The iPlant Collaborative: Cyberinfrastructure for Plant Biology

The iPlant Collaborative (iPlant) is a United States National Science Foundation (NSF) funded project that aims to create an innovative, comprehensive, and foundational cyberinfrastructure in support of plant biology research (PSCIC, 2006). iPlant is developing cyberinfrastructure that uniquely enables scientists throughout the diverse fields that comprise plant biology to address Grand Challenges in new ways, to stimulate and facilitate cross-disciplinary research, to promote biology and computer science research interactions, and to train the next generation of scientists on the use of cyberinfrastructure in research and education. Meeting humanity's projected demands for agricultural and forest products and the expectation that natural ecosystems be managed sustainably will require synergies from the application of information technologies. The iPlant cyberinfrastructure design is based on an unprecedented period of research community input, and leverages developments in high-performance computing, data storage, and cyberinfrastructure for the physical sciences. iPlant is an open-source project with application programming interfaces that allow the community to extend the infrastructure to meet its needs. iPlant is sponsoring community-driven workshops addressing specific scientific questions via analysis tool integration and hypothesis testing. These workshops teach researchers how to add bioinformatics tools and/or datasets into the iPlant cyberinfrastructure enabling plant scientists to perform complex analyses on large datasets without the need to master the command-line or high-performance computational services

The iPlant Collaborative: Cyberinfrastructure for Plant Biology

The iPlant Collaborative (iPlant) is a United States National Science Foundation (NSF) funded project that aims to create an innovative, comprehensive, and foundational cyberinfrastructure in support of plant biology research (PSCIC, 2006). iPlant is developing cyberinfrastructure that uniquely enables scientists throughout the diverse fields that comprise plant biology to address Grand Challenges in new ways, to stimulate and facilitate cross-disciplinary research, to promote biology and computer science research interactions, and to train the next generation of scientists on the use of cyberinfrastructure in research and education. Meeting humanity's projected demands for agricultural and forest products and the expectation that natural ecosystems be managed sustainably will require synergies from the application of information technologies. The iPlant cyberinfrastructure design is based on an unprecedented period of research community input, and leverages developments in high-performance computing, data storage, and cyberinfrastructure for the physical sciences. iPlant is an open-source project with application programming interfaces that allow the community to extend the infrastructure to meet its needs. iPlant is sponsoring community-driven workshops addressing specific scientific questions via analysis tool integration and hypothesis testing. These workshops teach researchers how to add bioinformatics tools and/or datasets into the iPlant cyberinfrastructure enabling plant scientists to perform complex analyses on large datasets without the need to master the command-line or high-performance computational services

From shallow sands to deep-sea trenches: Towards integrative systematics of Solenogastres (Aplacophora, Mollusca)

