26 research outputs found
Genome of the Asian Longhorned Beetle (\u3cem\u3eAnoplophora glabripennis\u3c/em\u3e), a Globally Significant Invasive Species, Reveals Key Functional and Evolutionary Innovations at the Beetle-Plant Interface
Background: Relatively little is known about the genomic basis and evolution of wood-feeding in beetles. We undertook genome sequencing and annotation, gene expression assays, studies of plant cell wall degrading enzymes, and other functional and comparative studies of the Asian longhorned beetle, Anoplophora glabripennis, a globally significant invasive species capable of inflicting severe feeding damage on many important tree species. Complementary studies of genes encoding enzymes involved in digestion of woody plant tissues or detoxification of plant allelochemicals were undertaken with the genomes of 14 additional insects, including the newly sequenced emerald ash borer and bull-headed dung beetle. Results: The Asian longhorned beetle genome encodes a uniquely diverse arsenal of enzymes that can degrade the main polysaccharide networks in plant cell walls, detoxify plant allelochemicals, and otherwise facilitate feeding on woody plants. It has the metabolic plasticity needed to feed on diverse plant species, contributing to its highly invasive nature. Large expansions of chemosensory genes involved in the reception of pheromones and plant kairomones are consistent with the complexity of chemical cues it uses to find host plants and mates. Conclusions: Amplification and functional divergence of genes associated with specialized feeding on plants, including genes originally obtained via horizontal gene transfer from fungi and bacteria, contributed to the addition, expansion, and enhancement of the metabolic repertoire of the Asian longhorned beetle, certain other phytophagous beetles, and to a lesser degree, other phytophagous insects. Our results thus begin to establish a genomic basis for the evolutionary success of beetles on plants
Genome of the Asian longhorned beetle (Anoplophora glabripennis), a globally significant invasive species, reveals key functional and evolutionary innovations at the beetle–plant interface
Background
Relatively little is known about the genomic basis and evolution of wood-feeding in beetles. We undertook genome sequencing and annotation, gene expression assays, studies of plant cell wall degrading enzymes, and other functional and comparative studies of the Asian longhorned beetle, Anoplophora glabripennis, a globally significant invasive species capable of inflicting severe feeding damage on many important tree species. Complementary studies of genes encoding enzymes involved in digestion of woody plant tissues or detoxification of plant allelochemicals were undertaken with the genomes of 14 additional insects, including the newly sequenced emerald ash borer and bull-headed dung beetle.
Results
The Asian longhorned beetle genome encodes a uniquely diverse arsenal of enzymes that can degrade the main polysaccharide networks in plant cell walls, detoxify plant allelochemicals, and otherwise facilitate feeding on woody plants. It has the metabolic plasticity needed to feed on diverse plant species, contributing to its highly invasive nature. Large expansions of chemosensory genes involved in the reception of pheromones and plant kairomones are consistent with the complexity of chemical cues it uses to find host plants and mates.
Conclusions
Amplification and functional divergence of genes associated with specialized feeding on plants, including genes originally obtained via horizontal gene transfer from fungi and bacteria, contributed to the addition, expansion, and enhancement of the metabolic repertoire of the Asian longhorned beetle, certain other phytophagous beetles, and to a lesser degree, other phytophagous insects. Our results thus begin to establish a genomic basis for the evolutionary success of beetles on plants
Autonomous Multimodal Metabolomics Data Integration for Comprehensive Pathway Analysis and Systems Biology
Comprehensive
metabolomic data can be achieved using multiple orthogonal
separation and mass spectrometry (MS) analytical techniques. However,
drawing biologically relevant conclusions from this data and combining
it with additional layers of information collected by other omic technologies
present a significant bioinformatic challenge. To address this, a
data processing approach was designed to automate the comprehensive
prediction of dysregulated metabolic pathways/networks from multiple
data sources. The platform autonomously integrates multiple MS-based
metabolomics data types without constraints due to different sample
preparation/extraction, chromatographic separation, or MS detection
method. This multimodal analysis streamlines the extraction of biological
information from the metabolomics data as well as the contextualization
within proteomics and transcriptomics data sets. As a proof of concept,
this multimodal analysis approach was applied to a colorectal cancer
(CRC) study, in which complementary liquid chromatography–mass
spectrometry (LC–MS) data were combined with proteomic and
transcriptomic data. Our approach provided a highly resolved overview
of colon cancer metabolic dysregulation, with an average 17% increase
of detected dysregulated metabolites per pathway and an increase in
metabolic pathway prediction confidence. Moreover, 95% of the altered
metabolic pathways matched with the dysregulated genes and proteins,
providing additional validation at a systems level. The analysis platform
is currently available via the XCMS Online (XCMSOnline.scripps.edu)
Interactive XCMS Online: simplifying advanced metabolomic data processing and subsequent statistical analyses.
