RNA sequences and transcriptome assemblies of Varroa jacobsoni (honey bee Varroa mites)

By Gladys K. Andino1, Michael Gribskov1, Denis Anderson2, Jay Evans3, Greg Hunt1

1. Purdue University 2. Abu Dhabi Food Control Authority, Kuwaitat Research Station 3. Agricultural Research Services, USDA United States Department of Agriculture

Category

Databases

Published on

Abstract

image
Ventral view of a female Varroa mite

 

 

Varroa mites are widely considered the biggest honey bee health problem worldwide [1-4]. Until recently, Varroa jacobsoni has been found to live and reproduce only in Asian honey bee (Apis cerana) colonies, while V. destructor successfully reproduces in both A. cerana and A. mellifera colonies. However, we have identified an island population of V. jacobsoni that is highly destructive to A. mellifera, the primary species used for pollination and honey production. The ability of these populations of mites to cross the species boundary represents a potentially enormous threat to apiculture. This ability is presumably due to genetic variation that exists among populations of V. jacobsoni and influences gene expression and reproductive status. In this work, we investigate differences in gene expression between populations of V. jacobsoni reproducing on A. cerana and those reproducing on A. mellifera in order to gain insight into the differences that allow V. jacobsoni to overcome its normal species tropism.

Database

This database contains information regarding sample collection of Varroa jacobsoni mites, RNA sequences (raw reads), newly discovered transcripts assemblies and Blast searches of V. jacobsoni mites. The database is presented as a spreadsheet which can be viewed by clicking the Dataview (blue button) at the top of the page. Scroll to the right on the Dataview to see the Reports and Data columns, these fields contains fasta files, Blast searches and fastq files. All fields in the database are described below.

Transcriptome assemblies of V. jacobsoni

Assembly TypePutative TranscriptsFasta FilesDescription
Vj Trinity de novo 374,530 de novo assembly README.txt
Vj Trinity genome-guided 428,912 genome-guided assembly README.txt
Vj Hybrid Trinity/PASA 319,231 hybrid Trinity/PASA assembly README.txt

Database Fields

Title: Geographical location from where Varroa jacobsoni mites were collected
Experiment or Case ID: Sample ID assigned by the source to the sample
Source: Names of the people who collected the mite samples
Keywords: Words describing the dataset, which can be used for searching
Report(s): Transcript assemblies (fasta fortmat) created by assembling all reads from all samples described in this experiment. Transcript assemblies (fasta fortmat) created by assembling all reads from all samples described in this experiment and Blastx results.
Latitude: Latitude of the location where data was collected, if applicable
Longitude: Longitude of the location where data was collected, if applicable
Parameters: Parameters or description chosen by the researcher to describe the data
Drawings/Diagrams: Drawing and diagram files needed to interpret the data, if applicable
Data: Data files generated through project. Tabular text, fasta or fastq format, is preferred (e.g., *.txt, *.fasta, *.fasta)
It is recommended that data files are organized in columns with each column having a descriptive header (e.g., sensor ID and unit)
Photos, Videos, etc.: Media files including photos, videos, audio generated through project, if applicable
Compiled by: names of the people who compiled the data
Date: Date when the dataset was compiled. (format: yyyy-mm-dd)

DOI: http://dx.doi.org/10.4231/H4159K

Cite this work

Researchers should cite this work as follows:

  • Following are references cited in the abstract: [1] Vanengelsdorp D, Hayes J, Underwood RM, Pettis J: A Survey of Honey Bee Colony Losses in the US, Fall 2007 to Spring 2008. PloS one 2008, 3(12). [2] Currie RW, Pernal SF, Guzmán-Novoa E: Honey bee colony losses in Canada. J Apicult Res 2010, 49(1):104-106. [3] Dahle B: role of Varroa destructor for honey bee colony losses in Norway. J Apicult Res 2010. [4] Guzmán-Novoa E, Eccles L, Calvete Y, McGowan J, Kelly PG, Correa-Benítez A: Varroa destructor is the main culprit for the death and reduced populations of overwintered honey bee ( Apis mellifera) colonies in Ontario, Canada. Apidologie 2010, 41(4):443-450.

  • Gladys K. Andino; Michael Gribskov; Denis Anderson; Jay Evans; Greg Hunt (2015), "RNA sequences and transcriptome assemblies of Varroa jacobsoni (honey bee Varroa mites)," https://datacenterhub.org/resources/382.