The marine realm encompasses a plethora of habitats: from light-flooded tropical coral reefs down to chemosynthetic vents and seeps to oceanic trenches several kilometers below the ocean’s surface. Habitat destruction, pollution, and effects of climate change accelerate rates of species extinction and pose a massive threat to marine ecosystems and biodiversity. Lack of baseline knowledge on species diversity is the key shortfall of current biodiversity research and especially prevalent among small-size invertebrates which constitute the larger part of global, metazoan biodiversity. Solenogastres (or Neomeniomorpha), an enigmatic class of molluscs are one of those understudied and neglected marine taxa. Instead of bearing a shell, these worm-shaped molluscs are densely covered in aragonitic spicules (the scleritome). They have been found from the tropics to the poles and occur from shallow waters down to the deep sea, with a peak in diversity along the continental shelfs. Despite their circumglobal occurrence, less than 300 species of Solenogastres have been described during the last 150 years since their first discovery. However, natural history collections alone have been estimated to contain at least ten-times more undescribed species than are currently known. Taxonomy of Solenogastres is bulky, requiring a mosaic of morphological and anatomical characters even for higher classification and is thus considered notoriously complex among zoologists. Novel approaches to characterize solenogaster diversity are urgently needed in order to catch up with discovery rates and modernize the taxonomic process. During my dissertation, I aimed to explore the diversity and evolution of Solenogastres in two understudied marine environments: the shallow-water interstitial habitat (i.e. the pore spaces between sand grains) and the deep oceans beyond the bathyal zone. For this purpose, I developed a novel integrative taxonomic workflow combining morphological characters of traditional taxonomy with DNA barcoding for molecular approaches to species delineation, supplemented with state-of-the-art anatomical 3D reconstructions of selected key lineages. My dissertation research is based on Solenogastres collected by colleagues and myself during sampling trips targeting marine interstitial malacofauna in Bermuda, Hawaii, Azores, Honshu and Okinawa (Japan). I joined two out of a series of four international deep-sea expeditions collecting benthic fauna in the Northwest Pacific, sampling across a depth range from 1,600 m down to almost 10,000 m in the Kuril-Kamchatka Trench. Overall, these expeditions covered different areas in the Northwest Pacific of varying geological age and stages of isolation. Additional material was made available through the natural history collection of the Section Mollusca, Bavarian State Collection of Zoology (SNSB-ZSM München), resulting in a total of 347 Solenogastres investigated during the course of my dissertation. Based on my work we are now able to identify main clades of meiofaunal Solenogastres, in a first step towards elucidating their global diversity of the clade in the interstitial habitat. The discovery of a putative widely distributed mesopsammic lineage of Dondersiidae (order Pholidoskepia) at sampling sites in the Atlantic and Pacific is challenged by the presence of co-occurring morphologically cryptic species revealed through anatomical 3D reconstructions. This highlights 1.) the risk of chimeric species descriptions if several individuals are used to extract all sets of taxonomically relevant characters and 2.) the importance of molecular data to reliably test hypothesis on conspecificity and distribution patterns in this taxonomically challenging group. Northwest Pacific Solenogastres were delineated based on unique morphological characters (i.e. scleritome data) and, if possible, cross-validated via molecular-based phylogenetic analyses. This integrative approach resulted in 60 candidate species across regions and depth zones in the Northwest Pacific (additional 13 candidate species lack molecular data), with the majority constituting species new to science. Their diversity covers all four orders, at least nine families, and 15 genera – therein presenting an immense boost in regional diversity. On a global scale, the number of abyssal Solenogastres has been more than doubled by these studies, and the animals collected from the bottom of the Kuril-Kamchatka Trench provide the first evidence of this molluscan class from the hadal zone and hold its depth record at almost 10,000 meters. The established baseline dataset of alpha-diversity from adjacent areas and depths zones enabled a first glimpse into distribution patterns. While there was overall little faunal overlap between the investigated regions and depths, several unique links were revealed: 1.) across depth by an eurybathic species occurring in the Kuril Basin (3,350 m) and at the bottom of the trench (9,580 m); 2) across the Kuril-Kamchatka Trench: Kruppomenia genslerae Ostermair, Brandt, Haszprunar, Jörger & Bergmeier, 2018 was found in the Sea of Okhotsk and on the open abyssal plain, thereby indicating that a hadal trench does not pose an insurmountable dispersal barrier for benthic invertebrates; and 3) potentially across oceans: anatomical investigations suggest that an abyssal species from the Atlantic is also present on the Northwest Pacific Plain, albeit molecular data from the putative Atlantic conspecifics to support pan-oceanic distribution is lacking. In order to gain insights into the feeding ecology of deep-sea Solenogastres, we sequenced their gut contents from genomic DNA extracts. This molecular-based approach showed that they are highly specialized micropredators with taxon-specific prey preferences. While anthozoan and hydrozoan cnidarians have been generally assumed as the main food source of Solenogastres, Siphonophora, Nemertea, Annelida and Bivalvia have now been added to their menu. The molecular phylogeny used as a backbone for our integrative approach to characterize their diversity has also several implications for solenogaster systematics. As two fast evolving mitochondrial markers were used in its analyses, without counterbalancing conservative markers the phylogeny cannot reliably resolve deep relationships within a group that has been hypothesized to date back to the early Paleozoic. Nevertheless, as our dataset contains multiple species and genera across several families, we were able to test the validity of existing taxonomic units: several classificatory entities (i.e. the largest order Cavibelonia, families Acanthomeniidae and Pruvotinidae) were retrieved as polyphyletic which will thus necessitate major systematic revisions in the future. The integrative approach developed during my dissertation allows for fast and efficient species delineation. Scleritome characters were chosen as the main morphological trait, as they are comparatively easy to access and provide the necessary link to the existing classificatory system to prevent a parallel system of DNA-based taxonomy. At the same time, reducing the amount of required characters presents an efficient solution when confronted with small-sized animals and high proportions of singletons that hamper the use of single individuals for multiple lines of investigation (e.g. morphology, anatomy, DNA). The set-up of our community-curated online database AplacBase currently serves as an openly accessible repository and initial identification tool, providing supporting information and guiding researchers through the essence of aplacophoran taxonomy. However, in order to overcome the taxonomic deficits prevalent in Solenogastres, novel approaches need to aim beyond the characterization of their diversity and consequently provide efficient solutions to the currently complicated process of species descriptions and diagnosis. Based on a backbone phylogeny stabilized by mitochondrial genomes, a streamlined approach combining “deep taxonomy” with rapid, DNA-based taxonomy is proposed to tackle the emerging wealth of novel Solenogastres species

