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The phylogenetic range of bacterial and viral pathogens of vertebrates [article]

Liam P. Shaw, Alethea D. Wang, David Dylus, Magda Meier, Grega Pogacnik, Christophe Dessimoz, Francois Balloux
2019 bioRxiv   pre-print
AbstractPathogenic microorganisms can often infect more than one host. Furthermore, many major human pathogens are multi-host pathogens. Describing the general patterns of host-pathogen associations is therefore important to understand risk factors for human disease emergence. However, there is a lack of comprehensive curated databases for this purpose. Here, we report a manually compiled host-pathogen association database, covering 2,595 bacteria and viruses infecting 2,656 vertebrate hosts.
more » ... also built a multi-mitochondrial gene tree for host species, allowing us to show that the phylogenetic similarity of hosts is the dominant factor for greater pathogen sharing. We find that the majority of bacteria and viruses are specialists infecting only a single host species. Bacteria include a significantly higher proportion of specialists compared to viruses. Conversely, multi-host viruses have a more restricted host range than multi-host bacteria. Several traits are significantly associated with host range. For viruses, having an RNA genome and a larger viral genome size were independently associated with a broader host range. For bacteria, motile and aerobic pathogens had a wider host range, with the largest number of hosts found for facultative anaerobes. Unexpectedly, intracellular and extracellular bacteria had similar host ranges, despite a priori looser association of the latter with their hosts. We find that zoonotic pathogens typically have a larger phylogenetic range, and that the fraction of pathogens shared between two hosts decreases with the phylogenetic distance between them. This result suggests that host phylogenetic similarity is the primary factor for host-switching in pathogens.
doi:10.1101/670315 fatcat:jj6scmk7evcmzmmqyiidwoxbwe

Skeletal regeneration in the brittle star Amphiura filiformis

Anna Czarkwiani, Cinzia Ferrario, David Viktor Dylus, Michela Sugni, Paola Oliveri
2016 Frontiers in Zoology  
Brittle stars regenerate their whole arms post-amputation. Amphiura filiformis can now be used for molecular characterization of arm regeneration due to the availability of transcriptomic data. Previous work showed that specific developmental transcription factors known to take part in echinoderm skeletogenesis are expressed during adult arm regeneration in A. filiformis; however, the process of skeleton formation remained poorly understood. Here, we present the results of an in-depth
more » ... c analysis of skeletal morphogenesis during regeneration, using calcein staining, EdU labeling and in situ hybridization. Results: To better compare different samples, we propose a staging system for the early A. filiformis arm regeneration stages based on morphological landmarks identifiable in living animals and supported by histological analysis. We show that the calcified spicules forming the endoskeleton first appear very early during regeneration in the dermal layer of regenerates. These spicules then mature into complex skeletal elements of the differentiated arm during late regeneration. The mesenchymal cells in the dermal area express the skeletal marker genes Afi-c-lectin, Afi-p58b and Afi-p19; however, EdU labeling shows that these dermal cells do not proliferate. Conclusions: A. filiformis arms regenerate through a consistent set of developmental stages using a distalization-intercalation mode, despite variability in regeneration rate. Skeletal elements form in a mesenchymal cell layer that does not proliferate and thus must be supplied from a different source. Our work provides the basis for future cellular and molecular studies of skeleton regeneration in brittle stars.
doi:10.1186/s12983-016-0149-x pmid:27110269 pmcid:PMC4841056 fatcat:rqrgai26fvcoppztoj6qmp2w3e

How to build phylogenetic species trees with OMA

David Dylus, Yannis Nevers, Adrian M. Altenhoff, Antoine Gürtler, Christophe Dessimoz, Natasha M. Glover
2022 F1000Research  
Knowledge of species phylogeny is critical to many fields of biology. In an era of genome data availability, the most common way to make a phylogenetic species tree is by using multiple protein-coding genes, conserved in multiple species. This methodology is composed of several steps: orthology inference, multiple sequence alignment and inference of the phylogeny with dedicated tools. This can be a difficult task, and orthology inference, in particular, is usually computationally intensive and
more » ... rror prone if done ad hoc. This tutorial provides protocols to make use of OMA Orthologous Groups, a set of genes all orthologous to each other, to infer a phylogenetic species tree. It is designed to be user-friendly and computationally inexpensive, by providing two options: (1) Using only precomputed groups with species available on the OMA Browser, or (2) Computing orthologs using OMA Standalone for additional species, with the option of using precomputed orthology relations for those present in OMA. A protocol for downstream analyses is provided as well, including creating a supermatrix, tree inference, and visualization. All protocols use publicly available software, and we provide scripts and code snippets to facilitate data handling. The protocols are accompanied with practical examples.
doi:10.12688/f1000research.23790.2 fatcat:7yv6eewhq5dzfajmbluksvzmua

