Aquerium: A web application for comparative exploration of domain‐based protein occurrences on the taxonomically clustered genome tree

Gene duplication and loss are major driving forces in evolution. While many important genomic resources provide information on gene presence, there is a lack of tools giving equal importance to presence and absence information as well as web platforms enabling easy visual comparison of multiple domain‐based protein occurrences at once. Here, we present Aquerium, a platform for visualizing genomic presence and absence of biomolecules with a focus on protein domain architectures. The web server offers advanced domain organization querying against the database of pre‐computed domains for ～26,000 organisms and it can be utilized for identification of evolutionary events, such as fusion, disassociation, duplication, and shuffling of protein domains. The tool also allows alternative inputs of custom entries or BLASTP results for visualization. Aquerium will be a useful tool for biologists who perform comparative genomic and evolutionary analyses. The web server is freely accessible at http://aquerium.utk.edu . Proteins 2016; 85:72–77. © 2016 Wiley Periodicals, Inc.     

The RAINFOR database: monitoring forest biomass and dynamics

Problem: Data from over 100 permanent sample plots which have been studied for 10–20 years need a suitable system for storage which allows simple data manipulation and retrieval for analysis. Methods: A relational database linking tree records, taxonomic nomenclature and corresponding environmental data has been built in MS Access as part of the RAINFOR project. Conclusion: The database allows flexible and long‐term use of a large amount of data: more than 100 tree plots across Amazonia, incorporating over 80 000 records of individual trees and over 300 000 total records of tree diameter measurements from successive censuses. The database is designed to enable linkages to existing soil, floristic or plant‐trait databases. This database will be a useful tool for exploring the impact of environmental factors on forest structure and dynamics at local to continental scales, and long term changes in forest ecology. As an early example of its potential, we explore the impact of different methodological assumptions on estimates of tropical forest biomass and carbon storage.     

林木蛋白质组学研究进展

近年来,应用新的基因组学技术来研究林木生长发育以及林木对生物与非生物胁迫的反应已使得人们对林木生物学有了相当大的了解。蛋白质组学是林木生物学的重要内容。本文综述了林木蛋白质组学在群体遗传、遗传作图、逆境生理、组织器官以及木材形成等方面的研究进展,并简要介绍了林木蛋白质组数据库。最后展望了林木蛋白质组学的发展前景。     

CoryneBase: Corynebacterium Genomic Resources and Analysis Tools at Your Fingertips

Corynebacteria are used for a wide variety of industrial purposes but some species are associated with human diseases. With increasing number of corynebacterial genomes having been sequenced, comparative analysis of these strains may provide better understanding of their biology, phylogeny, virulence and taxonomy that may lead to the discoveries of beneficial industrial strains or contribute to better management of diseases. To facilitate the ongoing research of corynebacteria, a specialized central repository and analysis platform for the corynebacterial research community is needed to host the fast-growing amount of genomic data and facilitate the analysis of these data. Here we present CoryneBase, a genomic database for Corynebacterium with diverse functionality for the analysis of genomes aimed to provide: (1) annotated genome sequences of Corynebacterium where 165,918 coding sequences and 4,180 RNAs can be found in 27 species; (2) access to comprehensive Corynebacterium data through the use of advanced web technologies for interactive web interfaces; and (3) advanced bioinformatic analysis tools consisting of standard BLAST for homology search, VFDB BLAST for sequence homology search against the Virulence Factor Database (VFDB), Pairwise Genome Comparison (PGC) tool for comparative genomic analysis, and a newly designed Pathogenomics Profiling Tool (PathoProT) for comparative pathogenomic analysis. CoryneBase offers the access of a range of Corynebacterium genomic resources as well as analysis tools for comparative genomics and pathogenomics. It is publicly available at http://corynebacterium.um.edu.my/.     

Genome Annotator Light (GAL): A Docker-based package for genome analysis and visualization

Next generation sequencing techniques produce enormous data but its analysis and visualization remains a big challenge. To address this, we have developed Genome Annotator Light(GAL), a Docker based package for genome analysis and data visualization. GAL integrated several existing tools and in-house programs inside a Docker Container for systematic analysis and visualization of genomes through web browser. GAL takes varieties of input types ranging from raw Fasta files to fully annotated files, processes them through a standard annotation pipeline and visualizes on a web browser. Comparative genomic analysis is performed automatically within a given taxonomic class. GAL creates interactive genome browser with clickable genomic feature tracks; local BLAST-able database; query page, on-fly downstream data analysis using EMBOSS etc. Overall, GAL is an extremely convenient, portable and platform independent. Fully integrated web-resources can be easily created and deployed, e.g. www.eumicrobedb.org/cglab, for our in-house genomes. GAL is freely available at https://hub.docker.com/u/cglabiicb/.     

