Evidence for an ancient whole genome duplication in the cycad lineage

Contrary to the many whole genome duplication events recorded for angiosperms (flowering plants), whole genome duplications in gymnosperms (non-flowering seed plants) seem to be much rarer. Although ancient whole genome duplications have been reported for most gymnosperm lineages as well, some are still contested and need to be confirmed. For instance, data for ginkgo, but particularly cycads have remained inconclusive so far, likely due to the quality of the data available and flaws in the analysis. We extracted and sequenced RNA from both the cycad Encephalartos natalensis and Ginkgo biloba. This was followed by transcriptome assembly, after which these data were used to build paralog age distributions. Based on these distributions, we identified remnants of an ancient whole genome duplication in both cycads and ginkgo. The most parsimonious explanation would be that this whole genome duplication event was shared between both species and had occurred prior to their divergence, about 300 million years ago

The 18S ribosomal RNA sequence of the sea anemone <i>Ammonia sulcata</i> and its evolutionary position among other eukaryotes

Evolutionary trees based on partial small ribosomal subunit RNA sequences of 22 metazoa species have been published [(1988) Science 239, 748-753]. In these trees, cnidarians (Radiata) seemed to have evolved independently from the Bilateria, which is in contradiction with the general evolutionary view. In order to further investigate this problem, the complete srRNA sequence of the sea anemone Ammonia sulcata was determined and evolutionary trees were constructed using a matrix optimization method. In the tree thus obtained the sea anemone and Bilateria together form a monophyletic cluster, with the sea anemone forming the first line of descent of the metazoan group

Oidium neolycopersici: Intra-specific variability inferred from AFLP analysis and relationship with closely related powdery mildew fungi infecting various plant species

Previous works indicated a considerable variation in the pathogenicity, virulence, and host range of Oidium neolycopersici isolates causing tomato powdery mildew epidemics in many parts of the world. In this study, rDNA internal transcribed spacer (ITS) sequences, and amplified fragment length polymorphism (AFLP) patterns were analyzed in 17 O. neolycopersici samples collected in Europe, North America, and Japan, including those which overcame some of the tomato major resistance genes. The ITS sequences were identical in all 10 samples tested and were also identical to ITS sequences of eight previously studied O. neolycopersici specimens. The AFLP analysis revealed a high genetic diversity in O. neolycopersici and indicated that all 17 samples represented different genotypes. This might suggest the existence of either a yet unrevealed sexual reproduction or other genetic mechanisms that maintain a high genetic variability in O. neolycopersici. No clear correlation was found between the virulence and the AFLP patterns of the O. neolycopersici isolates studied. The relationship between O. neolycopersici and powdery mildew anamorphs infecting Aquilegia vulgaris, Chelidonium majus, Passiflora caerulea, and Sedum alboroseum was also investigated. These anamorphs are morphologically indistinguishable from and phylogenetically closely related to O. neolycopersici. The cross-inoculation tests and the analyses of ITS sequences and AFLP patterns jointly indicated that the powdery mildew anamorphs collected from the above mentioned plant species all represent distinct, but closely related species according to the phylogenetic species recognition. All these species were pathogenic only to their original host plant species, except O. neolycopersici which infected S. alboroseum, tobacco, petunia, and Arabidopsis thaliana, in addition to tomato, in cross-inoculation tests. This is the first genome-wide study that investigates the relationships among powdery mildews that are closely related based on ITS sequences and morphology. The results indicate that morphologically indistinguishable powdery mildews that differed in only one to five single nucleotide positions in their ITS region are to be considered as different taxa with distinct host ranges

Semigroup evolution in Wigner Weisskopf pole approximation with Markovian spectral coupling

We establish the relation between the Wigner-Weisskopf theory for the description of an unstable system and the theory of coupling to an environment. According to the Wigner-Weisskopf general approach, even within the pole approximation (neglecting the background contribution) the evolution of a total system subspace is not an exact semigroup for the multi-channel decay, unless the projectors into eigesntates of the reduced evolution generator $W(z)$ are orthogonal. In this case these projectors must be evaluated at different pole locations $z_\alpha\neq z_\beta$. Since the orthogonality relation does not generally hold at different values of $z$, for example, when there is symmetry breaking, the semigroup evolution is a poor approximation for the multi-channel decay, even for a very weak coupling. Nevertheless, there exists a possibility not only to ensure the orthogonality of the $W(z)$ projectors regardless the number of the poles, but also to simultaneously suppress the effect of the background contribution. This possibility arises when the theory is generalized to take into account interactions with an environment. In this case $W(z)$, and hence its eigenvectors as well, are {\it independent} of $z$, which corresponds to a structure of the coupling to the continuum spectrum associated with the Markovian limit.Comment: 9 pages, 3 figure

The role of cryptotephra in refining the chronology of Late Pleistocene human evolution and cultural change in North Africa

