.
This article is part of the themed issue ‘Dating species divergences using rocks and clocks’.
doi:10.1098/rstb.2015.0133
PMCID: PMC4920334  PMID: 27325830
terrestrialization; molecular palaeobiology; arthropod evolution; molecular clock; phylogeny
7.  The genome of the yellow potato cyst nematode, Globodera rostochiensis, reveals insights into the basis of parasitism and virulence 
Genome Biology  2016;17:124.
Background
The yellow potato cyst nematode, Globodera rostochiensis, is a devastating plant pathogen of global economic importance. This biotrophic parasite secretes effectors from pharyngeal glands, some of which were acquired by horizontal gene transfer, to manipulate host processes and promote parasitism. G. rostochiensis is classified into pathotypes with different plant resistance-breaking phenotypes.
Results
We generate a high quality genome assembly for G. rostochiensis pathotype Ro1, identify putative effectors and horizontal gene transfer events, map gene expression through the life cycle focusing on key parasitic transitions and sequence the genomes of eight populations including four additional pathotypes to identify variation. Horizontal gene transfer contributes 3.5 % of the predicted genes, of which approximately 8.5 % are deployed as effectors. Over one-third of all effector genes are clustered in 21 putative ‘effector islands’ in the genome. We identify a dorsal gland promoter element motif (termed DOG Box) present upstream in representatives from 26 out of 28 dorsal gland effector families, and predict a putative effector superset associated with this motif. We validate gland cell expression in two novel genes by in situ hybridisation and catalogue dorsal gland promoter element-containing effectors from available cyst nematode genomes. Comparison of effector diversity between pathotypes highlights correlation with plant resistance-breaking.
Conclusions
These G. rostochiensis genome resources will facilitate major advances in understanding nematode plant-parasitism. Dorsal gland promoter element-containing effectors are at the front line of the evolutionary arms race between plant and parasite and the ability to predict gland cell expression a priori promises rapid advances in understanding their roles and mechanisms of action.
Electronic supplementary material
The online version of this article (doi:10.1186/s13059-016-0985-1) contains supplementary material, which is available to authorized users.
doi:10.1186/s13059-016-0985-1
PMCID: PMC4901422  PMID: 27286965
Plant-parasitic nematode; Genome sequence; Virulence; Effectors; Horizontal gene transfer
8.  Stage-specific Proteomes from Onchocerca ochengi, Sister Species of the Human River Blindness Parasite, Uncover Adaptations to a Nodular Lifestyle* 
Despite 40 years of control efforts, onchocerciasis (river blindness) remains one of the most important neglected tropical diseases, with 17 million people affected. The etiological agent, Onchocerca volvulus, is a filarial nematode with a complex lifecycle involving several distinct stages in the definitive host and blackfly vector. The challenges of obtaining sufficient material have prevented high-throughput studies and the development of novel strategies for disease control and diagnosis. Here, we utilize the closest relative of O. volvulus, the bovine parasite Onchocerca ochengi, to compare stage-specific proteomes and host-parasite interactions within the secretome. We identified a total of 4260 unique O. ochengi proteins from adult males and females, infective larvae, intrauterine microfilariae, and fluid from intradermal nodules. In addition, 135 proteins were detected from the obligate Wolbachia symbiont. Observed protein families that were enriched in all whole body extracts relative to the complete search database included immunoglobulin-domain proteins, whereas redox and detoxification enzymes and proteins involved in intracellular transport displayed stage-specific overrepresentation. Unexpectedly, the larval stages exhibited enrichment for several mitochondrial-related protein families, including members of peptidase family M16 and proteins which mediate mitochondrial fission and fusion. Quantification of proteins across the lifecycle using the Hi-3 approach supported these qualitative analyses. In nodule fluid, we identified 94 O. ochengi secreted proteins, including homologs of transforming growth factor-β and a second member of a novel 6-ShK toxin domain family, which was originally described from a model filarial nematode (Litomosoides sigmodontis). Strikingly, the 498 bovine proteins identified in nodule fluid were strongly dominated by antimicrobial proteins, especially cathelicidins. This first high-throughput analysis of an Onchocerca spp. proteome across the lifecycle highlights its profound complexity and emphasizes the extremely close relationship between O. ochengi and O. volvulus. The insights presented here provide new candidates for vaccine development, drug targeting and diagnostic biomarkers.
doi:10.1074/mcp.M115.055640
PMCID: PMC4974336  PMID: 27226403
9.  Proteomic analysis of secretory products from the model gastrointestinal nematode Heligmosomoides polygyrus reveals dominance of Venom Allergen-Like (VAL) proteins 
Journal of proteomics  2011;74(9):1573-1594.
