[Medicago] Medicago Genome in Nature

medicago from net.bio.net via medicago%40net.bio.net (by medicago from net.bio.net)
Mon Nov 21 23:21:56 EST 2011


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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