Genomic and Phenotypic Analyses of Polychaete Sibling Species <i>Platynereis dumerilii</i> and <i>Platynereis massiliensis</i> in Relation to Ocean Acidification

The increase of anthropogenic carbon dioxide emissions and the subsequent uptake of CO2 by the sea, is leading to a decrease in the pH of the oceans, a process known as Ocean Acidification. One of the main challenges of the current research on climate change is to determine how marine species respond to low pH/elevated pCO2 conditions. This thesis has investigated the effects of natural OA on the polychaete species Platynereis dumerilii and its sibling P. massiliensis (Annelida, Nereididae) as driver of genetic differentiation and phenotype/genotype selection. Platynereis spp. populations were sampled in five geographical areas situated along a thermo-latitudinal gradient along the Italian coasts, characterized by different pH conditions (acid vs normal). A multidisciplinary approach, focused on different aspects of the target species biology, was chosen and the following analyses were performed: (a) morphological and morphometric analyses of different populations/genotypes; (b) laboratory rearing of different populations to study the reproductive biology and gamete morphology; (c) population genetics by the amplification of a mitochondrial DNA marker (COI); (d) population genomics by a next-generation sequencing approach (RAD-seq); (e) background analyses and a long term laboratory experiment on selected genotypes/populations to study physiological responses to different pH conditions. This work has confirmed that Platynereis dumerilii and P. massiliensis represent two complexes of sibling species characterized by contrasting life history traits, reproductive biology and gamete morphology. The overall Platynereis massiliensis predominance in the CO2 vent systems is not a direct consequence of elevated pCO2, but it seems to derive from a winning reproductive strategy (brooding habit) in low pH conditions. Unlike Platynereis dumerilii, P. massiliensis is potentially able to thrive in the CO2 vents thanks to the higher stability of its antioxidant defence systems over temporal scale and its greater responsiveness to extreme hypercapnia conditions

Cryptic reservoirs of micro-eukaryotic parasites in ecologically relevant intertidal invertebrates from temperate coastal ecosystems unveiled by a combined histopathological, ultrastructural, and molecular approach