The intestinal helminth parasite, Heligmosomoides polygyrus offers a tractable experimental model for human hookworm infections such as Ancylostoma duodenale and veterinary parasites such as Haemonchus contortus. Parasite excretory-secretory (ES) products represent the major focus for immunological and biochemical analyses, and contain immunomodulatory molecules responsible for nematode immune evasion. In a proteomic analysis of adult H. polygyrus secretions (termed HES) matched to an extensive transcriptomic dataset, we identified 374 HES proteins by LC-MS/MS, which were distinct from those in somatic extract HEx, comprising 446 identified proteins, confirming selective export of ES proteins. The predominant secreted protein families were proteases (astacins and other metalloproteases, aspartic, cysteine and serine-type proteases), lysozymes, apyrases and acetylcholinesterases. The most abundant products were members of the highly divergent venom allergen-like (VAL) family, related to Ancylostoma secreted protein (ASP); 25 homologues were identified, with VAL-1 and -2 also shown to be associated with the parasite surface. The dominance of VAL proteins is similar to profiles reported for Ancylostoma and Haemonchus ES products. Overall, this study shows that the secretions of H. polygyrus closely parallel those of clinically important GI nematodes, confirming the value of this parasite as a model of helminth infection.
doi:10.1016/j.jprot.2011.06.002
PMCID: PMC4794625  PMID: 21722761
10.  Formin Is Associated with Left-Right Asymmetry in the Pond Snail and the Frog 
Current Biology  2016;26(5):654-660.
Summary
While components of the pathway that establishes left-right asymmetry have been identified in diverse animals, from vertebrates to flies, it is striking that the genes involved in the first symmetry-breaking step remain wholly unknown in the most obviously chiral animals, the gastropod snails. Previously, research on snails was used to show that left-right signaling of Nodal, downstream of symmetry breaking, may be an ancestral feature of the Bilateria [1, 2]. Here, we report that a disabling mutation in one copy of a tandemly duplicated, diaphanous-related formin is perfectly associated with symmetry breaking in the pond snail. This is supported by the observation that an anti-formin drug treatment converts dextral snail embryos to a sinistral phenocopy, and in frogs, drug inhibition or overexpression by microinjection of formin has a chirality-randomizing effect in early (pre-cilia) embryos. Contrary to expectations based on existing models [3, 4, 5], we discovered asymmetric gene expression in 2- and 4-cell snail embryos, preceding morphological asymmetry. As the formin-actin filament has been shown to be part of an asymmetry-breaking switch in vitro [6, 7], together these results are consistent with the view that animals with diverse body plans may derive their asymmetries from the same intracellular chiral elements [8].
Highlights
•Animals tend to be outwardly symmetric but internally are asymmetric•Unlike other animals, snails show inherited variation in asymmetry•We found that both snails and frogs use a common gene to define left and right•Asymmetry is probably an ancient and conserved property of cells and animals
Davison et al. have discovered a cell scaffolding protein in snails and frogs that controls body asymmetry, either the direction a snail shell coils, or whether a frog heart is placed to the left or right. Body asymmetry in animals, including humans, likely arises from a highly conserved, intrinsic asymmetry of the cell.
doi:10.1016/j.cub.2015.12.071
PMCID: PMC4791482  PMID: 26923788
11.  A single chromosome assembly of Bacteroides fragilis strain BE1 from Illumina and MinION nanopore sequencing data 
GigaScience  2015;4:60.
Background
Second and third generation sequencing technologies have revolutionised bacterial genomics. Short-read Illumina reads result in cheap but fragmented assemblies, whereas longer reads are more expensive but result in more complete genomes. The Oxford Nanopore MinION device is a revolutionary mobile sequencer that can produce thousands of long, single molecule reads.
Results
We sequenced Bacteroides fragilis strain BE1 using both the Illumina MiSeq and Oxford Nanopore MinION platforms. We were able to assemble a single chromosome of 5.18 Mb, with no gaps, using publicly available software and commodity computing hardware. We identified gene rearrangements and the state of invertible promoters in the strain.