Characterization of an alpine tree line using airborne LiDAR data and physiological modeling

Understanding what environmental drivers control the position of the alpine tree line is important for refining our understanding of plant stress and tree development, as well as for climate change studies. However, monitoring the location of the tree line position and potential movement is difficult due to cost and technical challenges, as well as a lack of a clear boundary. Advanced remote sensing technologies such as Light Detection and Ranging (LiDAR) offer significant potential to map short individual tree crowns within the transition zone despite the lack of predictive capacity. Process‐based forest growth models offer a complementary approach by quantifying the environmental stresses trees experience at the tree line, allowing transition zones to be defined and ultimately mapped. In this study, we investigate the role remote sensing and physiological, ecosystem‐based modeling can play in the delineation of the alpine tree line. To do so, we utilize airborne LiDAR data to map tree height and stand density across a series of altitudinal gradients from below to above the tree line within the Swiss National Park (SNP), Switzerland. We then utilize a simple process‐based model to assess the importance of seasonal variations on four climatically related variables that impose non‐linear constraints on photosynthesis. Our results indicate that all methods predict the tree line to within a 50 m altitudinal zone and indicate that aspect is not a driver of significant variations in tree line position in the region. Tree cover, rather than tree height is the main discriminator of the tree line at higher elevations. Temperatures in fall and spring are responsible for the major differences along altitudinal zones, however, changes in evaporative demand also control plant growth at lower altitudes. Our results indicate that the two methods provide complementary information on tree line location and, when combined, provide additional insights into potentially endangered forest/grassland transition zones.     

Analysis and visualization of H7 influenza using genomic,evolutionary and geographic information in a modular web service

We have reported previously on use of a web‐based application, Supramap ( http://supramap.org ) for the study of biogeographic, genotypic, and phenotypic evolution. Using Supramap we have developed maps of the spread of drug‐resistant influenza and host shifts in H1N1 and H5N1 influenza and coronaviruses such as SARS. Here we report on another zoonotic pathogen, H7 influenza, and provide an update on the implementation of Supramap as a web service. We find that the emergence of pathogenic strains of H7 is labile with many transitions from high to low pathogenicity, and from low to high pathogenicity. We use Supramap to put these events in a temporal and geospatial context. We identify several lineages of H7 influenza with biomarkers of high pathogenicity in regions that have not been reported in the scientific literature. The original implementation of Supramap was built with tightly coupled client and server software. Now we have decoupled the components to provide a modular web service for POY ( http://poyws.org ) that can be consumed by a data provider to create a novel application. To demonstrate the web service, we have produced an application, Geogenes ( http://geogenes.org ). Unlike in Supramap, in which the user is required to create and upload data files, in Geogenes the user works from a graphical interface to query an underlying dataset. Geogenes demonstrates how the web service can provide underlying processing for any sequence and metadata database. © The Willi Hennig Society 2012.     

Xylella fastidiosa comparative genomic database is an information resource to explore the annotation, genomic features, and biology of different strains

The Xylella fastidiosa comparative genomic database is a scientific resource with the aim to provide a user-friendly interface for accessing high-quality manually curated genomic annotation and comparative sequence analysis, as well as for identifying and mapping prophage-like elements, a marked feature of Xylella genomes. Here we describe a database and tools for exploring the biology of this important plant pathogen. The hallmarks of this database are the high quality genomic annotation, the functional and comparative genomic analysis and the identification and mapping of prophage-like elements. It is available from web site http://www.xylella.lncc.br.     

PolysacDB: a database of microbial polysaccharide antigens and their antibodies

Vaccines based on microbial cell surface polysaccharides have long been considered as attractive means to control infectious diseases. To realize this goal, detailed systematic information about the antigenic polysaccharide is necessary. However, only a few databases that provide limited knowledge in this area are available. This paper describes PolysacDB, a manually curated database of antigenic polysaccharides. We collected and compiled comprehensive information from literature and web resources about antigenic polysaccharides of microbial origin. The current version of the database has 1,554 entries of 149 different antigenic polysaccharides from 347 different microbes. Each entry provides comprehensive information about an antigenic polysaccharide, i.e., its origin, function, protocols for its conjugation to carriers, antibodies produced, details of assay systems, specificities of antibodies, proposed epitopes involved and antibody utilities. For convenience to the user, we have integrated web interface for searching, advanced searching and browsing data in database. This database will be useful for researchers working on polysaccharide-based vaccines. It is freely available from the URL: http://crdd.osdd.net/raghava/polysacdb/.     