XCMS Online (xcmsonline.scripps.edu) is a cloud-based informatic platform designed to process and visualize mass-spectrometry-based, untargeted metabolomic data. Initially, the platform was developed for two-group comparisons to match the independent, "control" versus "disease" experimental design. Here, we introduce an enhanced XCMS Online interface that enables users to perform dependent (paired) two-group comparisons, meta-analysis, and multigroup comparisons, with comprehensive statistical output and interactive visualization tools. Newly incorporated statistical tests cover a wide array of univariate analyses. Multigroup comparison allows for the identification of differentially expressed metabolite features across multiple classes of data while higher order meta-analysis facilitates the identification of shared metabolic patterns across multiple two-group comparisons. Given the complexity of these data sets, we have developed an interactive platform where users can monitor the statistical output of univariate (cloud plots) and multivariate (PCA plots) data analysis in real time by adjusting the threshold and range of various parameters. On the interactive cloud plot, metabolite features can be filtered out by their significance level (p-value), fold change, mass-to-charge ratio, retention time, and intensity. The variation pattern of each feature can be visualized on both extracted-ion chromatograms and box plots. The interactive principal component analysis includes scores, loadings, and scree plots that can be adjusted depending on scaling criteria. The utility of XCMS functionalities is demonstrated through the metabolomic analysis of bacterial stress response and the comparison of lymphoblastic leukemia cell lines
Data Streaming for Metabolomics: Accelerating Data Processing and Analysis from Days to Minutes
The speed and throughput
of analytical platforms has been a driving
force in recent years in the “omics” technologies and
while great strides have been accomplished in both chromatography
and mass spectrometry, data analysis times have not benefited at the
same pace. Even though personal computers have become more powerful,
data transfer times still represent a bottleneck in data processing
because of the increasingly complex data files and studies with a
greater number of samples. To meet the demand of analyzing hundreds
to thousands of samples within a given experiment, we have developed
a data streaming platform, XCMS Stream, which capitalizes on the acquisition
time to compress and stream recently acquired data files to data processing
servers, mimicking just-in-time production strategies from the manufacturing
industry. The utility of this XCMS Online-based technology is demonstrated
here in the analysis of T cell metabolism and other large-scale metabolomic
studies. A large scale example on a 1000 sample data set demonstrated
a 10 000-fold time savings, reducing data analysis time from
days to minutes. Further, XCMS Stream has the capability to increase
the efficiency of downstream biochemical dependent data acquisition
(BDDA) analysis by initiating data conversion and data processing
on subsets of data acquired, expanding its application beyond data
transfer to smart preliminary data decision-making prior to full acquisition
Smartphone Analytics: Mobilizing the Lab into the Cloud for Omic-Scale Analyses
Active data screening is an integral
part of many scientific activities,
and mobile technologies have greatly facilitated this process by minimizing
the reliance on large hardware instrumentation. In order to meet with
the increasingly growing field of metabolomics and heavy workload
of data processing, we designed the first remote metabolomic data
screening platform for mobile devices. Two mobile applications (apps),
XCMS Mobile and METLIN Mobile, facilitate access to XCMS and METLIN,
which are the most important components in the computer-based XCMS
Online platforms. These mobile apps allow for the visualization and
analysis of metabolic data throughout the entire analytical process.
Specifically, XCMS Mobile and METLIN Mobile provide the capabilities
for remote monitoring of data processing, real time notifications
for the data processing, visualization and interactive analysis of
processed data (e.g., cloud plots, principle component analysis, box-plots,
extracted ion chromatograms, and hierarchical cluster analysis), and
database searching for metabolite identification. These apps, available
on Apple iOS and Google Android operating systems, allow for the migration
of metabolomic research onto mobile devices for better accessibility
beyond direct instrument operation. The utility of XCMS Mobile and
METLIN Mobile functionalities was developed and is demonstrated here
through the metabolomic LC-MS analyses of stem cells, colon cancer,
aging, and bacterial metabolism
Autonomous Metabolomics for Rapid Metabolite Identification in Global Profiling
An autonomous metabolomic workflow
combining mass spectrometry
analysis with tandem mass spectrometry data acquisition was designed
to allow for simultaneous data processing and metabolite characterization.
Although previously tandem mass spectrometry data have been generated
on the fly, the experiments described herein combine this technology
with the bioinformatic resources of XCMS and METLIN. As a result of
this unique integration, we can analyze large profiling datasets and
simultaneously obtain structural identifications. Validation of the
workflow on bacterial samples allowed the profiling on the order of
a thousand metabolite features with simultaneous tandem mass spectra
data acquisition. The tandem mass spectrometry data acquisition enabled
automatic search and matching against the METLIN tandem mass spectrometry
database, shortening the current workflow from days to hours. Overall,
the autonomous approach to untargeted metabolomics provides an efficient
means of metabolomic profiling, and will ultimately allow the more
rapid integration of comparative analyses, metabolite identification,
and data analysis at a systems biology level