    BibTex | EndNote

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  19. 1 × SELECT *
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  20. 1 × SELECT *
      FROM `jos_resources`
  21. 1 × SELECT jos_template_styles.id,jos_template_styles.home,jos_template_styles.template,jos_template_styles.params,jos_extensions.protected
      FROM `jos_template_styles`
      INNER JOIN jos_extensions
      ON jos_extensions.element = jos_template_styles.template
  22. 1 × SELECT *
      FROM `jos_resource_ratings`
OTHER Tables:
  1. 1 × UPDATE `jos_session`
      SET `data` = '__default|a:9:{s:15:\"session.counter\";i:1;s:19:\"session.timer.start\";i:1593872093;s:18:\"session.timer.last\";i:1593872093;s:17:\"session.timer.now\";i:1593872093;s:8:\"registry\";O:23:\"Hubzero\\Config\\Registry\":2:{s:7:\"\0*\0data\";O:8:\"stdClass\":2:{s:1:\"0\";s:7:\"session\";s:10:\"Components\";O:8:\"stdClass\":1:{s:9:\"Resources\";O:8:\"stdClass\":2:{s:6:\"Models\";O:8:\"stdClass\":1:{s:6:\"Author\";O:8:\"stdClass\":2:{s:7:\"orderby\";s:8:\"ordering\";s:8:\"orderdir\";s:3:\"asc\";}}s:7:\"Reviews\";O:8:\"stdClass\":1:{s:6:\"Models\";O:8:\"stdClass\":1:{s:6:\"Review\";O:8:\"stdClass\":2:{s:7:\"orderby\";s:7:\"created\";s:8:\"orderdir\";s:4:\"desc\";}}}}}}s:9:\"separator\";s:1:\".\";}s:4:\"user\";C:17:\"Hubzero\\User\\User\":22:{a:1:{s:5:\"guest\";b:1;}}s:11:\"tracker.sid\";s:32:\"411ca179e8795699593042b378fece19\";s:12:\"tracker.ssid\";s:32:\"411ca179e8795699593042b378fece19\";s:12:\"tracker.rsid\";s:32:\"411ca179e8795699593042b378fece19\";}',`time` = '1593872093',`ip` = '3.235.239.156'
  2. 1 × SHOW FULL COLUMNS
      FROM `jos_resource_assoc
  3. 1 × INSERT INTO `jos_session` (`session_id`,`client_id`,`time`,`ip`)
      VALUES ('411ca179e8795699593042b378fece19','0','1593872093','3.235.239.156'
  4. 1 × DELETE
      FROM `jos_session`
  • onAfterInitialise Method plgSystemP3p::onAfterInitialise /core/plugins/system/p3p/p3p.php:21
  • onAfterInitialise Method plgSystemRemember::onAfterInitialise /core/plugins/system/remember/remember.php:20
  • onAfterInitialise Method plgSystemHubzero::onAfterInitialise /core/plugins/system/hubzero/hubzero.php:21
  • onAfterInitialise Method plgSystemXFeed::onAfterInitialise /core/plugins/system/xfeed/xfeed.php:21
  • onAfterInitialise Method plgSystemSupergroup::onAfterInitialise /core/plugins/system/supergroup/supergroup.php:113
  • onAfterInitialise Method plgSystemReferrerpolicy::onAfterInitialise /core/plugins/system/referrerpolicy/referrerpolicy.php:21
  • onAfterRoute Method plgSystemJquery::onAfterRoute /core/plugins/system/jquery/jquery.php:21
  • onAfterRoute Method plgSystemSpamjail::onAfterRoute /core/plugins/system/spamjail/spamjail.php:21
  • onAfterRoute Method plgSystemPassword::onAfterRoute /core/plugins/system/password/password.php:21
  • onAfterRoute Method plgSystemIncomplete::onAfterRoute /core/plugins/system/incomplete/incomplete.php:21
  • onAfterRoute Method plgSystemUnconfirmed::onAfterRoute /core/plugins/system/unconfirmed/unconfirmed.php:21
  • onAfterRoute Method plgSystemUnapproved::onAfterRoute /core/plugins/system/unapproved/unapproved.php:21
  • onResourcesAreas Method plgResourcesAbout::onResourcesAreas /core/plugins/resources/about/about.php:32
  • onResourcesAreas Method plgResourcesReviews::onResourcesAreas /core/plugins/resources/reviews/reviews.php:43
  • onResourcesAreas Method plgResourcesUsage::onResourcesAreas /core/plugins/resources/usage/usage.php:29
  • onResourcesAreas Method plgResourcesVersions::onResourcesAreas /core/plugins/resources/versions/versions.php:29
  • onResourcesAreas Method plgResourcesShare::onResourcesAreas /core/plugins/resources/share/share.php:29
  • onResourcesAreas Method plgResourcesCitations::onResourcesAreas /core/plugins/resources/citations/citations.php:29
