Estimation of syntenic spans between the Oryza sativa genome and FPContigs from other species of the Oryza Genus
Step 1 - Loading the FPContig Map
The OMAP FPC maps for the wild rice species were loaded into the Gramene
'mappings' relational database such that the data model captured the
locations of clones on FPContigs as designated in the FPC map.
Step 2 - Sequence Loading
All GenBank GSS BAC end sequences (BES) for the wild rice species were
loaded into the 'mappings' database, and cross references were made
between the sequence entries and their parent clones. Pairs of clone end
reads could therefore be readily identified.
Step 3 - Sequence Alignment
The BAC end sequences were aligned to the O.sativa pseudomolecules (TIGR v4
assembly) using blat. The standard blat parameters were used, and the
alignments from the top 10 scoring hits loaded into the database.
Step 4 - Clone Mapping
Mappings between clones and the O. sativa genome were inferred where both
ends of a given clone aligned and were within two standard deviations of the
mean clone size. The mean clone size was determined by examining the band
counts for the clones in the FPC map and extrapolating the clone size in
base pairs using an estimated band size of 1195 bp. The BES for a clone
could map in either the same or different orientations to account for
possible inversions, but could not be mapped to different chromosomes or to
regions on the same chromosome that fell outside of the expected clone size
region (+/- 2 std dev. from the mean clone size). Clones could map to
multiple regions of the genome if the score for the hits in the region were
the same (multiple top hits).
Step 5 - FPContig Mapping
FPContigs mappings on the genome were inferred where three or more
overlapping clones on a given contig were located. The start and end of the
clones became the start and end points of each region. If a gap existed,
another region would be formed by the clones in that region. Discrete
sections of each FPContig were free to map to multiple locations on the
genome.
Step 6 - Ordered OMAP FPC maps
Sections of the wild rice FPContigs that were located on the O.sativa
pseudomolecules were used to directly anchor syntenic regions between
the contigs on the FPC map to the O. sativa pseudomolecules (TIGR v4
assembly). The anchored FPContigs from each wild rice species were then
ordered and stacked along the syntenic chromosome to create a map that
could be viewed side by side with the associated chromosome map from
O. sativa in CMap. From these views the user can drill down to the
associated clone and BAC end sequence positions that the FPContig mappings
are derived from.