red clover (trifolium pratense) genome to add

[adf-ncgr]

per email:

Hi,
Thanks for your interest.
Please let us known then if there is anything from us you may need.

Looking forward to the next release of legumeinfo.

Cheers
Jose

On 1 Dec 2015, at 13:11, Cannon, Steven [AGRON] wrote:

> Dear Dr. De Vega,
>
> We will be pleased to host the red clover in legumeinfo. In fact, we had
> begun discussing this yesterday after seeing the new genome paper.
>
> It takes us some time to incorporate a new genome and the associated
> analyses (gene family displays, etc.), but I would anticipate we may be
> able to do this for either the January or February releases of the website
> February may be more realistic, considering the winter holidays; but
> please let us know if there are any time-frame considerations from your
> perspective.
>
> Please feel free to notify the team that we will be working on adding red
> clover to the website.
>
> Thanks for contacting us,
> Steven
> -----
> Steven Cannon
> USDA-ARS and Department of Agronomy
> Iowa State University
> 515-294-6971
>
>
>
> On 12/1/15, 6:00 AM, "weeks@iastate.edu on behalf of
> jose.devega@tgac.ac.uk" > jose.devega@tgac.ac.uk> wrote:
>
>> Jose De Vega (jose.devega@tgac.ac.uk) sent a message using the contact
>> form
>> at http://legumeinfo.org/contact.
>>
>> Hi,
>>
>> We have just published the red clover (Trifolium pratense) genome in
>> http://www.nature.com/articles/srep17394 , red clover is a forage legume
>> crop
>> very close to the model plant Medicago truncatula, the first forage crop
>> to
>> be sequenced. Also, soybean and common bean belong to the same family
>> (family
>> tree in http://www.nature.com/articles/srep17394/figures/3).
>>
>> The assembly is at chromosome-scale, it covers 80% of the genome and the
>> N50
>> is 13.02Mb. Scaffolds were anchored to a physical map and two genetic
>> maps.
>> We have one third of the assembly in seven chromosome sequences, or half
>> of
>> the assembly in 353 scaffolds plus another 25% in scaffolds longer than
>> 50Kbp, details are in the supplementary table 1 of the paper.
>> This scale allowed us to do a synteny analysis with Medicago truncatula in
>> the paper (Circos plot in
>> http://www.nature.com/articles/srep17394/figures/1), and it will be a
>> quite
>> useful tool for similar analysis with other legumes or forage plants.
>>
>> Data are fully open, including raw reads and BAC end sequences
>> (http://www.nature.com/articles/srep17394#additional-information). We have
>> done a full annotation with ~40K genes, that looks quite accurate and
>> comparable to its relatives. We have also annotated the repeat content.
>> As it says there, you can download the assembly in FASTA format, and the
>> annotation in GFF3 format from http://dx.doi.org/10.5281/zenodo.17232
>>
>> I would like to highlight that this will not be a orphan genome. We have
>> ongoing projects in red clover to study the domestication of red clover
>> and a
>> breeding program where we are sequencing natural lines of red clover to
>> improve the elite commercial varieties. We aim to make available diversity
>> information and an improved second version of the genome based on
>> high-resolution maps from the new synthetic populations, but likely not
>> earlier than spring 2017.
>>
>> I am at your disposal for any further information you may need.
>>
>> Best,
>> Jose De Vega
>>

[LEGUME-476] created by adf_ncgr

[adf-ncgr]

Copying data on lis-dev at /legumeinfo/Trifolium_pratense from the links found in email above:

Genome assembly annotation:
http://zenodo.org/record/17232#.VmXgDXt-rmE

by peu

[adf-ncgr]

Longest transcripts fasta and peptide fasta is created using gffread utility as it was not directly provided by the source of this species. Andrew and I found out that the gene annotation file is producing peptides that look like bad translations, so we think there is something wrong in the gff and for now we are investigating more before proceeding with data loading.

by peu