Conclusions
The single chromosome assembly of Bacteroides fragilis strain BE1 was achieved using only modest amounts of data, publicly available software and commodity computing hardware. This combination of technologies offers the possibility of ultra-cheap, high quality, finished bacterial genomes.
doi:10.1186/s13742-015-0101-6
PMCID: PMC4670535  PMID: 26640692
12.  Supergroup C Wolbachia, mutualist symbionts of filarial nematodes, have a distinct genome structure 
Open Biology  2015;5(12):150099.
Wolbachia pipientis is possibly the most widespread endosymbiont of arthropods and nematodes. While all Wolbachia strains have historically been defined as a single species, 16 monophyletic clusters of diversity (called supergroups) have been described. Different supergroups have distinct host ranges and symbiotic relationships, ranging from mutualism to reproductive manipulation. In filarial nematodes, which include parasites responsible for major diseases of humans (such as Onchocerca volvulus, agent of river blindness) and companion animals (Dirofilaria immitis, the dog heartworm), Wolbachia has an obligate mutualist role and is the target of new treatment regimens. Here, we compare the genomes of eight Wolbachia strains, spanning the diversity of the major supergroups (A–F), analysing synteny, transposable element content, GC skew and gene loss or gain. We detected genomic features that differ between Wolbachia supergroups, most notably in the C and D clades from filarial nematodes. In particular, strains from supergroup C (symbionts of O. volvulus and D. immitis) present a pattern of GC skew, conserved synteny and lack of transposable elements, unique in the Wolbachia genus. These features could be the consequence of a distinct symbiotic relationship between C Wolbachia strains and their hosts, highlighting underappreciated differences between the mutualistic supergroups found within filarial nematodes.
doi:10.1098/rsob.150099
PMCID: PMC4703054  PMID: 26631376
Wolbachia; GC skew; filarial nematodes; genome characteristics
14.  Oviposition but Not Sex Allocation Is Associated with Transcriptomic Changes in Females of the Parasitoid Wasp Nasonia vitripennis 
G3: Genes|Genomes|Genetics  2015;5(12):2885-2892.
Linking the evolution of the phenotype to the underlying genotype is a key aim of evolutionary genetics and is crucial to our understanding of how natural selection shapes a trait. Here, we consider the genetic basis of sex allocation behavior in the parasitoid wasp Nasonia vitripennis using a transcriptomics approach. Females allocate offspring sex in line with the local mate competition (LMC) theory. Female-biased sex ratios are produced when one or a few females lay eggs on a patch. As the number of females contributing offspring to a patch increases, less female-biased sex ratios are favored. We contrasted the transcriptomic responses of females as they oviposit under conditions known to influence sex allocation: foundress number (a social cue) and the state of the host (parasitized or not). We found that when females encounter other females on a patch or assess host quality with their ovipositors, the resulting changes in sex allocation is not associated with significant changes in whole-body gene expression. We also found that the gene expression changes produced by females as they facultatively allocate sex in response to a host cue and a social cue are very closely correlated. We expanded the list of candidate genes associated with oviposition behavior in Nasonia, some of which may be involved in fundamental processes underlying the ability to facultatively allocate sex, including sperm storage and utilization.
doi:10.1534/g3.115.021220
PMCID: PMC4683659  PMID: 26511500
sex allocation; transcriptomics; behavior; gene expression; local mate competition
15.  A conserved set of maternal genes? Insights from a molluscan transcriptome 
The early animal embryo is entirely reliant on maternal gene products for a ‘jump-start’ that transforms a transcriptionally inactive embryo into a fully functioning zygote. Despite extensive work on model species, it has not been possible to perform a comprehensive comparison of maternally-provisioned transcripts across the Bilateria because of the absence of a suitable dataset from the Lophotrochozoa. As part of an ongoing effort to identify the maternal gene that determines left-right asymmetry in snails, we have generated transcriptome data from 1 to 2-cell and ~32-cell pond snail (Lymnaea stagnalis) embryos. Here, we compare these data to maternal transcript datasets from other bilaterian metazoan groups, including representatives of the Ecydysozoa and Deuterostomia. We found that between 5 and 10% of all L. stagnalis maternal transcripts (~300-400 genes) are also present in the equivalent arthropod (Drosophila melanogaster), nematode (Caenorhabditis elegans), urochordate (Ciona intestinalis) and chordate (Homo sapiens, Mus musculus, Danio rerio) datasets. While the majority of these conserved maternal transcripts (“COMATs”) have housekeeping gene functions, they are a non-random subset of all housekeeping genes, with an overrepresentation of functions associated with nucleotide binding, protein degradation and activities associated with the cell cycle. We conclude that a conserved set of maternal transcripts and their associated functions may be a necessary starting point of early development in the Bilateria. For the wider community interested in discovering conservation of gene expression in early bilaterian development, the list of putative COMATs may be useful resource.
