Toward 959 nematode genomes

The sequencing of the complete genome of the nematode Caenorhabditis elegans was a landmark achievement and ushered in a new era of whole-organism, systems analyses of the biology of this powerful model organism. The success of the C. elegans genome sequencing project also inspired communities working on other organisms to approach genome sequencing of their species. The phylum Nematoda is rich and diverse and of interest to a wide range of research fields from basic biology through ecology and parasitic disease. For all these communities, it is now clear that access to genome scale data will be key to advancing understanding, and in the case of parasites, developing new ways to control or cure diseases. The advent of second-generation sequencing technologies, improvements in computing algorithms and infrastructure and growth in bioinformatics and genomics literacy is making the addition of genome sequencing to the research goals of any nematode research program a less daunting prospect. To inspire, promote and coordinate genomic sequencing across the diversity of the phylum, we have launched a community wiki and the 959 Nematode Genomes initiative (www.nematodegenomes.org/). Just as the deciphering of the developmental lineage of the 959 cells of the adult hermaphrodite C. elegans was the gateway to broad advances in biomedical science, we hope that a nematode phylogeny with (at least) 959 sequenced species will underpin further advances in understanding the origins of parasitism, the dynamics of genomic change and the adaptations that have made Nematoda one of the most successful animal phyla

Symmetry witnesses

A symmetry witness is a suitable subset of the space of selfadjoint trace class operators that allows one to determine whether a linear map is a symmetry transformation, in the sense of Wigner. More precisely, such a set is invariant with respect to an injective densely defined linear operator in the Banach space of selfadjoint trace class operators (if and) only if this operator is a symmetry transformation. According to a linear version of Wigner's theorem, the set of pure states, the rank-one projections, is a symmetry witness. We show that an analogous result holds for the set of projections with a fixed rank (with some mild constraint on this rank, in the finite-dimensional case). It turns out that this result provides a complete classification of the set of projections with a fixed rank that are symmetry witnesses. These particular symmetry witnesses are projectable; i.e., reasoning in terms of quantum states, the sets of uniform density operators of corresponding fixed rank are symmetry witnesses too.Comment: 15 page

Reinforcement Learning Produces Dominant Strategies for the Iterated Prisoner's Dilemma

We present tournament results and several powerful strategies for the Iterated Prisoner's Dilemma created using reinforcement learning techniques (evolutionary and particle swarm algorithms). These strategies are trained to perform well against a corpus of over 170 distinct opponents, including many well-known and classic strategies. All the trained strategies win standard tournaments against the total collection of other opponents. The trained strategies and one particular human made designed strategy are the top performers in noisy tournaments also

The Evolution of Tyrosine-Recombinase Elements in Nematoda

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

Reconstructing the phylogenetic relationships of nematodes using draft genomes and transcriptomes

Nematoda is a very diverse animal phylum. Within Nematoda, species display a multitude of life styles, different reproductive strategies and parasitism has arisen independently several times. Furthermore, morphological conservation and a high rate of homoplasy have impeded the resolution of nematode systematics. To address these issues, single gene (usually the nuclear ribosomal small subunit gene) and mitochondrial gene phylogenies have been used, but the information contained within the sequence of these genes is not enough to resolve the topological relationships between clades that emerged during rapid cladogenesis. Next generation sequencing data have been shown to produce high quality genomic and transcriptomic assemblies at low cost, as a result more and more nematode species are being sequenced. Sequences were gathered or generated for 53 nematode species from ESTs, gene predictions from full genome assemblies and transcripts from RNA-Seq experiments. These sequences were screened for orthologous gene clusters, which were concatenated into a supermatrix with thousands of aminoacid sites. The analysis of the supermatrix with maximum likelihood and Bayesian inference methods sheds light into the early splitting clades of the phylogenetic tree of nematodes and the derived clades III, IV and V. Furthermore, the phylogenetic relationships within the parastitic family Onchocercidae were resolved, unveiling the evolutionary history of these important taxa. Finally, data produced in this work will be useful for subsequent evolutionary studies of the phylum Nematoda