271 p.La mayoría de los eucariotas son organismos unicelulares (protistas), muchos de ellos pertenecientes a linajes que divergieron temprano en la historia evolutiva de este Dominio de organismos nucleados. Microscópicos, enormemente diversos y fenotípicamente convergentes, su clasificación cladística ha sido históricamente compleja, dejando atrás un extenso registro de taxones y de términos parafiléticos y polifiléticos. Teniendo que investigar atributos estructurales, celulares, biológicos y ecológicos en un mundo de rápidas interacciones y difícilmente accesible a simple vista, la protistología es particularmente dependiente de la sistemática. Ésta permite inferir rasgos de especies crípticas a partir de especies evolutivamente relacionadas.Las moléculas de ADN (y ARN), representan un "registro" preciso de estos eventos de diversificación, que preceden incluso a los más antiguos registros fósiles. En los últimos años, la maduración de los métodos de filogenia molecular, catalizados por una mayor accesibilidad a la secuenciación de próxima generación (NGS), está permitiendo resolver preguntas e hipótesis sobre la evolución y la especiación de estos organismos micro-eucariotas que no se habían podido responder mediante otros métodos. Por una parte, arboles filogenéticos construidos mediante concatenaciones de cientos, incluso miles de genes, están permitiendo rastrear la historia evolutiva de los linajes protistas hasta el último ancestro común de todos los eucariotas (LECA). Concomitantemente, análisis moleculares basados en genes e incluso fragmentos cortos (especialmente 18S rRNA), recuperados principalmente de matrices ambientales u orgánicas (eDNA o ADN ambiental), están revelando una ¿caja de Pandora¿ de diversidad micro-eucariota. Ésta diversidad ¿oculta¿ está transformando nuestra percepción de los protistas en la cadena trófica y la estructura ecológica. En el medio marino, sus papeles como autótrofos, heterótrofos (predadores, saprófitos, parásitos) o mixótrofos crece en importancia día a día. El aumento simultáneo de diversidad e importancia ha sido particularmente pronunciado entre los linajes de parásitos protistas, que adaptados a la vida dentro de un huésped son más inaccesibles y morfológicamente indistinguibles que sus homólogos de vida libre. Muy competitivo como estilo de vida, el parasitismo ha evolucionado de forma independiente varias veces en prácticamente todos los grupos eucariotas, en algunos incluso cientos de veces. De hecho, es posible que el efecto parapátrico que implica una existencia endosimbiótica, haya exacerbado la especiación entre los parásitos, que representan la que posiblemente sea la más común estrategia de consumo entre los organismos vivos. Es más, el número de especies crípticas que están, a día de hoy, siendo descubiertas en la mayoría de los linajes de parásitos protistas sigue aumentando abruptamente o apenas comienza a mostrar una desaceleración. Cabe destacar, que el descubrimiento de esta diversidad oculta, incluidas las especies crípticas, va más allá de la escalada en el número de especies; afecta los estudios sobre biología celular, ciclos biológicos, y ecología. Inexorablemente, esta fuerza mostrada por los métodos de análisis y secuenciación del ADN está abriendo una brecha entre la diversidad genética existente y nuestra comprensión de la morfología, patología, transmisión y posibles hospedadores de los parásitos protistas que la constituyen. Este desequilibrio es particularmente evidente entre los parásitos que infectan linajes de invertebrados, los cuales, salvo algunos taxones con interés comercial, permanecen en gran parte sin analizar, a pesar de constituir un grupo mucho más diverso que los vertebrados. Por una parte, es lógico que los parásitos protistas causantes de infecciones en especies marinas de interés comercial (peces, bivalvos, crustáceos¿) hayan sido priorizadas, pero hay que tener en cuenta que muchos de estos micro-eucariotas tienen ciclos de vida complejos, en los que pequeños invertebrados actúan muchas veces como vectores o reservorios. Descubrir y contextualizar estas asociaciones puede ser determinante a la hora de comprender cuándo y dónde puede variar la presión y capacidad infectiva de algunas de estas infecciones en la comunidad o huéspedes específicos. Al mismo tiempo que su diversidad e importancia aumenta, la inclusión progresiva de parásitos en modelos ecológicos está experimentando variaciones de gran alcance en la dinámica poblacional de las especies animales, vegetales o fúngicas en los ecosistemas. En consecuencia, las asociaciones entre parásitos y hospedadores se investigan cada vez más como una parte importante de la estructura de la comunidad, y no exclusivamente como una "molestia" para el ser humano y sus intereses. Por desgracia la inclusión de parásitos en modelos ecológicos está siendo lastrada por un profundo desconocimiento de estas interacciones. A diferencia de los organismos multicelulares, que han podido ser observados por científicos y aficionados durante siglos, la distribución espaciotemporal de la mayoría de los organismos unicelulares sigue siendo un profundo misterio. No obstante, dadas sus importantes funciones como vectores, huéspedes intermediarios y reservorios, una comprensión mucho más profunda del patobioma (patógenos asociados a un hospedador) y su variabilidad espacio-temporal es de suma importancia para un mayor poder de predicción de los factores de presión causantes de epidemias o zoonosis en el huésped, la población y el medioambiente.En este contexto, la hipótesis de este estudio plantea que especies de invertebrados comunes en la zona inter-mareal de ecosistemas costeros en climas templados son reservorios crípticos de un número significativo de parásitos micro-eucariotas (protistas) de interés para el medio y los recursos marinos. Eldescubrimiento progresivo de estas asociaciones ocultas de parásitos-huéspedes (mediante exámenes combinando técnicas histopatológicas, ultraestructurales y moleculares) permite una mejor comprensión de la morfología, patología, biología celular y ciclo de vida de dichos patógenos, lo que a su vez consiente un seguimiento más estrecho de los factores y presiones que promueven epidemias y zoonosis en una escala espacio-temporal.PIE:Plentziako Itsas Estazio

Evolutionary Genomics of Transposable Elements in the Saccharomyces sensu lato Complex

