Helmholtz Zentrum München - German Research Center for Environmental Health

FPC - Fingerprinted Contigs

The physical map of barley genome (Hordeum vulgare cv. Morex) is based on high information content fingerprinting (HICF) of 650 000 BAC clones generated by IPK. The BACs were derived from 5 different BAC libraries (2x HindIII, EcoRI, MboI, random sheared). A total of 570,000 (13x genome coverage) high quality fingerprints were selected and entered the de novo contig assembly with FPC v9.0. The resulting FPcontig version, termed fpc_10 (9,435 contigs, 507,688 BAC clones) is currently displayed. It will later be replaced by a manually curated improved version.

The FPcontigs where anchored by their member sequences (BES, 454 sequenced BACs, Harvest35) to single chromosome arms with a method called Read Based Chromosome Assignment (RBCA). RBCA exploits the sequence homology of low copy (repeatfree) regions between the query sequence and the chromosome sorted 454reads. About 1,000 FPcontigs contain BACs, that are associated to a genetic marker from the Close_ilumina_consensus_2009 map. These FPcontigs where directly anchored to a specific chromosome location (cM scale) on one of the seven chromosomes and can be accessed via crowsnest (link to crows nest chromosome view). The other genetic maps of barley are in the process of being integrated. More sequence data from 50xWGS Illumina read assemblies will also be included soon.

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Genetic Marker Download

Visualisation Tools

Gbrowse

Gbrowse view for FPcontigs


CrowsNest

CrowsNest view of the physical map