Release VB-2017-12

We are pleased to announce the December 2017 release of VectorBase (VB-2017-12):
  • Aedes aegypti AaegL5 assembly update
    • In this release the old Aedes aegypti AaegL3 assembly has been retired and has been replaced by the latest AaegL5 assembly from the Aedes aegypt Genome Working group. All future annotation and updates at VectorBase will be made on the new AaegL5 assembly.
    • A completely new gene set has been generated for the AaegL5 assembly and is available as the NCBI Aedes aegypti annotation release 101.
    • The NCBI release 101 annotation has been used in this release of VectorBase, and old VectorBase gene ids have been mapped to the new gene set to help users transfer their work to the assembly. The mapping of some of the more complicated gene split and merge events is still ongoing and updates will be made in future releases of VectorBase
    • The AaegL3 assembly is no longer supported in the VectorBase BioMart, search, and Apollo gene annotation applications. A 'frozen' version of the data will continue to be made available via the genome browser, and VectorBase is assisting with the transfer of current AaegL3 based Apollo annotations to the new reference assembly. A new version of the Apollo gene editing application using the AaegL5 assembly will be made available as rapidly as possible.
    • Both Aedes aegypti assemblies used the Liverpool strain for genome sequencing, but to accomodate potential strain specific variation between laboratories these are now differentiated by the use of the suffixes LVP (old AaegL3 assembly) and LVPAGWG (new AaegL5 assembly).
    • Old bookmarks made to the Aedes_aegypti AaegL3 assembly will automatically try to resolve against the new assembly, but may fail if a gene or transcript no longer exists in the new assembly. To resolve this issue add the _lvp or _lvpagwg strain names into the URL to connect to the desired assembly. e.g.
    • RNAseq, expression microarray probes, and SNP variation data have been remapped from AaegL3 to AaegL5 where possible. Not all features could be successfully remapped and there will have been a drop in the overall number of variants mapped, as well as alterations to the derived gene expression profiles. Copy Number Variants (CNV) on the AaegL3 assembly have not been transferred as many of these regions were based on repetitive gene families which have undergone split/merge events on the new assembly.
  • Anopheles atroparvus AatrE2 assembly update
    • A new assembly and gene set have been created for Anopheles atroparvus based on the paper "Partial-arm translocations in evolution of malaria mosquitoes revealed by high- coverage physical mapping of the Anopheles atroparvus genome" (Sharakov et al, BMC Genomics, manuscript submitted).
    • The AatrE2 assembly is a rescaffolding of the sequence of the previous AatrE1 assembly; this has lead to aleration to the genomic feature coordinates, but there have been no changes to the underlying sequences or gene content.
  • The Anopheles gambiae variation database has been updated and variants from dbSNP that had no linked genotype data have been removed. Variants calls for non An. gambiae colonies that were aligned to the An. gambiae PEST sequence have also removed. These two revisions have lead to an ~2% drop in the total number of SNP variants for An. gambiae.
  • We have introduced a new Export feature, called Export STRUCTURE, to enhance Search functionality, for which the exported CSV file can be used with the STRUCTURE software. This can be done through the renovated Export (button) in the Search page where Export Download, Sequence, and STRUCTURE are available in the popup window. Please note that one needs to first select Population Biology (Domain) and Sample genotype (Sub-domain) from the Filter Results in order to activate Export STRUCTURE function (button).
  • The Tools page has been updated to include resources within the tools. We invite you to take a look, most are not new but you may have not noticed them before. One of these is 'Find a Data Display'.
  • Use 'Find a Data Display' to choose a gene, region or variant and then browse for relevant visualizations that include many different types of figures and tables. You can use these visualizations in your presentation, thesis or publication. Contact us if you need help using this resource or have doubts about how to cite the visualizations.
  • Three new differential expression experiments have been added to the expression browser, including the first expression data in VectorBase for Glossina and all Aedes aegypti datasets have been remapped for the new AaegL5 assembly.
  • Ten new insecticide resistance projects have been added to PopBio and a beta/prototype genotype view is available for testing. This shows allele frequencies for commonly assayed variant loci such as kdr and Ace1.
  • The schedule for outreach activities in the first semester of 2018 is available now, including open registration for the next VectorBase workshop and webinars.

For details please follow this link: vectorbase.org/release/release-vb-2017-12#

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