Amanita family genetics

Amanita family genetics

The Amanitaceae Studies site is collecting a reliably identified set of genetic sequences associated with samples belonging to the Amanitaceae.  These sequences are derived from type collections where that is possible; and, from modern collections identified by, or in the laboratories of, the site's editors.

This page is intended to be the parent page to a cluster of pages providing among other features the following:

1. a means of reviewing, sorting, or filtering our collection of GenBank accessioned sequences along with a summary of the assembled data
2. a draft quality control process for the processing chromatagraph data by our Roosevelt group
3. a template or templates for reporting sequences edited by our Roosevelt group
4. Informational documentation about the processing of raw sequences intended for a broad audience including nonexpert citizen scientists.
5. A limited bibliography providing some background on the work being done concerning the collection, termini of subloci of nrITS, and related topics.

Draft child pages available:

• Limited background bibliography for DNA studies relevant to the child pages which follow.
  
  
• Search-, Sort-, and Filterable List of Sequences and Statistics on the Collected Sequences from samples of the Amanitaceae - flexible access to a catalog of reliably named sequences for species of the Amanita family, with some statistical analysis.

  Our present dataset includes (as of 1.v.2013) 544 sequences from samples of 152 named, provisional, or code-numbered taxa.  To be included, a sequence must be derived from a type collection or from another voucher collection presently in existence and having been revised and determined by one of the editors or a trained person working under their direction.
  
  Clicking on GenBank accession numbers activates a query to GenBank so that sequence detail can be recovered by our users.
  
  Sequence length is provided so that the extent to which data may have been trimmed or unavailable for a given sequence can be judged by the user. Taxon names are linked to the relevant taxon pages on this site.
  
  

• nrITS Sublocus Terminal Motifs in the Amanitaceae - under development -

  At the minimum, this page provides
  

  • a record of observed variation in terminal motifs used to identify sublocus termini for 18S 3', 5.8S 5' and 3', and 28S 5' and
    
  • a record of observed variations in regions adjacent to these motifs in ITS1 or ITS2.
    

  This information may be useful for training new students or citizen scientists that might participate in the processes of trimming and annotating sequences.
  
  
• nrITS GenBank submission template for Amanitaceae -  Designed with the idea of recording as fully as is reasonable the origin and processing of nrITS sequences edited and submitted by the Roosevelt group, particularly in relation to the North American Mycoflora Project, the Amanitaceae Type Sequencing Project, and other collaborative efforts.