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The physical map of chromosome 1 was constructed using the data from 316 probes. The map contains 41 Assembly 19 sequence contigs. One discrepancy exists bestween this map and the Assembly 20 contig. The BRI map indicates that contig 19-2020 lies between 19-10097 and 19-10223. We failed to anchor this contig on our map using several probes. The optical map provided no helpful information.. Chromosome 1 is 3,190,737 bp in size. It contains SfiI fragments S, C2, A, B, J, E and L in that order from right to left. It contains one MRS between fragments B and J. The centromere is 100-120 Kb to the left of the MRS in the 1 B Sfi I fragment on 19-10205.
The 1 L telomere sequence was not assigned to any Assembly 19 contigs and does not exist in the BRI sequence. The physical map assumes that it follows 19-2507 because probes from the end of 19-2507 hybridize to fosmids hit by telomere probes. Probe data also indicate that perhaps the last 5 kb of 19-2507 needs to be trimmed. The optical map indicates that the actual end of the chromosome extends just another 15 Kb beyond this point.
The fosmid contig has two breaks in its continuity. One is near the right end of 19-10223. Several probes across a 40 Kb region only hit one of two fosmids indicating it is a region difficult to clone with fosmids. The second break is a 60 Kb portion within 19-10216. Although the probe coverage is good, about one probe every 10 Kb, the fosmid hits are not continuous and are rich in repeats. Both of these breaks are considered to be harmless because they are mid-Assembly 19 contig and there is strong support over the entire lengths of these contigs from both the optical map and the BRI map.
This is a schematic drawing of the chromosome 1 of strain 1006. The thin lines are SfiI sites, the thick lines are MRS locations.