Centromere positions are inferred from the locations of discontinuities in the optical maps and physical gaps in the pseudomolecules, supported by FISH data. The following describes how the centromere positions were determined for each chromosome. Gaps that are in bold are the ones selected as centromeres.
- The chromosome is entirely covered by OMcontig9 and OMcontig3
- The centromere should be placed between these two contigs
- Considering the tiling path file, the only gap that qualifies is feature 188; between AC229370 (ending at 14,537,610) and AC126011 (beginning at 14,687,611).
- The optical map sizes this gap at >=2.47 Mb.
- N-PERICEN BACAC145372 is located on OMcontig6. BACAC139356 is also located on OMcontig6.
- S-PERICEN BACAC135798 is located on OMcontig8.
- OMcontig21 sits between OMcontig6 and OMcontig8 based upon the alignment of part of this contig to the Chr2 pseudomoledcule between the pericentromric BACs.
- The centromere should be located either between OMcontig6 and OMcontig21 or between OMcontig21 and OMcontig8.
- If the centromere is placed north of OMcontig21, it could go into one of 2 gaps.
- (a) Between AC186134 (ending at 17,572,871) and CT030253 (beginning at 17,722,872)
- (b) Between CT030253 (ending at 17,813,058) and AC234238 (beginning at 17,963,059). Choice (a) is based on overhangs of OM contigs.
- If the centromere is placed south of OMcontig21 it would be placed in the gap between AC231336 (ending at 18,521,795) and AC234396 (beginning at 18,671,796).
The centromere appears to lie between ONcontig17 and OMcontig11. In this region, there are 3 candidate gaps:
- (a) feature 155; Between AC147201 (ending at 12,432,874) and AC147363 (beginning at 12,532,875).
- (b) feature 157; Between AC147363 (ending at 12,623,865) and AC225468 (beginning at 12,673,866).
- (c) feature 163, 164 between AC150247 (ending at 13,355,468) and CU571306 (beginning at 13,505,469). Gap ends at 13,455,468; the rest is a 50K clone.
- Centromere is between OMcontig 13 and OMcontig1. There is only one candidate gap in the pseudomolecule in this region:
- Features 171-173; 200K gap between AC225461 (ending at 13,595,301) and AC202466 (beginning at 13,795,302).
- Since there are flanking 50K clones on each side, actual gap is 100K starting 13,645,301.
- Centromere is between OMcontig5 and OMcontig20. There are two candidate gaps in this region:
- (a) Feature 206; Between FP700171 (ending at 20,808,648) and AC137509 (begining at 20,908,649)
- (b) feature 214, 215; Between AC121240 (ending at 21,259,590) and CU914127 (beginning at 21,374,591).
Choose (a) based on OM overhangs.
Several possible locations for centromere based on FISH data:
- 1. Between OMcontig10 and OMcontig 23; only one candidate gap- features 137-139; Between AC146806 and AC157779. Clones at each side; actual gap is between 10,990,682 and 11,090,681.
- 2. Between OMcontig23 and OMcontig22; 2 candidate gaps:
- (2a) features 145-147; Between AC146583 and AC148657. Flanking clones on both sides, so actual gap is feature 146 from 11,673,972 and 11,773,971.
- (2b) features 149-151. Between AC148657 and AC149806. Flanking clones on both sides, so actual gap is feature 150 from 11,994,233 and 12,094,332.
- 3. Between OMcontig22 and OMcontig16. Only one candidate gap- features 170-172. Actual gap is feature 171 from 13,632,152 to 13,732,151.
- Centromere should be located between OMcontig15 and OMcontig2.
- Only one candidate gap- features 133,134. Gap is feature 133; between 11,232,686 and 11,332,685.
Two possible locations:
- 1. Between OMcontig12 and OMcontig24
- 2. Between OMcontig24 and OMcontig4
In each region, there is one candidate gap.
- (1a) features 152-154; gap is feature 153 from 12,255,701 to 12,355,700.
- (2a) features 164,165; gap is feature 165 from 13,065,704 to 13,165,703.
FISH would place N-TEL on OMcontig24 and S-TEL on OMcontig 4, thus favoring the second gap. However, the location of AC140103 (stated perhaps to be associated with N-TEL) clouds the issue a little.