How to build phylogenetic species trees with OMA

David Dylus, Yannis Nevers, Adrian M. Altenhoff, Antoine Gürtler, Christophe Dessimoz, Natasha M. Glover
2020 F1000Research  
Knowledge of species phylogeny is critical to many fields of biology. In an era of genome data availability, the most common way to make a phylogenetic species tree is by using multiple protein-coding genes, conserved in multiple species. This methodology is composed of several steps: orthology inference, multiple sequence alignment and inference of the phylogeny with dedicated tools. This can be a difficult task, and orthology inference, in particular, is usually computationally intensive and
more » ... rror prone if done ad hoc. This tutorial provides protocols to make use of OMA Orthologous Groups, a set of genes all orthologous to each other, to infer a phylogenetic species tree. It is designed to be user-friendly and computationally inexpensive, by providing two options: (1) Using only precomputed groups with species available on the OMA Browser, or (2) Computing orthologs using OMA Standalone for additional species, with the option of using precomputed orthology relations for those present in OMA. A protocol for downstream analyses is provided as well, including creating a supermatrix, tree inference, and visualization. All protocols use publicly available software, and we provide scripts and code snippets to facilitate data handling. The protocols are accompanied with practical examples.
doi:10.12688/f1000research.23790.1 fatcat:36ddwvqlzbgyniwmjslfvd6omm

Expression of skeletogenic genes during arm regeneration in the brittle star Amphiura filiformis

Anna Czarkwiani, David V. Dylus, Paola Oliveri
2013 Gene Expression Patterns  
Skeleton ets1/2 tbr gataC foxB alx1 a b s t r a c t The brittle star Amphiura filiformis, which regenerates its arms post autotomy, is emerging as a useful model for studying the molecular underpinnings of regeneration, aided by the recent availability of some molecular resources. During regeneration a blastema initially is formed distally to the amputation site, and then a rapid rebuild is obtained by adding metameric units, which will eventually differentiate and become fully functional. In
more » ... is work we first characterize the developmental process of the regenerating arms using two differentiation markers for muscle and skeletal structures -Afi-trop-1 and Afiacoll. Both genes are not expressed in the blastema and newly added undifferentiated metameric units. Their expression at different regenerating stages shows an early segregation of muscle and skeletal cells during the regenerating process, long before the metameric units become functional. We then studied the expression of a set of genes orthologous of the sea urchin transcription factors involved in the development of skeletal and non-skeletal mesoderm: Afi-ets1/2, Afi-alx1, Afi-tbr, Afi-foxB and Afi-gataC. We found that Afi-ets1/2, Afi-alx1, Afi-foxB and Afi-gataC are all expressed at the blastemal stage. As regeneration progresses those genes are expressed in a similar small undifferentiated domain beneath the distal growth cap, while in more advanced metameric units they become restricted to different skeletal domains. Afi-foxB becomes expressed in non-skeletal structures. This suggests that they might play a combinatorial role only in the early cell specification process and that subsequently they function independently in the differentiation of different structures. Afi-tbr is not present in the adult arm tissue at any stage of regeneration. In situ hybridization results have been confirmed with a new strategy for quantitative PCR (QPCR), using a subdivision of the three stages of regeneration into proximal (differentiated) and distal (undifferentiated) arm segments.
doi:10.1016/j.gep.2013.09.002 pmid:24051028 pmcid:PMC3838619 fatcat:vje4vf2gmzdhbpotx55cw5ofzq

FGF signalling plays similar roles in development and regeneration of the skeleton in the brittle star Amphiura filiformis [article]