doi:10.1387/ijdb.140121ad
PMCID: PMC4594767  PMID: 25690965
maternal to zygotic transition; mollusk; MBT; MZT; Spiralia
16.  ReproPhylo: An Environment for Reproducible Phylogenomics 
PLoS Computational Biology  2015;11(9):e1004447.
The reproducibility of experiments is key to the scientific process, and particularly necessary for accurate reporting of analyses in data-rich fields such as phylogenomics. We present ReproPhylo, a phylogenomic analysis environment developed to ensure experimental reproducibility, to facilitate the handling of large-scale data, and to assist methodological experimentation. Reproducibility, and instantaneous repeatability, is built in to the ReproPhylo system and does not require user intervention or configuration because it stores the experimental workflow as a single, serialized Python object containing explicit provenance and environment information. This ‘single file’ approach ensures the persistence of provenance across iterations of the analysis, with changes automatically managed by the version control program Git. This file, along with a Git repository, are the primary reproducibility outputs of the program. In addition, ReproPhylo produces an extensive human-readable report and generates a comprehensive experimental archive file, both of which are suitable for submission with publications. The system facilitates thorough experimental exploration of both parameters and data. ReproPhylo is a platform independent CC0 Python module and is easily installed as a Docker image or a WinPython self-sufficient package, with a Jupyter Notebook GUI, or as a slimmer version in a Galaxy distribution.
doi:10.1371/journal.pcbi.1004447
PMCID: PMC4559436  PMID: 26335558
17.  Statistical models for RNA-seq data derived from a two-condition 48-replicate experiment 
Bioinformatics  2015;31(22):3625-3630.
Motivation: High-throughput RNA sequencing (RNA-seq) is now the standard method to determine differential gene expression. Identifying differentially expressed genes crucially depends on estimates of read-count variability. These estimates are typically based on statistical models such as the negative binomial distribution, which is employed by the tools edgeR, DESeq and cuffdiff. Until now, the validity of these models has usually been tested on either low-replicate RNA-seq data or simulations.
Results: A 48-replicate RNA-seq experiment in yeast was performed and data tested against theoretical models. The observed gene read counts were consistent with both log-normal and negative binomial distributions, while the mean-variance relation followed the line of constant dispersion parameter of ∼0.01. The high-replicate data also allowed for strict quality control and screening of ‘bad’ replicates, which can drastically affect the gene read-count distribution.
Availability and implementation: RNA-seq data have been submitted to ENA archive with project ID PRJEB5348.
Contact: g.j.barton@dundee.ac.uk
doi:10.1093/bioinformatics/btv425
PMCID: PMC4754627  PMID: 26206307
18.  The evolution of parasitism in Nematoda 
Parasitology  2014;142(Suppl 1):S26-S39.
SUMMARY
Nematodes are abundant and diverse, and include many parasitic species. Molecular phylogenetic analyses have shown that parasitism of plants and animals has arisen at least 15 times independently. Extant nematode species also display lifestyles that are proposed to be on the evolutionary trajectory to parasitism. Recent advances have permitted the determination of the genomes and transcriptomes of many nematode species. These new data can be used to further resolve the phylogeny of Nematoda, and identify possible genetic patterns associated with parasitism. Plant-parasitic nematode genomes show evidence of horizontal gene transfer from other members of the rhizosphere, and these genes play important roles in the parasite-host interface. Similar horizontal transfer is not evident in animal parasitic groups. Many nematodes have bacterial symbionts that can be essential for survival. Horizontal transfer from symbionts to the nematode is also common, but its biological importance is unclear. Over 100 nematode species are currently targeted for sequencing, and these data will yield important insights into the biology and evolutionary history of parasitism. It is important that these new technologies are also applied to free-living taxa, so that the pre-parasitic ground state can be inferred, and the novelties associated with parasitism isolated.
