Anoplophora glabripennis

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I5klogo4.jpg Anoplophora glabripennis

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People with a declared interest in Anoplophora glabripennis
Duane D. McKenna University of Memphis
Wayne Hunter US Horticultural Research Laboratory
Nomination is supported by 0 people


Transcriptome datasets for Anoplophora glabripennis
Species Description No. sequences Last update
Anoplophora glabripennis GenBank EST division (dbEST) 556556 2455686.55 May 2011

i5K Comments for Anoplophora glabripennis
The Asian longhorned beetle (Anoplophora glabripennis) (ALB) is an invasive pest from Asia that came to Canada, the United States and Europe concealed in solid wood packing material. It is a serious threat to deciduous hardwood trees in urban, suburban, and forested parts of the country. Larvae bore into a tree’s heartwood, damaging and eventually killing the tree. If it became widely established in North America (it is already established locally), it could be one of the most destructive and costly invasive species ever (USDA Prgm. Aid No.1655). A target of current USDA eradication efforts. These beetles are large (1-1.5 inches) and one beetle can provide more than 10 micrograms of DNA. Specimens in North America are all relatively closely related. Suitable specimens are available for sequencing. Duane D. McKenna


Anoplophora glabripennis
Anoplophora glabripennis
Asian longhorned beetle


Taxonomic classification
Class: Insecta
Order: Coleoptera
Family: Cerambycidae
Genus: Anoplophora
NCBI taxid: 485px-US-NLM-NCBI-Logo.png 217634
Resources
Collection: Baylor i5k pilot, UK Forestry Commision list of pests and diseases
Information
WorkingGroup: Plant pests and beneficials
Nomination: i5K initiative
Date: 2011/08/09


I5klogo4.jpg  i5K Arthropod Sequencing Initiative
 Supported by: 0 ()



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Analysis and Publication Plans for the ALB Genome (Posted 11 April 2014, last updated 30 May 2014: Duane McKenna: dmckenna@memphis.edu)


News

• New collaborations are welcome if compatible with existing plans (contact me to inquire).

• Add, confirm or modify contributions by logging into the i5k website. However, please contact me with major changes. Please communicate with other collaborators when your interests are similar and add notes to the analysis plan to clarify responsibilities in the event of overlap.

• Reminder: Manual genome annotation is ongoing via Web-Apollo (you can register for access to Web Apollo here: http://i5k.nal.usda.gov/web-apollo-registration) and will end on July 15, with an inclusive ALB genome consortium publication to follow. By July 15, please provide me with a 1+ paragraph summary (with citations) of the major/notable results from your subproject(s), along with a brief descriptive subheading. Please let me know ASAP if you anticipate not being able to meet the July 15 deadline. ALB genome data files (DNA and RNA) are available at: https://www.hgsc.bcm.edu/arthropods/asian-long-horned-beetle-genome-project

• Please discuss your publication plans with me now to avoid problems later, including piecemeal erosion of the content of our eventual genome consortium pub(s), missed opportunities for minor co-authorship, etc.


Analysis Plan

Project coordinator: Duane McKenna, University of Memphis: dmckenna@memphis.edu

Participating research groups: S. Ahn, S. Brown, J. DeMuth, M. Friedrich, S. Geib, M. Goodisman, S. Grath, K. Hoover, W. Hunter, J. Jones, A. Khila, D. Lance, J. Lynch, R. Mitchell, D. Nelson, K. Panfilio, Y. Pauchet, S. Richards, H. Robertson, T. Sutter, J. Werren, G. Yocum


Subprojects:


Automated annotation

Collaborators: Stephen Richards (Baylor); Dan Hughes (Baylor)

Publication plans: Contribution to genome consortium pub.


Bacterial symbionts/microbiome

Collaborators: Erin Scully (USDA/ARS) - contacted, please confirm; Kelli Hoover (Penn. State Univ.) - contacted, please confirm; Evan Braswell (USDA/APHIS) - contacted, please confirm; Jack Werren (Univ. of Rochester) - contacted, please confirm

Publication plans: Contribution to genome consortium pub.


Cellular transcytosis/immune mechanisms

Collaborators: Wayne Hunter (USDA/ARS); Laura Hunnicut (USDA/ARS)

Publication plans: Contribution to genome consortium pub.


CpG analysis & DNA methylation (including general molecular evolution)

Collaborators: Michael Goodisman (Georgia Tech); Karl Glastad (Georgia Tech); Sonja Grath (Univ. of Munich)

Publication plans: Contribution to genome consortium pub.


