Comparative Genomic Analysis of 31 Phytophthora Genomes Reveals Genome Plasticity and Horizontal Gene Transfer

Phytophthora species are oomycete plant pathogens that cause great economic and ecological impacts. The Phytophthora genus includes over 180 known species, infecting a wide range of plant hosts, including crops, trees, and ornamentals. We sequenced the genomes of 31 individual Phytophthora species and 24 individual transcriptomes to study genetic relationships across the genus. De novo genome assemblies revealed variation in genome sizes, numbers of predicted genes, and in repetitive element content across the Phytophthora genus. A genus-wide comparison evaluated orthologous groups of genes. Predicted effector gene counts varied across Phytophthora species by effector family, genome size, and plant host range. Predicted numbers of apoplastic effectors increased as the host range of Phytophthora species increased. Predicted numbers of cytoplasmic effectors also increased with host range but leveled off or decreased in Phytophthora species that have enormous host ranges. With extensive sequencing across the Phytophthora genus, we now have the genomic resources to evaluate horizontal gene transfer events across the oomycetes. Using a machine-learning approach to identify horizontally transferred genes with bacterial or fungal origin, we identified 44 candidates over 36 Phytophthora species genomes. Phylogenetic reconstruction indicates that the transfers of most of these 44 candidates happened in parallel to major advances in the evolution of the oomycetes and Phytophthora spp. We conclude that the 31 genomes presented here are essential for investigating genus-wide genomic associations in genus Phytophthora. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license

Augmented Virtuality Data Annotation and Human-in-the-Loop Refinement for RGBD Data in Industrial Bin-Picking Scenarios

Beyond conventional automated tasks, autonomous robot capabilities aside to human cognitive skills are gaining importance. This comprises goods commissioning and material supply in intralogistics as well as material feeding and assembly operations in production. Deep learning-based computer vision is considered as enabler for autonomy. Currently, the effort to generate specific datasets is challenging. Adaptation of new components often also results in downtimes. The objective of this paper is to propose an augmented virtuality (AV) based RGBD data annotation and refinement method. The approach reduces required effort in initial dataset generation to enable prior system commissioning and enables dataset quality improvement up to operational readiness during ramp-up. In addition, remote fault intervention through a teleoperation interface is provided to increase operational system availability. Several components within a real-world experimental bin-picking setup serve for evaluation. The results are quantified by comparison to established annotation methods and through known evaluation metrics for pose estimation in bin-picking scenarios. The results enable to derive accurate and more time-efficient data annotation for different algorithms. The AV approach shows a noticeable reduction in required effort and timespan for annotation as well as dataset refinement

Procedural modeling of plant ecosystems maximizing vegetation cover

Vegetation plays a major role in the realistic display of outdoor scenes. However, manual plant placement can be tedious. For this reason this paper presents a new proposal in the field of procedural modeling of natural scenes. This method creates plant ecosystems that maximizes the covered space by optimizing an objective function subject to a series of constraints defined by a system of inequalities. This system includes the constraints of the environment taking into account characteristics of the terrain and the plant species involved. Once the inequality system has been defined, a solution will be obtained that tries to maximize the radius of the projected area of the trees and therefore the extension of the vegetation cover on the ground. The technique eliminates the trees that do not achieve a minimum growth radius, simulating the typical competitive process of nature. Results show the good performance and the high visual quality of the ecosystems obtained by the proposed technique. The use of this kind of optimization techniques could be used to solve other procedural modeling problems in other fields of application.Funding for open access charge: CRUE-Universitat Jaume

An Evolutionary Approach to Adaptive Image Analysis for Retrieving and Long-term Monitoring Historical Land Use from Spatiotemporally Heterogeneous Map Sources

Land use changes have become a major contributor to the anthropogenic global change. The ongoing dispersion and concentration of the human species, being at their orders unprecedented, have indisputably altered Earth’s surface and atmosphere. The effects are so salient and irreversible that a new geological epoch, following the interglacial Holocene, has been announced: the Anthropocene. While its onset is by some scholars dated back to the Neolithic revolution, it is commonly referred to the late 18th century. The rapid development since the industrial revolution and its implications gave rise to an increasing awareness of the extensive anthropogenic land change and led to an urgent need for sustainable strategies for land use and land management. By preserving of landscape and settlement patterns at discrete points in time, archival geospatial data sources such as remote sensing imagery and historical geotopographic maps, in particular, could give evidence of the dynamic land use change during this crucial period. In this context, this thesis set out to explore the potentials of retrospective geoinformation for monitoring, communicating, modeling and eventually understanding the complex and gradually evolving processes of land cover and land use change. Currently, large amounts of geospatial data sources such as archival maps are being worldwide made online accessible by libraries and national mapping agencies. Despite their abundance and relevance, the usage of historical land use and land cover information in research is still often hindered by the laborious visual interpretation, limiting the temporal and spatial coverage of studies. Thus, the core of the thesis is dedicated to the computational acquisition of geoinformation from archival map sources by means of digital image analysis. Based on a comprehensive review of literature as well as the data and proposed algorithms, two major challenges for long-term retrospective information acquisition and change detection were identified: first, the diversity of geographical entity representations over space and time, and second, the uncertainty inherent to both the data source itself and its utilization for land change detection. To address the former challenge, image segmentation is considered a global non-linear optimization problem. The segmentation methods and parameters are adjusted using a metaheuristic, evolutionary approach. For preserving adaptability in high level image analysis, a hybrid model- and data-driven strategy, combining a knowledge-based and a neural net classifier, is recommended. To address the second challenge, a probabilistic object- and field-based change detection approach for modeling the positional, thematic, and temporal uncertainty adherent to both data and processing, is developed. Experimental results indicate the suitability of the methodology in support of land change monitoring. In conclusion, potentials of application and directions for further research are given