doi:10.1017/S0031182014000791
PMCID: PMC4413787  PMID: 24963797
Nematoda; nematodes; parasitism; evolution; genome; symbiont; Wolbachia; phylogeny; horizontal gene transfer
19.  The genomes of two key bumblebee species with primitive eusocial organization 
Sadd, Ben M | Barribeau, Seth M | Bloch, Guy | de Graaf, Dirk C | Dearden, Peter | Elsik, Christine G | Gadau, Jürgen | Grimmelikhuijzen, Cornelis JP | Hasselmann, Martin | Lozier, Jeffrey D | Robertson, Hugh M | Smagghe, Guy | Stolle, Eckart | Van Vaerenbergh, Matthias | Waterhouse, Robert M | Bornberg-Bauer, Erich | Klasberg, Steffen | Bennett, Anna K | Câmara, Francisco | Guigó, Roderic | Hoff, Katharina | Mariotti, Marco | Munoz-Torres, Monica | Murphy, Terence | Santesmasses, Didac | Amdam, Gro V | Beckers, Matthew | Beye, Martin | Biewer, Matthias | Bitondi, Márcia MG | Blaxter, Mark L | Bourke, Andrew FG | Brown, Mark JF | Buechel, Severine D | Cameron, Rossanah | Cappelle, Kaat | Carolan, James C | Christiaens, Olivier | Ciborowski, Kate L | Clarke, David F | Colgan, Thomas J | Collins, David H | Cridge, Andrew G | Dalmay, Tamas | Dreier, Stephanie | du Plessis, Louis | Duncan, Elizabeth | Erler, Silvio | Evans, Jay | Falcon, Tiago | Flores, Kevin | Freitas, Flávia CP | Fuchikawa, Taro | Gempe, Tanja | Hartfelder, Klaus | Hauser, Frank | Helbing, Sophie | Humann, Fernanda C | Irvine, Frano | Jermiin, Lars S | Johnson, Claire E | Johnson, Reed M | Jones, Andrew K | Kadowaki, Tatsuhiko | Kidner, Jonathan H | Koch, Vasco | Köhler, Arian | Kraus, F Bernhard | Lattorff, H Michael G | Leask, Megan | Lockett, Gabrielle A | Mallon, Eamonn B | Antonio, David S Marco | Marxer, Monika | Meeus, Ivan | Moritz, Robin FA | Nair, Ajay | Näpflin, Kathrin | Nissen, Inga | Niu, Jinzhi | Nunes, Francis MF | Oakeshott, John G | Osborne, Amy | Otte, Marianne | Pinheiro, Daniel G | Rossié, Nina | Rueppell, Olav | Santos, Carolina G | Schmid-Hempel, Regula | Schmitt, Björn D | Schulte, Christina | Simões, Zilá LP | Soares, Michelle PM | Swevers, Luc | Winnebeck, Eva C | Wolschin, Florian | Yu, Na | Zdobnov, Evgeny M | Aqrawi, Peshtewani K | Blankenburg, Kerstin P | Coyle, Marcus | Francisco, Liezl | Hernandez, Alvaro G | Holder, Michael | Hudson, Matthew E | Jackson, LaRonda | Jayaseelan, Joy | Joshi, Vandita | Kovar, Christie | Lee, Sandra L | Mata, Robert | Mathew, Tittu | Newsham, Irene F | Ngo, Robin | Okwuonu, Geoffrey | Pham, Christopher | Pu, Ling-Ling | Saada, Nehad | Santibanez, Jireh | Simmons, DeNard | Thornton, Rebecca | Venkat, Aarti | Walden, Kimberly KO | Wu, Yuan-Qing | Debyser, Griet | Devreese, Bart | Asher, Claire | Blommaert, Julie | Chipman, Ariel D | Chittka, Lars | Fouks, Bertrand | Liu, Jisheng | O’Neill, Meaghan P | Sumner, Seirian | Puiu, Daniela | Qu, Jiaxin | Salzberg, Steven L | Scherer, Steven E | Muzny, Donna M | Richards, Stephen | Robinson, Gene E | Gibbs, Richard A | Schmid-Hempel, Paul | Worley, Kim C
Genome Biology  2015;16(1):76.