Managing mature forest features: The production,accuracy and ecological relevance of a landscape‐scale map

Mature trees and forests contain structural features such as tree hollows, large coarse woody debris and large spreading crowns that provide critical habitat for a wide range of species. These features can take hundreds of years to develop and require careful management to ensure their continued availability. Managing these features requires spatial mapping layers to facilitate landscape‐scale management. This paper outlines how a map of mature forest habitat was developed for Tasmania, Australia. The map was produced using spatial data on vegetation type, mature crown density and senescence, a global layer of forest loss data derived from satellite imagery, a database on timber harvest plans and a spatial layer on the extent of fire. The relationship between mapped mature habitat availability (high, medium, low or negligible) and tree hollow availability in wet forest areas was explored, complementing a similar published study in dry forests. The number of large trees likely to have hollows significantly increased with mapped mature habitat availability, although there was considerable variation and overlap between map categories. Data from a fauna locality database and two radio‐tracking studies showed that three of the vertebrate hollow‐using species examined (Swift Parrot, Common Brushtail Possum and the Tasmanian Long‐eared Bat) and nest records of a species reliant on large tree crowns (the Wedge‐tailed Eagle) were all more likely to occur in areas of higher mapped mature habitat availability. It is concluded that this map reflects the relative availability of tree hollows, is ecologically meaningful and will be useful when managing mature forest habitat at large spatial scales, but the variable accuracy of the map at fine scales needs to be taken into account.     

Tree mortality in the eastern and central United States: patterns and drivers

Substantial uncertainty surrounds how forest ecosystems will respond to the simultaneous impacts of multiple global change drivers. Long‐term forest dynamics are sensitive to changes in tree mortality rates; however, we lack an understanding of the relative importance of the factors that affect tree mortality across different spatial and temporal scales. We used the US Forest Service Forest Inventory and Analysis database to evaluate the drivers of tree mortality for eastern temperate forest at the individual‐level across spatial scales from tree to landscape to region. We investigated 13 covariates in four categories: climate, air pollutants, topography, and stand characteristics. Overall, we found that tree mortality was most sensitive to stand characteristics and air pollutants. Different functional groups also varied considerably in their sensitivity to environmental drivers. This research highlights the importance of considering the interactions among multiple global change agents in shaping forest ecosystems.     

Quantifying Tropical Dry Forest Type and Succession: Substantial Improvement with LiDAR

Improved technologies are needed to advance our knowledge of the biophysical and human factors influencing tropical dry forests, one of the world's most threatened ecosystems. We evaluated the use of light detection and ranging (LiDAR) data to address two major needs in remote sensing of tropical dry forests, i.e., classification of forest types and delineation of forest successional status. We evaluated LiDAR‐derived measures of three‐dimensional canopy structure and subcanopy topography using classification‐tree techniques to separate different dry forest types and successional stages in the Guánica Biosphere Reserve in Puerto Rico. We compared the LiDAR‐based results with classifications made from commonly used remote sensing data, including Landsat satellite imagery and radar‐based topographic data. The accuracy of the LiDAR‐based forest type classification (including native‐ and exotic‐dominated forest classes) was substantially higher than those from previously available data (kappa = 0.90 and 0.63, respectively). The best result was obtained when combining LiDAR‐derived metrics of canopy structure and topography, and adding Landsat spectral data did not improve the classification. For the second objective, we observed that LiDAR‐derived variables of vegetation structure were better predictors of forest successional status (i.e., mid‐secondary, late‐secondary, and primary forests) than was spectral information from Landsat. Importantly, the key LiDAR predictors identified within each classification‐tree model agreed with previous ecological knowledge of these forests. Our study highlights the value of LiDAR remote sensing for assessing tropical dry forests, reinforcing the potential for this novel technology to advance research and management of tropical forests in general.     

MicroPhenoDB Associates Metagenomic Datawith Pathogenic Microbes,Microbial Core Genes,and Human Disease Phenotypes

Microbes play important roles in human health and disease. The interaction between microbes and hosts is a reciprocal relationship, which remains largely under-explored. Current computational resources lack manually and consistently curated data to connect metagenomic data to pathogenic microbes, microbial core genes, and disease phenotypes. We developed the MicroPhenoDB database by manually curating and consistently integrating microbe-disease association data. MicroPhenoDB provides 5677 non-redundant associations between 1781 microbes and 542 human disease phenotypes across more than 22 human body sites. MicroPhenoDB also provides 696,934 relationships between 27,277 unique clade-specific core genes and 685 microbes. Disease phenotypes are classified and described using the Experimental Factor Ontology (EFO). A refined score model was developed to prioritize the associations based on evidential metrics. The sequence search option in MicroPhenoDB enables rapid identification of existing pathogenic microbes in samples without running the usual metagenomic data processing and assembly. MicroPhenoDB offers data browsing, searching, and visualization through user-friendly web interfaces and web service application programming interfaces. MicroPhenoDB is the first database platform to detail the relationships between pathogenic microbes, core genes, and disease phenotypes. It will accelerate metagenomic data analysis and assist studies in decoding microbes related to human diseases. MicroPhenoDB is available through http://www.liwzlab.cn/microphenodb and http://lilab2.sysu.edu.cn/microphenodb.     