Cuticular adaptations, e.g., elytra, pigmentation, hydrophobicity

Collaborator: Kristen Panfilio (Univ. of Cologne); Sue Brown (Kansas State Univ.), Abdon Khila (ENS Lyon), David Armisen (ENS Lyon), Antonin Crumiere (ENS Lyon), Essia Sghaier (ENS Lyon), Peter Refki (ENS Lyon), Cedric Mendoza (ENS Lyon), Emilia Santos (ENS Lyon), Severine Viala (ENS Lyon).

Publication plans: Contribution to genome consortium pub.


Cytochrome P450’s

Collaborator: David Nelson (Univ. of TN, Memphis), Stephanie Haddad (Univ. of Memphis)

Publication plans: Contribution to genome consortium pub.


Diapause & stress tolerance

Collaborators: George Yocum (USDA/ARS); Anna Bennett (USDA/ARS), Julia Bowsher (NDSU), Jenna Johnson (NDSU), Joe Rinehart (USDA/ARS), Richard Roehrdanz (USDA/ARS), Alex Torson (NDSU)

Publication plans: Contribution to genome consortium pub.


DNA and RNA extraction and QC

Collaborator: Duane McKenna (Univ. of Memphis)

Publication plans: Contribution to genome consortium pub.


Embryo patterning genes/signaling pathways

Collaborator: Jeremy Lynch (Univ. of IL, Chicago)

Publication plans: Contribution to genome consortium pub., also separate companion paper. Is the Toll pathway already “taken” in relation to the immunity group? If not, could be covered here. Will also do BMP and EGF pathways and some transcription factors.

Publication plans: Contribution to genome consortium pub.


Fungal symbionts

Collaborators: Erin Scully (USDA-ARS) - contacted, please confirm; Kelli Hoover (Penn. State Univ.) - contacted, please confirm; additional potential collaborators?

Publication plans: Contribution to genome consortium pub.


Gene duplication and loss

Collaborator: Kristen Panfilio (Univ. of Cologne) - contacted, please confirm; additional potential collaborators?

Publication plans: Contribution to genome consortium pub.


Genome sequencing & assembly

Collaborators: Stephen Richards (Baylor); Other members of the i5k team at Baylor

Publication plans: Contribution to genome consortium pub.


Genome structure (e.g. synteny/rearrangement/translocation)

Collaborator: Jeff DeMuth (Univ. of Texas, Arlington)

Publication plans: Contribution to genome consortium pub.


Gustatory receptors

Collaborator: Hugh Robertson (Univ. of IL, Urbana-Champaign)

Publication plans: Contribution to genome consortium pub.


Hox genes

Collaborators: Kristen Panfilio (Univ. of Cologne); Others?: E. Schwager; W. Damen; Nikola-Michael Prpic; A. McGregor? - please confirm

Publication plans: Contribution to genome consortium pub.


Ionotropic receptors

Collaborator: ? Hugh Robertson (Univ. of IL, Urbana-Champaign)

Publication plans: Contribution to genome consortium pub.


Lateral gene transfer

Collaborators: Jack Werren (Univ. of Rochester)

Publication plans: Contribution to genome consortium pub.


Molecular phylogenetics & evolution

Collaborators: Duane McKenna (Univ. of Memphis); Stephanie Haddad (Univ. of Memphis); Yunke Wu (USDA-APHIS)

Publication plans: Contribution to genome consortium pub.


Odorant receptors & odorant binding proteins (chemoreception & olfaction)

Collaborator: Rob Mitchell (Univ. of AZ)

Publication plans: Contribution to genome consortium pub., also separate companion paper.


Opsins & light perception (across Coleoptera/Neuropteroidea)

Collaborators: Marcus Friedrich (Wayne State Univ.); Jeffery Jones (Oakland Univ.); Elke Buschbeck (Univ. of Cincinnati); Tiffany Cook (Cincinnati Childrens Hospital Medical Center).

Publication plans: Contribution to genome consortium pub., also separate companion paper.


Overarching functional annotation, gene ontology terms, pfam domain hits, etc

Collaborator: Scott Geib (USDA-ARS)

Publication plans: Contribution to genome consortium pub.


Plant cell wall degrading enzymes & other digestive-related genes; digestive physiology (details TBD)

Collaborators: Yannick Pauchet (Max Planck Inst. Chem. Ecol.) (1st companion paper in press IBMB); Roy Kirsch (Max Planck Inst. Chem. Ecol.); Kelli Hoover (Penn. State Univ.); Scott Geib (USDA-ARS); Erin Scully (USDA-ARS; also, interest in interactions with gut microbes - bacteria and fungi)

Publication plans: Contribution to genome consortium pub., also separate companion papers.