Realistic reconstruction and rendering of detailed 3D scenarios from multiple data sources

During the last years, we have witnessed significant improvements in digital terrain modeling, mainly through photogrammetric techniques based on satellite and aerial photography, as well as laser scanning. These techniques allow the creation of Digital Elevation Models (DEM) and Digital Surface Models (DSM) that can be streamed over the network and explored through virtual globe applications like Google Earth or NASA WorldWind. The resolution of these 3D scenes has improved noticeably in the last years, reaching in some urban areas resolutions up to 1m or less for DEM and buildings, and less than 10 cm per pixel in the associated aerial imagery. However, in rural, forest or mountainous areas, the typical resolution for elevation datasets ranges between 5 and 30 meters, and typical resolution of corresponding aerial photographs ranges between 25 cm to 1 m. This current level of detail is only sufficient for aerial points of view, but as the viewpoint approaches the surface the terrain loses its realistic appearance. One approach to augment the detail on top of currently available datasets is adding synthetic details in a plausible manner, i.e. including elements that match the features perceived in the aerial view. By combining the real dataset with the instancing of models on the terrain and other procedural detail techniques, the effective resolution can potentially become arbitrary. There are several applications that do not need an exact reproduction of the real elements but would greatly benefit from plausibly enhanced terrain models: videogames and entertainment applications, visual impact assessment (e.g. how a new ski resort would look), virtual tourism, simulations, etc. In this thesis we propose new methods and tools to help the reconstruction and synthesis of high-resolution terrain scenes from currently available data sources, in order to achieve realistically looking ground-level views. In particular, we decided to focus on rural scenarios, mountains and forest areas. Our main goal is the combination of plausible synthetic elements and procedural detail with publicly available real data to create detailed 3D scenes from existing locations. Our research has focused on the following contributions: - An efficient pipeline for aerial imagery segmentation - Plausible terrain enhancement from high-resolution examples - Super-resolution of DEM by transferring details from the aerial photograph - Synthesis of arbitrary tree picture variations from a reduced set of photographs - Reconstruction of 3D tree models from a single image - A compact and efficient tree representation for real-time rendering of forest landscapesDurant els darrers anys, hem presenciat avenços significatius en el modelat digital de terrenys, principalment gràcies a tècniques fotogramètriques, basades en fotografia aèria o satèl·lit, i a escàners làser. Aquestes tècniques permeten crear Models Digitals d'Elevacions (DEM) i Models Digitals de Superfícies (DSM) que es poden retransmetre per la xarxa i ser explorats mitjançant aplicacions de globus virtuals com ara Google Earth o NASA WorldWind. La resolució d'aquestes escenes 3D ha millorat considerablement durant els darrers anys, arribant a algunes àrees urbanes a resolucions d'un metre o menys per al DEM i edificis, i fins a menys de 10 cm per píxel a les fotografies aèries associades. No obstant, en entorns rurals, boscos i zones muntanyoses, la resolució típica per a dades d'elevació es troba entre 5 i 30 metres, i per a les corresponents fotografies aèries varia entre 25 cm i 1m. Aquest nivell de detall només és suficient per a punts de vista aeris, però a mesura que ens apropem a la superfície el terreny perd tot el realisme. Una manera d'augmentar el detall dels conjunts de dades actuals és afegint a l'escena detalls sintètics de manera plausible, és a dir, incloure elements que encaixin amb les característiques que es perceben a la vista aèria. Així, combinant les dades reals amb instàncies de models sobre el terreny i altres tècniques de detall procedural, la resolució efectiva del model pot arribar a ser arbitrària. Hi ha diverses aplicacions per a les quals no cal una reproducció exacta dels elements reals, però que es beneficiarien de models de terreny augmentats de manera plausible: videojocs i aplicacions d'entreteniment, avaluació de l'impacte visual (per exemple, com es veuria una nova estació d'esquí), turisme virtual, simulacions, etc. En aquesta tesi, proposem nous mètodes i eines per ajudar a la reconstrucció i síntesi de terrenys en alta resolució partint de conjunts de dades disponibles públicament, per tal d'aconseguir vistes a nivell de terra realistes. En particular, hem decidit centrar-nos en escenes rurals, muntanyes i àrees boscoses. El nostre principal objectiu és la combinació d'elements sintètics plausibles i detall procedural amb dades reals disponibles públicament per tal de generar escenes 3D d'ubicacions existents. La nostra recerca s'ha centrat en les següents contribucions: - Un pipeline eficient per a segmentació d'imatges aèries - Millora plausible de models de terreny a partir d'exemples d’alta resolució - Super-resolució de models d'elevacions transferint-hi detalls de la fotografia aèria - Síntesis d'un nombre arbitrari de variacions d’imatges d’arbres a partir d'un conjunt reduït de fotografies - Reconstrucció de models 3D d'arbres a partir d'una única fotografia - Una representació compacta i eficient d'arbres per a navegació en temps real d'escenesPostprint (published version