Phylogenomics and analysis of shared genes suggest a single transition to mutualism in Wolbachia of nematodes

Wolbachia, endosymbiotic bacteria of the order Rickettsiales, are widespread in arthropods but also present in nematodes. In arthropods, A and B supergroup Wolbachia are generally associated with distortion of host reproduction. In filarial nematodes, including some human parasites, multiple lines of experimental evidence indicate that C and D supergroup Wolbachia are essential for the survival of the host, and here the symbiotic relationship is considered mutualistic. The origin of this mutualistic endosymbiosis is of interest for both basic and applied reasons: How does a parasite become a mutualist? Could intervention in the mutualism aid in treatment of human disease? Correct rooting and high-quality resolution of Wolbachia relationships are required to resolve this question. However, because of the large genetic distance between Wolbachia and the nearest outgroups, and the limited number of genomes so far available for large-scale analyses, current phylogenies do not provide robust answers. We therefore sequenced the genome of the D supergroup Wolbachia endosymbiont of Litomosoides sigmodontis, revisited the selection of loci for phylogenomic analyses, and performed a phylogenomic analysis including available complete genomes (from isolates in supergroups A, B, C, and D). Using 90 orthologous genes with reliable phylogenetic signals, we obtained a robust phylogenetic reconstruction, including a highly supported root to the Wolbachia phylogeny between a (A + B) clade and a (C + D) clade. Although we currently lack data from several Wolbachia supergroups, notably F, our analysis supports a model wherein the putatively mutualist endosymbiotic relationship between Wolbachia and nematodes originated from a single transition event

A single chromosome assembly of Bacteroides fragilis strain BE1 from Illumina and MinION nanopore sequencing data

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

The genome of Romanomermis culicivorax:revealing fundamental changes in the core developmental genetic toolkit in Nematoda

Background: The genetics of development in the nematode Caenorhabditis elegans has been described in exquisite detail. The phylum Nematoda has two classes: Chromadorea (which includes C. elegans) and the Enoplea. While the development of many chromadorean species resembles closely that of C. elegans, enoplean nematodes show markedly different patterns of early cell division and cell fate assignment. Embryogenesis of the enoplean Romanomermis culicivorax has been studied in detail, but the genetic circuitry underpinning development in this species has not been explored. Results: We generated a draft genome for R. culicivorax and compared its gene content with that of C. elegans, a second enoplean, the vertebrate parasite Trichinella spiralis, and a representative arthropod, Tribolium castaneum. This comparison revealed that R. culicivorax has retained components of the conserved ecdysozoan developmental gene toolkit lost in C. elegans. T. spiralis has independently lost even more of this toolkit than has C. elegans. However, the C. elegans toolkit is not simply depauperate, as many novel genes essential for embryogenesis in C. elegans are not found in, or have only extremely divergent homologues in R. culicivorax and T. spiralis. Our data imply fundamental differences in the genetic programmes not only for early cell specification but also others such as vulva formation and sex determination. Conclusions: Despite the apparent morphological conservatism, major differences in the molecular logic of development have evolved within the phylum Nematoda. R. culicivorax serves as a tractable system to contrast C. elegans and understand how divergent genomic and thus regulatory backgrounds nevertheless generate a conserved phenotype. The R. culicivorax draft genome will promote use of this species as a research model

An open reproducible framework for the study of the iterated prisoner's dilemma

The Axelrod library is an open source Python package that allows for reproducible game theoretic research into the Iterated Prisoner's Dilemma. This area of research began in the 1980s but suffers from a lack of documentation and test code. The goal of the library is to provide such a resource, with facilities for the design of new strategies and interactions between them, as well as conducting tournaments and ecological simulations for populations of strategies. With a growing collection of 139 strategies, the library is a also a platform for an original tournament that, in itself, is of interest to the game theoretic community. This paper describes the Iterated Prisoner's Dilemma, the Axelrod library and its development, and insights gained from some novel research.Comment: 11 pages, Journal of Open Research Software 4.1 (2016