Anna Czarkwiani, David Viktor Dylus, Luisana Carballo, Paola Oliveri
2019 bioRxiv   pre-print
Regeneration is an adult developmental process considered to be an epiphenomenon of embryonic development. Although several studies have shown that various embryonic genes are expressed during regeneration, there have been no large-scale, direct and functional comparative studies between the development and regeneration of a specific structure in one animal. Here, we use the brittle star Amphiura filiformis to characterise the role of the FGF signalling pathway during skeletal development and
more » ... generation. In both processes, we find the ligands expressed in ectodermal cells flanking underlying mesodermal cells, and the receptors expressed specifically by these skeletogenic cells. Perturbation of FGF but not VEGF signalling during skeletogenesis completely inhibited skeleton formation in both embryogenesis and regeneration, without affecting other key developmental processes like cell migration or proliferation. Transcriptome-wide differential analysis identified a highly similar cohort of skeletogenic differentiation genes downstream of the FGF signalling pathway, whereas upstream transcription factors involved in the initial specification of the skeletogenic lineage where unaffected. Comparison to the sea urchin indicated that many of the affected genes are associated with differentiation. Moreover, several genes showed no homology to a cohort from other species, leading to the discovery of brittle star specific, downstream skeletogenic genes. In conclusion, our results show that the FGF pathway is crucial for skeletogenesis in the brittle star, as it is in other deuterostomes, and for the first time provide evidence for the re-deployment of a gene regulatory module during both regeneration and development.
doi:10.1101/632968 fatcat:mhqgw57onzgljpsqsesaiu5r5e

Bifurcation search via feedback loop breaking in biochemical signaling pathways with time delay

Steffen Waldherr, David Dylus, Frank Allgöwer
2011 Asian journal of control  
We develop a method to locate bifurcations in time delay systems with a potentially high-dimensional parameter space. It is based on the feedback loop breaking approach that we developed and applied earlier for bifurcation search in ordinary differential equations. The method is particularly suited for the analysis of biological networks, for example to determine which parameters are relevant for complex dynamical behavior in such networks. To illustrate the benefits that this approach yields
more » ... r biological network analysis, we apply it to study the effect of parameter variations on oscillations in a model of the MAP kinase cascade with a time delay.
doi:10.1002/asjc.383 fatcat:jmk4mgmxqnbkbnvmyiu5cskldu

OMA standalone: orthology inference among public and custom genomes and transcriptomes [article]

Adrian M Altenhoff, Jeremy Levy, Magdalena Zarowiecki, Bartłomiej Tomiczek, Alex Warwick Vesztrocy, Daniel Dalquen, Steven Müller, Maximilian Telford, Natasha Glover, David Dylus, Christophe Dessimoz
2018 bioRxiv   pre-print
Genomes and transcriptomes are now typically sequenced by individual labs, but analysing them often remains challenging. One essential step in many analyses lies in identifying orthologs — corresponding genes across multiple species — but this is far from trivial. The OMA (Orthologous MAtrix) database is a leading resource for identifying orthologs among publicly available, complete genomes. Here, we describe the OMA pipeline available as a standalone program for Linux and Mac. When run on a
more » ... ster, it has native support for the LSF, SGE, PBS Pro, and Slurm job schedulers and can scale up to thousands of parallel processes. Another key feature of OMA standalone is that users can combine their own data with existing public data by exporting genomes and pre-computed alignments from the OMA database, which currently contains over 2100 complete genomes. We compare OMA standalone to other methods in the context of phylogenetic tree inference, by inferring a phylogeny of the Lophotrochozoa, a challenging clade within the Protostomes. We also discuss other potential applications of OMA standalone, including identifying gene families having undergone duplications/losses in specific clades, and identifying potential drug targets in non-model organisms. OMA Standalone is available at http://omabrowser.org/standalone under the permissible open source Mozilla Public License Version 2.0.
doi:10.1101/397752 fatcat:uwc4hhtohvhfjeh2halzzwafya

Developmental transcriptomics of the brittle star Amphiura filiformis reveals gene regulatory network rewiring in echinoderm larval skeleton evolution [article]