Transposable elements (TEs) are almost ubiquitous components of eukaryotic genomes that have long been considered solely deleterious or ’junk DNA’. They are split into two main forms, retro-transposons and DNA transposons, depending on the method of replication employed. Hosts have developed strategies for combating TEs including RNAi, methylation and copy number con-trol. TEs have also evolved ways of persisting in the genome in order to survive, such as target site specificity. Two additional ways which may be utilised by TEs, positive selection and horizontal transfer, were investigated here primarily using the budding yeasts in the Saccharomyces sensu lato complex. These species typically contain up to five families of retrotransposons, designatedTy1-5, and multiple subfamilies, all of varying transpositional activity. Discoveries of insertions evolving under positive selection and providing benefits to their hosts have been sporadic and serendipitous findings in a number of organisms. Full genome screenings for such insertions are rarely published, despite the impact TE insertions have upon their hosts. A population genomics approach was performed to address this issue in the genomes of Saccha-romyces cerevisiae and sister species S. paradoxus. Signatures of positive selection acting upon Ty insertions were identified using Tajima’s statistical D test. Neighbouring genes were also analysed to ascertain the true target of selection where hitchhiking linked the two. A subset of LTR-gene pairings were explored using qPCR in order to identify any effects on host gene expression the occupied loci may cause. Two genes displayed significantly increased levels of expression, which may be due to the presence of positive selection candidate LTRs, which in turn may contribute to improving host fitness. This thesis further documents the systematic screening for Ty-like elements of all available genomes of budding yeast and related species. Extensive phylogenetic analyses estimated evolutionary relationships and possible horizontal transfer events of elements between the species. Evidence for in excess of 75 horizontal transfer events was uncovered here, around half of which were successful in propagating in new genomes. The occurrence of horizontal transfer of TEs in the genomes of budding yeast is therefore far more common than previously documented. During screening of genomes, a further potential method of avoiding host defences was uncovered. The divergence of the highly active Ty4 family, which coincided with population isolation of multiple Saccharomyces species into subfamilies, was surprising given previous reports of this family being of particularly low activity. Such events are rarely recorded in eukaryotic genomes, and may also illustrate the compulsive spread of a new subfamily via horizontal transfer. The investigations reported here represent the first genomic screening of Ty insertions in Saccharomyces for signatures of positive selection, and an updated, comprehensive search for evidence of HT between species of budding yeast. Both may act as methods for TE families to persist in the genomes of their hosts, and represent far more than simply ’junk DNA’

Evolutionary genomics : statistical and computational methods

This open access book addresses the challenge of analyzing and understanding the evolutionary dynamics of complex biological systems at the genomic level, and elaborates on some promising strategies that would bring us closer to uncovering of the vital relationships between genotype and phenotype. After a few educational primers, the book continues with sections on sequence homology and alignment, phylogenetic methods to study genome evolution, methodologies for evaluating selective pressures on genomic sequences as well as genomic evolution in light of protein domain architecture and transposable elements, population genomics and other omics, and discussions of current bottlenecks in handling and analyzing genomic data. Written for the highly successful Methods in Molecular Biology series, chapters include the kind of detail and expert implementation advice that lead to the best results. Authoritative and comprehensive, Evolutionary Genomics: Statistical and Computational Methods, Second Edition aims to serve both novices in biology with strong statistics and computational skills, and molecular biologists with a good grasp of standard mathematical concepts, in moving this important field of study forward

Evolutionary Genomics

This open access book addresses the challenge of analyzing and understanding the evolutionary dynamics of complex biological systems at the genomic level, and elaborates on some promising strategies that would bring us closer to uncovering of the vital relationships between genotype and phenotype. After a few educational primers, the book continues with sections on sequence homology and alignment, phylogenetic methods to study genome evolution, methodologies for evaluating selective pressures on genomic sequences as well as genomic evolution in light of protein domain architecture and transposable elements, population genomics and other omics, and discussions of current bottlenecks in handling and analyzing genomic data. Written for the highly successful Methods in Molecular Biology series, chapters include the kind of detail and expert implementation advice that lead to the best results. Authoritative and comprehensive, Evolutionary Genomics: Statistical and Computational Methods, Second Edition aims to serve both novices in biology with strong statistics and computational skills, and molecular biologists with a good grasp of standard mathematical concepts, in moving this important field of study forward