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PhasIbeAm (A CYTED-sponsored genome project)

"Unveiling of the genome of the common bean for the exploitation of natural resources in Latin America"

In Africa and Latin America common beans (P. vulgaris) are the main source of protein for over five hundred million people. The project is an International collaboration whose main goal is to increase genetic resources and technological tools available for this crop, and specially, cDNA and genomic sequences to support selection and design of new bean varieties.

The objectives of this Project include the sequencing of the common bean (Mesoamerican line BAT93), which has an expected genome size of approximately 600 Mbp.

An hybrid sequencing strategy will be used based on pyrosequencing (454Titanium) plus ligation based sequencing (SOLiD) in order to achieve a 16-18X coverage. Furthermore, in order to facilitate assembly of the sequenced genome 300 thousand BAC ends will be sequenced. Transcriptional activity of the predicted genes will be supported by data from pyrosequencing of a cDNA library generated from a complex RNA mixture obtained from different organs, developmental stages, and under different biotic and abiotic stress conditions. Additionally, when the physical map and more complete information about the sequence of the genome are obtained, the Consortium will proceed with ultra-sequencing of some BACs.

This project will also include a gene annotation sub-task whose goal is to generate a reliable gene catalogue for this species. This annotation strategy will involve the use of tools to combine ab initio and evidence-based gene predictors plus existing common bean annotation and other well established gene annotation strategies used in other plant genomics projects

Finally, we will offer a series of courses and workshops that will be the basis for future exploitation of the data generated.


Join the PhasIBeam google group to stay up-to-date.

Project Information

Description of the project in Spanish project description

A list of coordinators of the PhasIbeAm team info



Assembly

PhasIbeAm Team is making available the raw sequence data from this genome-sequencing project before scientific publication. The purpose of this policy is to make available the common bean genomic sequence to the scientific community as soon as possible with the reasonable expectation that the collaborators will publish their results without concerns about potential preemption by other groups that did not participate in the effort.

By accessing these data, you agree not to publish any articles containing analyses of genes or genomic data on a whole genome or chromosome scale prior to publication by the PhasIbeAm team and its collaborators of its comprehensive genome analysis. These restrictions will be lifted on the publication of the whole genome description. During this waiting period, the data will be available for any kind of publication that does not compete directly with planned publications (e.g. reserved analyses) of the PhasIbeAm team and collaborators. Scientists are strongly encouraged to contact a coordinator about their intentions and any potential collaboration.

To read the entire data usage policy and download the sequence data please click here

Assembly and annotation statistics phasIbeam.v10

Links

  1. P.vulgaris BAT93 at CoGe http://https://genomevolution.org/CoGe
  2. P.vulgaris BAT93 at NCBI PRJNA221782 http://www.ncbi.nlm.nih.gov/bioproject/PRJNA221782
  3. Genome Browser http://denovo.cnag.cat/genomes/bean
  4. PhylomeDB http://www.phylomedb.org


Images

Linkage groups with anchored scaffolds

  • Development stages of Bean [1]


Additional information

Mapping between BAT93 (column 1: PhylomeDB IDs, column 2: Project Gene IDs) and G19833 genes (column 3: PhylomeDB IDs, column 4: Phytozome IDs). Column 5 indicates whether the mapped gene pair has been placed on the BAT93 linkage groups. Slightly (and very minor) differences in terms of counts as compared with the published paper due to two or more genes with identical sequences in one accession mapping to an unique gene in the counterpart accession.

File:25.GeneMapping.ExternalIDs.public.gz


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