David V Dylus, Liisa M Blowes, Anna Czarkwiani, Maurice R Elphick, Paola Oliveri
2017 bioRxiv   pre-print
It stage, embryos were collected for RNA extraction and/or fixed for WMISH as described in (Dylus et mRNA sequencing protocol.  ...  INTRODUCTION Given the similarity of development between sea urchin and brittle star (Dylus et al. 2016; expression profiles of representatives of these two classes of echinoderms.  ... 
doi:10.1101/166991 fatcat:cdbhq4cfmrcqtpfa76kxnts6b4

FGF signalling plays similar roles in development and regeneration of the skeleton in the brittle star Amphiura filiformis

Anna Czarkwiani, David V. Dylus, Luisana Carballo, Paola Oliveri
2021 Development  
Regeneration as an adult developmental process is in many aspects similar to embryonic development. Although many studies point out similarities and differences, no large-scale, direct and functional comparative analyses between development and regeneration of a specific cell type or structure in one animal exist. Here, we use the brittle star Amphiura filiformis to characterise the role of the FGF signalling pathway during skeletal development in embryos and arm regeneration. In both
more » ... we find ligands expressed in ectodermal cells that flank underlying skeletal mesenchymal cells, which express the receptors. Perturbation of FGF signalling showed inhibited skeleton formation in both embryogenesis and regeneration, without affecting other key developmental processes. Differential transcriptome analysis finds mostly differentiation genes rather than transcription factors to be downregulated in both contexts. Moreover, comparative gene analysis allowed us to discover brittle star-specific differentiation genes. In conclusion, our results show that the FGF pathway is crucial for skeletogenesis in the brittle star, as in other deuterostomes, and provide evidence for the re-deployment of a developmental gene regulatory module during regeneration.
doi:10.1242/dev.180760 pmid:34042967 fatcat:bk46ltztbvf2nikmnm2ro24y7m

RecPhyloXML: a format for reconciled gene trees

Wandrille Duchemin, Guillaume Gence, Anne-Muriel Arigon Chifolleau, Lars Arvestad, Mukul S Bansal, Vincent Berry, Bastien Boussau, François Chevenet, Nicolas Comte, Adrián A Davín, Christophe Dessimoz, David Dylus (+10 others)
2018 Bioinformatics  
Motivation: A reconciliation is an annotation of the nodes of a gene tree with evolutionary events-for example, speciation, gene duplication, transfer, loss, etc-along with a mapping onto a species tree. Many algorithms and software produce or use reconciliations but often using different reconciliation formats, regarding the type of events considered or whether the species tree is dated or not. This complicates the comparison and communication between different programs. Results: Here, we
more » ... r a consortium of software developers in gene tree species tree reconciliation to propose and endorse a format that aims to promote an integrative-albeit flexible-specification of phylogenetic reconciliations. This format, named recPhyloXML, is accompanied by several tools such as a reconciled tree visualizer and conversion utilities. Availability: http://phylariane.univ-lyon1.fr/recphyloxml/ Contact: wandrille.duchemin@univ-lyon1.fr Supplementary information: There is no supplementary data associated with this publication.
doi:10.1093/bioinformatics/bty389 pmid:29762653 fatcat:4x5yhdsxvzex5fe3vvc3mml6gy

OMA standalone: orthology inference among public and custom genomes and transcriptomes

Adrian M. Altenhoff, Jeremy Levy, Magdalena Zarowiecki, Bartłomiej Tomiczek, Alex Warwick Vesztrocy, Daniel A. Dalquen, Steven Müller, Maximilian J. Telford, Natasha M. Glover, David Dylus, Christophe Dessimoz
2019 Genome Research  
Genomes and transcriptomes are now typically sequenced by individual laboratories but analyzing them often remains challenging. One essential step in many analyses lies in identifying orthologs-corresponding genes across multiple species-but this is far from trivial. The Orthologous MAtrix (OMA) database is a leading resource for identifying orthologs among publicly available, complete genomes. Here, we describe the OMA pipeline available as a standalone program for Linux and Mac. When run on a
more » ... cluster, it has native support for the LSF, SGE, PBS Pro, and Slurm job schedulers and can scale up to thousands of parallel processes. Another key feature of OMA standalone is that users can combine their own data with existing public data by exporting genomes and precomputed alignments from the OMA database, which currently contains over 2100 complete genomes. We compare OMA standalone to other methods in the context of phylogenetic tree inference, by inferring a phylogeny of Lophotrochozoa, a challenging clade within the protostomes. We also discuss other potential applications of OMA standalone, including identifying gene families having undergone duplications/losses in specific clades, and identifying potential drug targets in nonmodel organisms. OMA standalone is available under the permissive open source Mozilla Public License Version 2.0.
doi:10.1101/gr.243212.118 pmid:31235654 pmcid:PMC6633268 fatcat:6vr6fs2wgbedhckeif3kcgoeba

