Estimation of Syntenic Spans between Maize and Rice
The source data for the analysis were;
- Zea mays Agarose FPC Map
- Oryza sativa (japonica) pseudomolecule assembly
- Zea mays EST sequences
- Zea mays clustered EST sequences (unigenes)
EST clusters and EST singletons attached to the maize FPC map were
identified via correspondence with overgos
placed on the map as physical markers. Of these sequences, only those
that hit an FPContig through multiple clones (BACs) were considered
for further analysis.
The sequences associated with the resulting list of overgos were
aligned to the rice pseudomolecule assembly using BLAT (with
parameters -minIdentity=50 followed by PslReps with -singleHit). The
alignments were further filtered using the following criteria;
- Alignment length was greater than 150 basepairs and,
- Sequences with more than 3 hits to the genome of equal
value were discarded.
The alignments were used to construct a sorted pairwise list of
locations on the maize FPC map and their corresponding locations on
the rice genome. For each location on a given maize FPContig, if the
distance between adjacent points on rice fell within a distance of
300kb, a syntenic span was constructed.