Project logo

Collaborator: Rob Mitchell (Univ. of AZ)


Sex-biased genes, sex-determination (similar to next – please resolve any overlap)

Collaborators: Sonja Grath (Univ. of Munich); Evan Braswell (USDA/APHIS) - contacted, please confirm


Germline genes (across Coleoptera/Neuropteroidea) (similar to previous – please resolve any overlap)

Collaborator: Jeremy Lynch (Univ. of IL, Chicago)

Publication plans: Contribution to genome consortium pub., also separate companion paper


RNAi machinery

Collaborators: Scott Geib (USDA-ARS); Bernarda Calla (USDA-ARS); Kelli Hoover (Penn. State Univ.)

Publication plans: Contribution to genome consortium pub.


Specimens for DNA and RNA

Collaborators: Duane McKenna (Univ. of Memphis); Dave Lance (USDA/APHIS-PPQ-S&T)

Publication plans: Contribution to genome consortium pub.


Transposable elements

Collaborator: Jeff DeMuth (Univ. of Texas, Arlington)

Publication plans: Contribution to genome consortium pub.


UDP-glycosyltransferase (UGT) multigene family

Collaborator: Seung-Joon Ahn (Max Planck Inst. Chem. Ecol.)

Publication plans: Contribution to genome consortium pub.


Web Apollo

Collaborator: Monica Poelchau (USDA/ARS); Monica Munoz-Torres (Lawrence Berkeley National Lab)

Publication plans: Contribution to genome consortium pub.


Wnt ligands and the canonical pathway

Collaborators: Susan Brown (Kansas State Univ.); Jason Phelps (Kansas State Univ.)


Mitochondrion

Collaborators: ???


Non-coding RNAs

Collaborators: ???


Viruses

Collaborators: ???


Other contributions?


Other collaborators not yet listed above

Michael Dickens (Univ. of Memphis)


Other beetle genomes available for comparative study

Agrilus planipennis (emerald ash borer: suborder Polyphaga) i5k contacts Jian Duan (Jian.Duan@ars.usda.gov) and Kristen Kuhn (Kristen.Kuhn@ars.usda.gov)

Dendroctonus ponderosae (mountain pine beetle: Polyphaga) published

Leptinotarsa decemlineata (Colorado potato beetle: Polyphaga) i5k contact Yolanda Chen (Yolanda.Chen@uvm.edu)

Mengenilla moldrzyki (order Strepsiptera - the sister group of beetles) published

Onthophagus taurus (dung beetle: Polyphaga) i5k contact: Armin Moczek (armin@indiana.edu)

Tribolium castaneum (flour beetle: Polyphaga) published (other Tribolium spp. likely available through i5k collaborators)

• "Incomplete" draft assemblies (unannotated) are available from the McKenna lab for exemplars from the other 3 beetle suborders (all i5k and published beetle genomes are from suborder Polyphaga), and from a neuropterid (order Megaloptera), for use in comparative studies that can make use of such data (contig NG50 from ~1.5kb to 20kb, depending on the species).

Taxa available: Calosoma scrutator (fiery searcher: suborder Adephaga)

Chauliodes pectinicornis (summer fishfly: order Megaloptera)

Harmonia axyridis (Asian multicolored ladybug: suborder Polyphaga)

Hydroscapha redfordi (minute bog beetle: suborder Myxophaga)

Priacma serrata (bleach beetle: suborder Archostemata).

Contact me (dmckenna@memphis.edu) for more information.


Publication Plan

Manual annotation and other data collection will be completed on July 15, 2014, with an inclusive ALB genome consortium publication to follow. The nature and scope of the publication will be dictated by the subprojects completed. Additional companion papers, many of which will cover a single topic (e.g., “molecular evolution of …”) across all of Coleoptera or all of Neuropteroidea (Coleoptera plus Strepsiptera plus Neuropterida) will expand on topics included in the main genome paper and will cover other aspects of beetle evolution, genetics and genomics that do not fit in the genome publication. If you think your contribution would be most appropriately published as a companion paper, please contact me to discuss this, including policies for minor coauthorship, acknowledgment, etc. If you are currently working only with ALB data and would like to annotate your genes across other beetle genomes or near relatives of beetles, send me a note with cc to Stephen (Fringy) Richards, Monica Poelchau, and the community leads on the genomes of interest (see above) indicating the species and genes you would like to work on. If these genes are not already being studied by other collaborators, you should be able to get access to the needed data.

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