  • onResourcesAreas Method plgResourcesQuestions::onResourcesAreas /core/plugins/resources/questions/questions.php:29
  • onResourcesAreas Method plgResourcesSupportingDocs::onResourcesAreas /core/plugins/resources/supportingdocs/supportingdocs.php:30
  • onResourcesAreas Method plgResourcesWishlist::onResourcesAreas /core/plugins/resources/wishlist/wishlist.php:29
  • onResourcesAreas Method plgResourcesFindThisText::onResourcesAreas /core/plugins/resources/findthistext/findthistext.php:29
  • onResourcesAreas Method plgResourcesWindowstools::onResourcesAreas /core/plugins/resources/windowstools/windowstools.php:214
  • onContentPrepare Method plgContentLoadmodule::onContentPrepare /core/plugins/content/loadmodule/loadmodule.php:35
  • onContentPrepare Method plgContentEmailcloak::onContentPrepare /core/plugins/content/emailcloak/emailcloak.php:25
  • onContentPrepare Method plgContentPagebreak::onContentPrepare /core/plugins/content/pagebreak/pagebreak.php:35
  • onContentPrepare Method plgContentXhubtags::onContentPrepare /core/plugins/content/xhubtags/xhubtags.php:25
  • onContentPrepare Method plgContentFormathtml::onContentPrepare /core/plugins/content/formathtml/formathtml.php:105
  • onContentPrepare Method plgContentExternalhref::onContentPrepare /core/plugins/content/externalhref/externalhref.php:41
  • onResources Method plgResourcesAbout::onResources /core/plugins/resources/about/about.php:54
  • onResources Method plgResourcesReviews::onResources /core/plugins/resources/reviews/reviews.php:91
  • onResources Method plgResourcesUsage::onResources /core/plugins/resources/usage/usage.php:51
  • onResources Method plgResourcesVersions::onResources /core/plugins/resources/versions/versions.php:50
  • onResources Method plgResourcesShare::onResources /core/plugins/resources/share/share.php:50
  • onResources Method plgResourcesCitations::onResources /core/plugins/resources/citations/citations.php:51
  • onResources Method plgResourcesQuestions::onResources /core/plugins/resources/questions/questions.php:60
  • onResources Method plgResourcesSupportingDocs::onResources /core/plugins/resources/supportingdocs/supportingdocs.php:52
  • onResources Method plgResourcesWishlist::onResources /core/plugins/resources/wishlist/wishlist.php:50
  • onResources Method plgResourcesFindThisText::onResources /core/plugins/resources/findthistext/findthistext.php:51
  • onResources Method plgResourcesWindowstools::onResources /core/plugins/resources/windowstools/windowstools.php:235
  • onResources Method plgResourcesGooglescholar::onResources /core/plugins/resources/googlescholar/googlescholar.php:25
  • onResources Method plgResourcesOpengraph::onResources /core/plugins/resources/opengraph/opengraph.php:25
  • onResources Method plgResourcesDublincore::onResources /core/plugins/resources/dublincore/dublincore.php:25
  • onResources Method plgResourcesCoins::onResources /core/plugins/resources/coins/coins.php:25
  • onResourcesSub Method plgResourcesGroups::onResourcesSub /core/plugins/resources/groups/groups.php:45
  • onResourcesSub Method plgResourcesRelated::onResourcesSub /core/plugins/resources/related/related.php:45
  • onResourcesSub Method plgResourcesSponsors::onResourcesSub /core/plugins/resources/sponsors/sponsors.php:45
  • onResourcesSub Method plgResourcesWatch::onResourcesSub /core/plugins/resources/watch/watch.php:46
  • onResourcesSub Method plgResourcesCollections::onResourcesSub /core/plugins/resources/collections/collections.php:31
  • onAfterDispatch Method plgSystemDebug::onAfterDispatch /core/plugins/system/debug/debug.php:60
  • onAfterDispatch Method PlgSystemHighlight::onAfterDispatch /core/plugins/system/highlight/highlight.php:25
  • onAfterRender Method plgSystemSef::onAfterRender /core/plugins/system/sef/sef.php:21