e-infrastructure Roadmap for Open Science in Agriculture

A bibliometric study

The e-ROSA project seeks to build a shared vision of a future sustainable e-infrastructure for research and education in agriculture in order to promote Open Science in this field and as such contribute to addressing related societal challenges. In order to achieve this goal, e-ROSA’s first objective is to bring together the relevant scientific communities and stakeholders and engage them in the process of coelaboration of an ambitious, practical roadmap that provides the basis for the design and implementation of such an e-infrastructure in the years to come.

This website highlights the results of a bibliometric analysis conducted at a global scale in order to identify key scientists and associated research performing organisations (e.g. public research institutes, universities, Research & Development departments of private companies) that work in the field of agricultural data sources and services. If you have any comment or feedback on the bibliometric study, please use the online form.

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Multiple evolutionary mechanisms drive papillomavirus diversification


The circular, double-stranded 8-kb DNA genome of papillomaviruses (PVes) consists mainly of 4 large genes, E1, E2, L2, and L1. Approximately 150 papillomavirus genomes have been sequenced to date. We analyzed a representative sample of 53 PVes genomes using maximum likelihood, Bayesian inference, maximum parsimony, and distance-based methods both on nucleotide (nt) and on amino acid (aa) alignments. When the 4 genes were analyzed separately, aa-inferred phylogenies contradicted each other less than nt-inferred trees (judged by partition homogeneity tests). In particular, gene combinations including the L2 gene generated significant incongruence (P < 0.001). Combined analyses of the remaining genes E1-E2-L1 produced a well-supported phylogeny including supertaxon beta + gamma + pi + xi-PVes (infecting Artiodactyla, Carnivora, Primates, and Rodentia) and supertaxon K + lambda + mu + nu + sigma-PVes (infecting Carnivora, Lagomorpha, Primates, and Rodentia). Based on the tree topology, host-linked evolution appears plausible at shallow, rather than deeper, taxonomic levels. Diversification within PVes may also involve adaptive radiation establishing different niches (within a single-host species) and recombination events (within single-host cells). Heterogeneous groups of closely related PVes infecting, for example, humans and domestic animals such as hamster, dog, and cattle suggest multiple infections across species borders. Additional evolutionary phenomena such as strong codon usage preferences, and computational biases including reconstruction artifacts and insufficient taxon sampling, may contribute to the incomplete resolution of deep phylogenetic nodes. The molecular data globally supports a complex evolutionary scenario for PVes, which is driven by multiple mechanisms but not exclusively by coevolution with corresponding hosts.

  • DE
  • CH
  • Helmholtz_Assoc (DE)
  • EPFL_Swiss_Fed_Inst_Technol_Lausanne (CH)
  • Charite_Univ_Med_Berlin (DE)
Data keywords
  • high performance computing
Agriculture keywords
  • cattle
Data topic
  • big data
Document type

Inappropriate format for Document type, expected simple value but got array, please use list format

Institutions 10 co-publis
  • Helmholtz_Assoc (DE)
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e-ROSA - e-infrastructure Roadmap for Open Science in Agriculture has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 730988.
Disclaimer: The sole responsibility of the material published in this website lies with the authors. The European Union is not responsible for any use that may be made of the information contained therein.