Advances in ecological genomics in forest trees and applications to genetic resources conservation and breeding

Forest trees are an unparalleled group of organisms in their combined ecological, economic and societal importance. With widespread distributions, predominantly random mating systems and large population sizes, most tree species harbour extensive genetic variation both within and among populations. At the same time, demographic processes associated with Pleistocene climate oscillations and land‐use change have affected contemporary range‐wide diversity and may impinge on the potential for future adaptation. Understanding how these adaptive and neutral processes have shaped the genomes of trees species is therefore central to their management and conservation. As for many other taxa, the advent of high‐throughput sequencing methods is expected to yield an understanding of the interplay between the genome and environment at a level of detail and depth not possible only a few years ago. An international conference entitled ‘Genomics and Forest Tree Genetics’ was held in May 2016, in Arcachon (France), and brought together forest geneticists with a wide range of research interests to disseminate recent efforts that leverage contemporary genomic tools to probe the population, quantitative and evolutionary genomics of trees. An important goal of the conference was to discuss how such data can be applied to both genome‐enabled breeding and the conservation of forest genetic resources under land use and climate change. Here, we report discoveries presented at the meeting and discuss how the ecological genomic toolkit can be used to address both basic and applied questions in tree biology.     

Linking woodland key habitat inventory and forest inventory data to prioritize districts needing conservation efforts

Woodland key habitat (WKH) inventories have been conducted in northern European countries, with the aim to create networks of minimally disturbed forest stands for protection. The goal of national forest inventory is to provide information relevant to forest management, such as on forest types, trees species composition, age structure and wood volume. The aim of this study was to link these two inventory databases to identify districts of Latvia most deficient in connectivity and habitat quality, in order to prioritize districts needing conservation effort. As an example, the area of deciduous forest with nemoral tree species (oak, ash, lime, maple and elm) and aspen was chosen. These forests provide habitat for a specific community of epiphytes. Using information in the WKH database, habitat quality in different districts of Latvia was estimated by the frequencies of occurrence of structural elements and selected indicator epiphyte species in nemoral tree species and aspen WKHs. Using digital data in the national forest inventory database, fragmentation metrics were determined for forests that, according to age and tree species composition, could potentially be nemoral tree and aspen WKHs. On a regional level, the lowest habitat quality in WKH occurred in districts that had the least fragmentation of potential WKH forest. In the less fragmented areas, the habitat quality of the existing WKH will likely increase in the future, and could be promoted by management to create structural elements typical of natural forests. The districts with the most fragmented nemoral and aspen forests, contained WKHs with the best habitat quality. A focus on protection should be given to these stands as they are the most likely to support source populations, and there is a need to improve spatial continuity of suitable tree substrate in these areas.     

MorphoBank: phylophenomics in the “cloud”

A highly interoperable informatics infrastructure rapidly emerged to handle genomic data used for phylogenetics and was instrumental in the growth of molecular systematics. Parallel growth in software and databases to address needs peculiar to phylophenomics has been relatively slow and fragmented. Systematists currently face the challenge that Earth may hold tens of millions of species (living and fossil) to be described and classified. Grappling with research on this scale has increasingly resulted in work by teams, many constructing large phenomic supermatrices. Until now, phylogeneticists have managed data in single‐user, file‐based desktop software wholly unsuitable for real‐time, team‐based collaborative work. Furthermore, phenomic data often differ from genomic data in readily lending themselves to media representation (e.g. 2D and 3D images, video, sound). Phenomic data are a growing component of phylogenetics, and thus teams require the ability to record homology hypotheses using media and to share and archive these data. Here we describe MorphoBank, a web application and database leveraging software as a service methodology compatible with “cloud” computing technology for the construction of matrices of phenomic data. In its tenth year, and fully available to the scientific community at‐large since inception, MorphoBank enables interactive collaboration not possible with desktop software, permitting self‐assembling teams to develop matrices, in real time, with linked media in a secure web environment. MorphoBank also provides any user with tools to build character and media ontologies (rule sets) within matrices, and to display these as directed acyclic graphs. These rule sets record the phylogenetic interrelatedness of characters (e.g. if X is absent, Y is inapplicable, or X–Z characters share a media view). MorphoBank has enabled an order of magnitude increase in phylophenomic data collection: a recent collaboration by more than 25 researchers has produced a database of > 4500 phenomic characters supported by > 10 000 media.
© The Willi Hennig Society 2011.