MOESM1 of Large-scale gene expression study in the ophiuroid Amphiura filiformis provides insights into evolution of gene regulatory networks

David Dylus, Anna Czarkwiani, Josefine StĂĽngberg, Olga Ortega-Martinez, Sam Dupont, Paola Oliveri
2016 Figshare  
Additional file 1. Additional figures and tables; Contains figures and tables supporting data in the main text.
doi:10.6084/m9.figshare.c.3614990_d2 fatcat:yabcbfkylnbgnogxjxvhcmi32y

Large-scale gene expression study in the ophiuroid Amphiura filiformis provides insights into evolution of gene regulatory networks

David Viktor Dylus, Anna Czarkwiani, Josefine Stångberg, Olga Ortega-Martinez, Sam Dupont, Paola Oliveri
2016 EvoDevo  
The evolutionary mechanisms involved in shaping complex gene regulatory networks (GRN) that encode for morphologically similar structures in distantly related animals remain elusive. In this context, echinoderm larval skeletons found in brittle stars and sea urchins provide an ideal system. Here, we characterize for the first time the development of the larval skeleton in the ophiuroid Amphiura filiformis and compare it systematically with its counterpart in sea urchin. Results: We show that
more » ... iuroids and euechinoids, that split at least 480 Million years ago (Mya), have remarkable similarities in tempo and mode of skeletal development. Despite morphological and ontological similarities, our high-resolution study of the dynamics of genetic regulatory states in A. filiformis highlights numerous differences in the architecture of their underlying GRNs. Importantly, the A.filiformis pplx, the closest gene to the sea urchin double negative gate (DNG) repressor pmar1, fails to drive the skeletogenic program in sea urchin, showing important evolutionary differences in protein function. hesC, the second repressor of the DNG, is co-expressed with most of the genes that are repressed in sea urchin, indicating the absence of direct repression of tbr, ets1/2, and delta in A. filiformis. Furthermore, the absence of expression in later stages of brittle star skeleton development of key regulatory genes, such as foxb and dri, shows significantly different regulatory states. Conclusion: Our data fill up an important gap in the picture of larval mesoderm in echinoderms and allows us to explore the evolutionary implications relative to the recently established phylogeny of echinoderm classes. In light of recent studies on other echinoderms, our data highlight a high evolutionary plasticity of the same nodes throughout evolution of echinoderm skeletogenesis. Finally, gene duplication, protein function diversification, and cis-regulatory element evolution all contributed to shape the regulatory program for larval skeletogenesis in different branches of echinoderms.
doi:10.1186/s13227-015-0039-x pmid:26759711 pmcid:PMC4709884 fatcat:surjszpfnfcabjv3g2qzgjwctq

Developmental transcriptomics of the brittle star Amphiura filiformis reveals gene regulatory network rewiring in echinoderm larval skeleton evolution

David V. Dylus, Anna Czarkwiani, Liisa M. Blowes, Maurice R. Elphick, Paola Oliveri
2018 Genome Biology  
INTRODUCTION Given the similarity of development between sea urchin and brittle star (Dylus et al. 2016; expression profiles of representatives of these two classes of echinoderms.  ...  Dylus DV et al. 2016. Large-scale gene expression study in the ophiuroid Amphiura filiformis provides insights into evolution of gene regulatory networks.  ... 
doi:10.1186/s13059-018-1402-8 pmid:29490679 pmcid:PMC5831733 fatcat:o2rkzorkgva75mw2gy3avvbe5m
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