© 2014.Sites in North Africa hold key information for dating the presence of Homo sapiens and the distribution of Middle Stone Age (MSA), Middle Palaeolithic (MP) and Later Stone Age (LSA) cultural activity in the Late Pleistocene. Here we present new and review recently published tephrochronological evidence for five cave sites in North Africa with long MSA/MP and LSA cultural sequences. Four tephra horizons have been identified at the Haua Fteah (Cyrenaica, Libya). They include cryptotephra evidence for the Campanian Ignimbrite (CI) eruption dating to ~39 ka that allows correlation with other Palaeolithic sequences in the eastern Mediterranean and as far north as Russia. Cryptotephra have also been recorded from the Moroccan sites of Taforalt, Rhafas and Dar es-Soltane 1. At Taforalt the geochemical composition suggests a provenance in the Azores, while examples from Sodmein (Egypt) appear to derive from central Anatolia and another unknown source. In these latter examples chemical compositional data from relevant proximal volcanic centres is currently lacking so the identification of tephra in layers of known age and cultural association provides the first reliable age determinations for distal volcanic events and their geographical extent. The future potential for tephrochronological research in North Africa is also discussed

Improved chromosome-level genome assembly and annotation of the seagrass, Zostera marina (eelgrass)

Background: Seagrasses (Alismatales) are the only fully marine angiosperms. Zostera marina (eelgrass) plays a crucial role in the functioning of coastal marine ecosystems and global carbon sequestration. It is the most widely studied seagrass and has become a marine model system for exploring adaptation under rapid climate change. The original draft genome (v.1.0) of the seagrass Z. marina (L.) was based on a combination of Illumina mate-pair libraries and fosmid-ends. A total of 25.55 Gb of Illumina and 0.14 Gb of Sanger sequence was obtained representing 47.7× genomic coverage. The assembly resulted in ~2000 unordered scaffolds (L50 of 486 Kb), a final genome assembly size of 203MB, 20,450 protein coding genes and 63% TE content. Here, we present an upgraded chromosome-scale genome assembly and compare v.1.0 and the new v.3.1, reconfirming previous results from Olsen et al. (2016), as well as pointing out new findings. Methods: The same high molecular weight DNA used in the original sequencing of the Finnish clone was used. A high-quality reference genome was assembled with the MECAT assembly pipeline combining PacBio long-read sequencing and Hi-C scaffolding. Results: In total, 75.97 Gb PacBio data was produced. The final assembly comprises six pseudo-chromosomes and 304 unanchored scaffolds with a total length of 260.5Mb and an N50 of 34.6 MB, showing high contiguity and few gaps (~0.5%). 21,483 protein-encoding genes are annotated in this assembly, of which 20,665 (96.2%) obtained at least one functional assignment based on similarity to known proteins. Conclusions: As an important marine angiosperm, the improved Z. marina genome assembly will further assist evolutionary, ecological, and comparative genomics at the chromosome level. The new genome assembly will further our understanding into the structural and physiological adaptations from land to marine life

Evidence for an ancient whole genome duplication in the cycad lineage

Contrary to the many whole genome duplication events recorded for angiosperms (flowering plants), whole genome duplications in gymnosperms (non-flowering seed plants) seem to be much rarer. Although ancient whole genome duplications have been reported for most gymnosperm lineages as well, some are still contested and need to be confirmed. For instance, data for ginkgo, but particularly cycads have remained inconclusive so far, likely due to the quality of the data available and flaws in the analysis. We extracted and sequenced RNA from both the cycad Encephalartos natalensis and Ginkgo biloba. This was followed by transcriptome assembly, after which these data were used to build paralog age distributions. Based on these distributions, we identified remnants of an ancient whole genome duplication in both cycads and ginkgo. The most parsimonious explanation would be that this whole genome duplication event was shared between both species and had occurred prior to their divergence, about 300 million years ago.The UP Research Development Programme (RDP), the Genomics Research Institute (GRI), Multidisciplinary Research Partnership `Bioinformatics: from nucleotides to networks' Project (no. 01MR0310W) of Ghent University, and funding from the European Union Seventh Framework Programme (FP7/2007-2013) under European Research Council Advanced Grant Agreement 322739 ± DOUBLEUP.http://www.plosone.orgam2017Forestry and Agricultural Biotechnology Institute (FABI)Genetic

Multi-Target Prediction: A Unifying View on Problems and Methods

Multi-target prediction (MTP) is concerned with the simultaneous prediction of multiple target variables of diverse type. Due to its enormous application potential, it has developed into an active and rapidly expanding research field that combines several subfields of machine learning, including multivariate regression, multi-label classification, multi-task learning, dyadic prediction, zero-shot learning, network inference, and matrix completion. In this paper, we present a unifying view on MTP problems and methods. First, we formally discuss commonalities and differences between existing MTP problems. To this end, we introduce a general framework that covers the above subfields as special cases. As a second contribution, we provide a structured overview of MTP methods. This is accomplished by identifying a number of key properties, which distinguish such methods and determine their suitability for different types of problems. Finally, we also discuss a few challenges for future research