Background
The shift from solitary to social behavior is one of the major evolutionary transitions. Primitively eusocial bumblebees are uniquely placed to illuminate the evolution of highly eusocial insect societies. Bumblebees are also invaluable natural and agricultural pollinators, and there is widespread concern over recent population declines in some species. High-quality genomic data will inform key aspects of bumblebee biology, including susceptibility to implicated population viability threats.
Results
We report the high quality draft genome sequences of Bombus terrestris and Bombus impatiens, two ecologically dominant bumblebees and widely utilized study species. Comparing these new genomes to those of the highly eusocial honeybee Apis mellifera and other Hymenoptera, we identify deeply conserved similarities, as well as novelties key to the biology of these organisms. Some honeybee genome features thought to underpin advanced eusociality are also present in bumblebees, indicating an earlier evolution in the bee lineage. Xenobiotic detoxification and immune genes are similarly depauperate in bumblebees and honeybees, and multiple categories of genes linked to social organization, including development and behavior, show high conservation. Key differences identified include a bias in bumblebee chemoreception towards gustation from olfaction, and striking differences in microRNAs, potentially responsible for gene regulation underlying social and other traits.
Conclusions
These two bumblebee genomes provide a foundation for post-genomic research on these key pollinators and insect societies. Overall, gene repertoires suggest that the route to advanced eusociality in bees was mediated by many small changes in many genes and processes, and not by notable expansion or depauperation.
Electronic supplementary material
The online version of this article (doi:10.1186/s13059-015-0623-3) contains supplementary material, which is available to authorized users.
doi:10.1186/s13059-015-0623-3
PMCID: PMC4414376  PMID: 25908251
20.  Ancient and Novel Small RNA Pathways Compensate for the Loss of piRNAs in Multiple Independent Nematode Lineages 
PLoS Biology  2015;13(2):e1002061.
Small RNA pathways act at the front line of defence against transposable elements across the Eukaryota. In animals, Piwi interacting small RNAs (piRNAs) are a crucial arm of this defence. However, the evolutionary relationships among piRNAs and other small RNA pathways targeting transposable elements are poorly resolved. To address this question we sequenced small RNAs from multiple, diverse nematode species, producing the first phylum-wide analysis of how small RNA pathways evolve. Surprisingly, despite their prominence in Caenorhabditis elegans and closely related nematodes, piRNAs are absent in all other nematode lineages. We found that there are at least two evolutionarily distinct mechanisms that compensate for the absence of piRNAs, both involving RNA-dependent RNA polymerases (RdRPs). Whilst one pathway is unique to nematodes, the second involves Dicer-dependent RNA-directed DNA methylation, hitherto unknown in animals, and bears striking similarity to transposon-control mechanisms in fungi and plants. Our results highlight the rapid, context-dependent evolution of small RNA pathways and suggest piRNAs in animals may have replaced an ancient eukaryotic RNA-dependent RNA polymerase pathway to control transposable elements.
A survey of the nematode phylum reveals loss of the Piwi/piRNA pathway in several lineages, but RNA-dependent RNA polymerases control transposable elements in its absence.
Author Summary
Transposable elements are segments of DNA that have the ability to copy themselves independently of the host genome and thus pose a severe threat to the integrity of the genome. Organisms have evolved mechanisms to restrict the spread of transposable elements, with small RNA molecules being one of the most important defense mechanisms. In animals, the predominant small RNA transposon-silencing mechanism is the piRNA pathway, which appears to be widely conserved. However, little is known about how small RNA pathways that target transposons evolve. In order to study this question we investigated small RNA pathways across the nematode phylum, using a well-studied model organism—the nematode Caenorhabditis elegans—as the starting point. Surprisingly we found that the piRNA pathway has been completely lost in all groups of nematodes bar those most closely related to C. elegans. This finding raises the intriguing question of how these nematodes are able to control transposable element mobilization without piRNAs. We discovered that there are other small RNA pathways that target transposable elements in these nematodes, employing RNA-dependent RNA polymerases in order to make small RNAs antisense to transposable elements. Intriguingly, the most ancient of these mechanisms, found in the most basal nematodes, is a Dicer-dependent RNA-directed DNA methylation pathway. This pathway shares strong similarity to transposon-silencing mechanisms in plants and fungi, suggesting that it might have been present in an ancient common ancestor of all eukaryotes. Our results highlight the rapid evolution of small RNA pathways and demonstrate the importance of examining molecular pathways in detail across a range of evolutionary distances.
doi:10.1371/journal.pbio.1002061
PMCID: PMC4323106  PMID: 25668728
21.  Extracellular Onchocerca-derived small RNAs in host nodules and blood 
Parasites & Vectors  2015;8:58.
