Mostrando entradas con la etiqueta Ensembl Plants. Mostrar todas las entradas
Mostrando entradas con la etiqueta Ensembl Plants. Mostrar todas las entradas

7 de febrero de 2024

Browsing barley pangenes

Hi,

late last year we published a paper describing GET_PANGENES, a protocol to call pangenes, which are clusters of gene models/alleles found in genomic assemblies in a similar location. You can read all about it at https://doi.org/10.1186/s13059-023-03071-z . Using this approach you can produce figures like this, where you can see the pangene of interest in green:

Genomic context of barly pangene cluster HORVU.MOREX.r3.3HG0311160 (green arrows), which corresponds to barley locus HvOS2. Figure from https://doi.org/10.1186/s13059-023-03071-z
 

As we do research on barley breeding and adaptation, we thought it would be useful for us and others out there to have way of inspecting barley pangenes, for instance to check whether a gene of interest is conserved or polymorphic across the barleys sampled by in the pangenome (n=20) put together by Jayakodi et al.

This exactly what you can do, at the protein sequence level, at https://eead-csic-compbio.github.io/barley_pangenes , where you can scroll pangenes along chromosomes, with MorexV3 positions; genes not found in MorexV3 lack a position therefore and are shown with a hash (#):


You will notice that pangenes with occupancy > 1, ie containing gene models found it at least two barleys, can be clicked to display a multiple protein alignment with help from the NCBI msaviewer:


There you can easily zoom in to regions of interest and print or export the alignment in FASTA, PDF or SVG format (high quality).

Hope this can be useful to the barley genomics community,

Bruno

 

23 de diciembre de 2022

RSAT::Plants updated (Dec2022)

Hi, 

if you use the Plants server of the Regulatory Sequence Analysis Tools (RSAT), you might want to know that it has just been updated. Here's a short summary of the changes:

  • The updated URL is https://rsat.eead.csic.es/plants
  •  It now supports HTTPS connections powered by certbot
  •  It now uses the source code at https://github.com/rsa-tools/rsat-code (I have updated some documentation along the way)
  •  Nine new species have been imported from Ensembl Plants: Lolium perenne, Brassica juncea, Echinochloa crusgalli, Digitaria exilis, Vigna unguiculata, Brassica rapa ro18, Corylus avellana, Ficus carica, Lactuca sativa
  •  One species renamed: Physcomitrium patens
  •  Three updated with a new assembly: Vitis vinifera, Triticum urartum, sunflower
  • This leaves the total number of supported assemblies in 100; you can see their stats at https://rsat.eead.csic.es/plants/data/stats
  • Most species now correspond to release 55 of Ensembl Plants, but note that the sequence data is unchanged in many cases. This means that, for instance, that Hordeum_vulgare.MorexV3_pseudomolecules_assembly.52 becomes        Hordeum_vulgare.MorexV3_pseudomolecules_assembly.55, but the sequence is exactly the same.         

  


Have a nice break,

Bruno