[Medicago] RE: Medicago Genome in Nature

medicago from net.bio.net via medicago%40net.bio.net (by medicago from net.bio.net)
Tue Nov 22 21:09:38 EST 2011

Dear Medicago community,

Taking advantage of the note about the outstanding new Medicago resources at JCVI (and GenBank), I'd like to also point to some additional new complimentary resources at the Legume Information System (LIS), http://comparative-legumes.org . This is among a growing set of tools that the genome sequence and IMGAG gene models have made possible.

 o A Medicago genome browser. A useful feature is a set of synteny tracks that establish associations with 
    soybean and Lotus (and browsers for the same):

 o A multi-sequence search tool that displays queries against the full Medicago, soybean, or Lotus genomes, 
    and provides synteny information and linkouts to the respective browsers:

 o A set of legume-focused gene family pages, with capacity for flexible key-word or sequence searches:

 o A sequence search tool that reports matches to various legume resources, including browser locations at JCVI
   and expression information at Noble.

The LIS tools are the work of the teams at NCGR (led by Dr. John Crow) and at USDA-ARS at Ames, and of course make use of the great work of the many participants in the international Medicago genome consortium, and the other outstanding genomics data being generated for the group of related plants. Congratulations on the recent Medicago paper in Nature, and thanks to all.

We would be happy to receive your questions, feedback, or requests: lis_feedback from ncgr.org; or direct to me (scannon from iastate.edu) or John Crow (jac from ncgr.org).

Wishing you a happy Thanksgiving or "thanks-giving" (whether the holiday is celebrated officially by you or not).
Steven Cannon
scannon from iastate.edu
USDA-ARS and Department of Agronomy
Iowa State University

Steven Cannon
scannon from iastate.edu
USDA-ARS and Department of Agronomy
Iowa State University

From: medicago-bounces from oat.bio.indiana.edu [medicago-bounces from oat.bio.indiana.edu] On Behalf Of medicago from oat.bio.indiana.edu [medicago from oat.bio.indiana.edu]
Sent: Monday, November 21, 2011 10:21 PM
To: medicago from net.bio.net
Subject: [Medicago] Medicago Genome in Nature

Greetings, Leguminous Colleagues!

As many of you will have seen, the Medicago genome paper is now published in the journal Nature. Our thanks to all the people who have coordinated and contributed to the production and analyses of the genome sequence.

We are pleased to announce that the assembly and predicted gene models of Medicago truncatula are now deposited in GenBank. We also want to take this opportunity to announce the launching of a revamped JCVI website devoted to the distribution and curation of related genomic resources in Medicago.

GenBank assembly and annotation release

The Medicago pseudomolecules (constructed from the BAC tiling path) and associated gene annotations are available on GenBank (http://www.ncbi.nlm.nih.gov/bioproject/10791). The current version (MedtrA17_3.5) consists of 8 chromosomes with identifiers CM001217-CM001224 and 146 unplaced BACs with identifiers GL982851 - GL982996. This assembly release has a total size of 314Mb (262Mb excluding gaps), and contains 46,016 predicted proteins.

For members in the Medicago sequencing consortium, we would like to point out a few changes that occurred during the GenBank release process:

During submission, we found that there were contaminants in the pseudomolecule assembly (un-removed vector, E. coli, etc., 106K bases in total), so we masked these regions and replaced them with the same number of Ns in order to preserve the coordinate system. Consequently any genes that intersect these contaminant ranges were either edited or dropped.

The gene naming scheme has been changed slightly, in order to conform to the GenBank standard. Specifically, the locus tag prefix is now "MTR_", instead of "Medtr", e.g. Medtr1g005000 has been converted to MTR_1g005000. The old Medtr names are still available in the "note" field in the GenBank records; therefore both names are available for search on the GenBank website.

The Illumina WGS assembly has NOT been deposited in the GenBank but is available on JCVI FTP (see below). We are working on an improved version of Illumina WGS assembly by adding more sequences, in an effort to fill the gaps on the pseudomolecules. You can blast against these updated assemblies on our web site.

JCVI Medicago website
In conjunction with the release of the Medicago truncatula genome paper, the project pages at JCVI (http://medicago.jcvi.org/medicago) have been updated with new data and functionalities.  Several new features include:
The Golden Path Viewer allows you to look at the tiling path of each pseudomolecule in a movable and scalable way.  You can view the placement of individual BACs and the gaps, and move along the pseudomolecule by scrolling.
The Gene Curation Page, which is accessible by the locus search, has been made available for each gene.  This page contains the gene structure, attributes (reference sequence, coordinates, length, etc), supporting evidences, HMM search results, GO terms, SwissProt, TMHMM, SignalP, TargetP, and BLAST search results.  You can also view and download the genomic, CDS and protein sequences for each locus.
View of the BAC assembly in an image that shows Draft/Finished BACs as seen on each chromosome, with respect to the length and centromeres.  You can hover over or click on any region to see the coordinates, and quickly navigate to a particular region in GBrowse.
Various search functions:
Putative function search - to search for a particular gene by keyword (ex. "aldolase")
Locus search - to search for a particular gene by locus name (ex. Medtr5g024510, AC225458.91)
Clone Name Search- to search for a particular clone by pseudomolecule, BAC or contig ID.
The Community Annotation pipeline is now available for use!  We are now accepting data to improve the annotation of various gene families at this time. Please help us improve the annotation - structural and functional. We are working to implement a direct web submission process, but for now you will need to e-mail us.
The Download page contains FTP links to the updated datasets. Previous versions of the assembly and annotations are also available. The differences between the release versions are explained.

We appreciate all of your comments and suggestions! Please send your feedback to mtruncatula from jcvi.org<mailto:mtruncatula from jcvi.org>.

The Medicago truncatula Genome Project is supported by grants DBI-0321460, DBI-0604966 and DBI-0821966 from the National Science Foundation.

Your friends at JCVI:
Haibao Tang (Senior Bioinformatics Engineer)
Vivek Krishnakumar (Bioinformatics Engineer)
Shelby Bidwell (Bioinformatics Analyst)
Chris Town (Project Lead)

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