Background
microRNAs (miRNAs), a class of short, non-coding RNA can be found in a highly stable, cell-free form in mammalian body fluids. Specific miRNAs are secreted by parasitic nematodes in exosomes and have been detected in the serum of murine and dog hosts infected with the filarial nematodes Litomosoides sigmodontis and Dirofilaria immitis, respectively. Here we identify extracellular, parasite-derived small RNAs associated with Onchocerca species infecting cattle and humans.
Methods
Small RNA libraries were prepared from total RNA extracted from the nodule fluid of cattle infected with Onchocerca ochengi as well as serum and plasma from humans infected with Onchocerca volvulus in Cameroon and Ghana. Parasite-derived miRNAs were identified based on the criteria that sequences unambiguously map to hairpin structures in Onchocerca genomes, do not align to the human genome and are not present in European control serum.
Results
A total of 62 mature miRNAs from 52 distinct pre-miRNA candidates were identified in nodule fluid from cattle infected with O. ochengi of which 59 are identical in the genome of the human parasite O. volvulus. Six of the extracellular miRNAs were also identified in sequencing analyses of serum and plasma from humans infected with O. volvulus. Based on sequencing analysis the abundance levels of the parasite miRNAs in serum or plasma range from 5 to 127 reads/per million total host miRNA reads identified, comparable to our previous analyses of Schistosoma mansoni and L. sigmodontis miRNAs in serum. All six of the O. volvulus miRNAs identified have orthologs in other filarial nematodes and four were identified in the serum of mice infected with L. sigmodontis.
Conclusions
We have identified parasite-derived miRNAs associated with onchocerciasis in cattle and humans. Our results confirm the conserved nature of RNA secretion by diverse nematodes. Additional species-specific small RNAs from O. volvulus may be present in serum based on the novel miRNA sequences identified in the nodule fluid. In our analyses comparison to European control serum illuminates the scope for false-positives, warranting caution in criteria that should be applied to identification of biomarkers of infection.
Electronic supplementary material
The online version of this article (doi:10.1186/s13071-015-0656-1) contains supplementary material, which is available to authorized users.
doi:10.1186/s13071-015-0656-1
PMCID: PMC4316651  PMID: 25623184
microRNAs; Extracellular RNA; Filarial nematode; Onchocerciasis; Host-pathogen
22.  Exosomes secreted by nematode parasites transfer small RNAs to mammalian cells and modulate innate immunity 
Nature Communications  2014;5:5488.
In mammalian systems RNA can move between cells via vesicles. Here we demonstrate that the gastrointestinal nematode Heligmosomoides polygyrus, which infects mice, secretes vesicles containing microRNAs (miRNAs) and Y RNAs as well as a nematode Argonaute protein. These vesicles are of intestinal origin and are enriched for homologues of mammalian exosome proteins. Administration of the nematode exosomes to mice suppresses Type 2 innate responses and eosinophilia induced by the allergen Alternaria. Microarray analysis of mouse cells incubated with nematode exosomes in vitro identifies Il33r and Dusp1 as suppressed genes, and Dusp1 can be repressed by nematode miRNAs based on a reporter assay. We further identify miRNAs from the filarial nematode Litomosoides sigmodontis in the serum of infected mice, suggesting that miRNA secretion into host tissues is conserved among parasitic nematodes. These results reveal exosomes as another mechanism by which helminths manipulate their hosts and provide a mechanistic framework for RNA transfer between animal species.
Mammalian cell-derived exosomes can carry RNA and proteins from cell to cell, but this mode of transport has not been shown in nematodes. Here the authors show that a gastrointestinal parasite secretes exosomes that transfer microRNAs to mammalian cells and regulate innate immunity.
doi:10.1038/ncomms6488
PMCID: PMC4263141  PMID: 25421927
23.  Transcriptome analyses of Anguillicola crassus from native and novel hosts 
PeerJ  2014;2:e684.
