The i5k Workspace@NAL—enabling genomic data access, visualization and curation of arthropod genomes

Poelchau, Monica F.; Childers, Christopher P.; Moore, Gary T.; Tsavatapalli, Vijaya; Evans, Jay D.; Lee, Chien‐Yueh; Lin, Han; Lin, Jun-Wei; Hackett, Kevin J.

doi:10.1093/nar/gku983

Cited by 159 publications

(156 citation statements)

References 20 publications

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“…All functional information was included in the OGS. Information on the A. glabripennis genome project is collated at the i5k Workspace [67] (https://i5k.nal.usda.gov/Anoplophora_glabripennis), and the genome, transcript, and protein sets can be searched via BLAST and browsed via the JBrowse genome browser [68] (https://apollo.nal.usda.gov/anogla/jbrowse). All manually curated genes and transcripts and their curation actions are provided in Additional file 2: Table S6.…”

Section: Methodsmentioning

confidence: 99%

Genome of the Asian longhorned beetle (Anoplophora glabripennis), a globally significant invasive species, reveals key functional and evolutionary innovations at the beetle–plant interface

et al. 2016

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BackgroundRelatively 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.ResultsThe 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.ConclusionsAmplification 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-016-1088-8) contains supplementary material, which is available to authorized users.

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Section: Methodsmentioning

confidence: 99%

Genome of the Asian longhorned beetle (Anoplophora glabripennis), a globally significant invasive species, reveals key functional and evolutionary innovations at the beetle–plant interface

et al. 2016

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“…Amino acid sequences of homologs for these genes were found in GenBank for Tribolium castaneum , which has a well-annotated genome. Subsequently, the genome of ACP available on the i5k Workspace@NAL platform (https://i5k.nal.usda.gov/webapp/blast/)59, was searched against the genes in this list, using sequences of homologs as query. Hits (contigs) obtained from this search were subsequently used in BLASTX searches to verify their identity and to detect functional domains.…”

Section: Methodsmentioning

confidence: 99%

Asian Citrus Psyllid RNAi Pathway – RNAi evidence

Taning

Andrade

Hunter

et al. 2016

Sci Rep

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Diaphorina citri, known as the Asian citrus psyllid, is an important pest of citrus because it transmits a phloem-limited bacteria strongly implicated in huanglongbing (citrus greening disease). Emerging biotechnologies, such as RNA interference, could provide a new sustainable and environmentally friendly strategy for the management of this pest. In this study, genome and functional analysis were performed to verify whether the RNAi core genes are present in the Asian psyllid genome and if the RNAi machinery could be exploited to develop a management strategy for this pest. Analyses of RNAi-related genes in the Asian citrus psyllid genome showed an absence of sequences encoding R2D2, a dsRNA-binding protein that functions as a cofactor of Dicer-2 in Drosophila. Nevertheless, bioassays using an in Planta System showed that the Asian citrus psyllid was very sensitive to ingested dsRNA, demonstrating a strong RNAi response. A small dose of dsRNA administered through a citrus flush was enough to trigger the RNAi mechanism, causing significant suppression of the targeted transcript, and increased psyllid mortality. This study provides evidence of a functional RNAi machinery, which could be further exploited to develop RNAi based management strategies for the control of the Asian citrus psyllid.

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“…Over the past several years there has been a steady increase in the availability of genome sequence information for a variety of insect species, including several bee species [5]. Additional sequencing and analyses substantially improved the A. mellifera genome in 2014, resulting in the identification of more than 5000 additional protein coding genes [6].…”

Section: Comparative Analyses Of Immune Genesmentioning

confidence: 99%

The power and promise of applying genomics to honey bee health

Grozinger

Robinson

2015

Current Opinion in Insect Science

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New genomic tools and resources are now being used to both understand honey bee health and develop tools to better manage it. Here, we describe the use of genomic approaches to identify and characterize bee parasites and pathogens, examine interactions among these parasites and pathogens, between them and their bee hosts, and to identify genetic markers for improved breeding of more resilient bee stocks. We also discuss several new genomic techniques that can be used to more efficiently study, monitor and improve bee health. In the case of using RNAi-based technologies to mitigate diseases in bee populations, we highlight advantages, disadvantages and strategies to reduce risk. The increased use of genomic analytical tools and manipulative technologies has already led to significant advances, and holds great promise for improvements in the health of honey bees and other critical pollinator species.

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The i5k Workspace@NAL—enabling genomic data access, visualization and curation of arthropod genomes

Cited by 159 publications

References 20 publications

Genome of the Asian longhorned beetle (Anoplophora glabripennis), a globally significant invasive species, reveals key functional and evolutionary innovations at the beetle–plant interface

Genome of the Asian longhorned beetle (Anoplophora glabripennis), a globally significant invasive species, reveals key functional and evolutionary innovations at the beetle–plant interface

Asian Citrus Psyllid RNAi Pathway – RNAi evidence

The power and promise of applying genomics to honey bee health

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