Anguillicola crassus is a swim bladder nematode of eels. The parasite is native to the Asian eel Anguilla japonica, but was introduced to Europe and the European eel Anguilla anguilla in the early 1980s. A Taiwanese source has been proposed for this introduction. In the new host in the recipient area, the parasite appears to be more pathogenic. As a reason for these differences, genetically fixed differences in infectivity and development between Taiwanese and European A.crassus have been described and disentangled from plasticity induced by different host environments. To explore whether transcriptional regulation is involved in these lifecycle differences, we have analysed a “common garden”, cross infection experiment, using deep-sequencing transcriptomics. Surprisingly, in the face of clear phenotypic differences in life history traits, we identified no significant differences in gene expression between parasite populations or between experimental host species. From 120,000 SNPs identified in the transcriptome data we found that European A. crassus were not a genetic subset of the Taiwanese nematodes sampled. The loci that have the major contribution to the European-Taiwanese population differentiation show an enrichment of synonymous and non-coding polymorphism. This argues against positive selection in population differentiation. However, genes involved in protein processing in the endoplasmatic reticulum membrane and genes bearing secretion signal sequences were enriched in the set of genes most differentiated between European and Taiwanese A. crassus. These genes could be a source for the phenotypically visible genetically fixed differences between European and Taiwanese A. crassus.
doi:10.7717/peerj.684
PMCID: PMC4250067  PMID: 25469324
Anguillicola crassus; SNPs; Population differentiation; Gene expression; Transcriptome; Discriminant analysis of principal components (DAPC); Anguilla; Eel; Invasive parasite; Anguillicoloides crassus
24.  The Evolution of Tyrosine-Recombinase Elements in Nematoda 
PLoS ONE  2014;9(9):e106630.
Transposable elements can be categorised into DNA and RNA elements based on their mechanism of transposition. Tyrosine recombinase elements (YREs) are relatively rare and poorly understood, despite sharing characteristics with both DNA and RNA elements. Previously, the Nematoda have been reported to have a substantially different diversity of YREs compared to other animal phyla: the Dirs1-like YRE retrotransposon was encountered in most animal phyla but not in Nematoda, and a unique Pat1-like YRE retrotransposon has only been recorded from Nematoda. We explored the diversity of YREs in Nematoda by sampling broadly across the phylum and including 34 genomes representing the three classes within Nematoda. We developed a method to isolate and classify YREs based on both feature organization and phylogenetic relationships in an open and reproducible workflow. We also ensured that our phylogenetic approach to YRE classification identified truncated and degenerate elements, informatively increasing the number of elements sampled. We identified Dirs1-like elements (thought to be absent from Nematoda) in the nematode classes Enoplia and Dorylaimia indicating that nematode model species do not adequately represent the diversity of transposable elements in the phylum. Nematode Pat1-like elements were found to be a derived form of another Pat1-like element that is present more widely in animals. Several sequence features used widely for the classification of YREs were found to be homoplasious, highlighting the need for a phylogenetically-based classification scheme. Nematode model species do not represent the diversity of transposable elements in the phylum.
doi:10.1371/journal.pone.0106630
PMCID: PMC4157794  PMID: 25197791
25.  poRe: an R package for the visualization and analysis of nanopore sequencing data 
Bioinformatics  2014;31(1):114-115.
Motivation: The Oxford Nanopore MinION device represents a unique sequencing technology. As a mobile sequencing device powered by the USB port of a laptop, the MinION has huge potential applications. To enable these applications, the bioinformatics community will need to design and build a suite of tools specifically for MinION data.
Results: Here we present poRe, a package for R that enables users to manipulate, organize, summarize and visualize MinION nanopore sequencing data. As a package for R, poRe has been tested on Windows, Linux and MacOSX. Crucially, the Windows version allows users to analyse MinION data on the Windows laptop attached to the device.
Availability and implementation: poRe is released as a package for R at http://sourceforge.net/projects/rpore/. A tutorial and further information are available at https://sourceforge.net/p/rpore/wiki/Home/
Contact: mick.watson@roslin.ed.ac.uk
Supplementary information: Supplementary data are available at Bioinformatics online.
doi:10.1093/bioinformatics/btu590
PMCID: PMC4271141  PMID: 25173419

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