Spreadsheet: 2b90c8dc-a14d-4777-b82c-4c0a86a42fbb
Sheet: Sheet1

Table S3.  Predicted rearrangements between the chicken and turkey genomes. | Unnamed: 1 | Unnamed: 2 | Unnamed: 3 | Unnamed: 4 | Unnamed: 5
GGA | Bld2 GGA start coord. | Bld2 GGA end coord. | MGA* | Nature of the rearrangement | Notes
1 | 9713416 | 10050000 | MGA1 | segment relocated to chr1:74570000, could be misplacement of GGA contig 180 | translocated segment is internal to direct repeat of SEMA3 genes
1 | 75800000 | 76000000 | MGA1 | small inversion | possible unequal recombination within KCN gene cluster
1 | 104450000 | 104459439 | MGA1 | likely error in chick assembly, misplaced fragment of rDNA | the genetic map places this short segment near 1q telomere
1 | 125900000 | 126300000 | MGA1 | small interchromosomal translocation | insertion of GGA4:25,500,000-25,550,000 at repetitive locus (see also below)
1 | 156600000 | 156600001 | MGA1 | small interchromosomal translocation | may be misplacement of Ctg13.1004 in GGA seq or LINE-based translocation of a small segment from GGA4:73,089,000-73,090,000
1 | 172822000 | 172900000 | MGA1 | possible small inversion | may be mis-assembly of GGA ctg3.1161
2 | 54870224 | 56560442 | MGA3 | inversion with 56.560 Mb coordinate being telomeric in MGA3 | (together one inversion and two translocations or assembly errors)
2 | 54398341 | 54413232 | MGA3 | small translocation or mis-assembly of GGA seq., inverted rel. to GGA seq. coord. | (together one inversion and two translocations or assembly errors)
2 | 54641337 | 54845268 | MGA3 | probably inverted relative to GGA sequence coordinates | (together one inversion and two translocations or assembly errors)
2 | 54290000 | 54330000 | MGA3 | small translocation or mis-assembly of GGA seq., orientation uncertain | (together one inversion and two translocations or assembly errors)
2 | 54452395 | 54545188 | MGA3 | probably inverted relative to GGA sequence coordinates | (together one inversion and two translocations or assembly errors)
2 | 53804240 | 54263147 | MGA3 | inverted relative to GGA seq. coordinates with 53.8 Mb joined to 56.6 Mb in MGA | (together one inversion and two translocations or assembly errors)
3 | 6218 | 2344838 | MGA2 | inversion, telomeric | FISH CONFIRMED, order is [NAME]5.6Mb]-[11.605-5.605Mb]-[13.16Mb-------]
3 | 5605686 | 11605484 | MGA2 | inversion (agrees with genetic map) | FISH CONFIRMED, order is [NAME]5.6Mb]-[11.605-5.605Mb]-[13.16Mb-------]
4 | 25500000 | 25550000 | MGA4 | small interchromosomal translocation to about 125.90 Mb orthologous coord. on MGA1 | see also chr1:125900000
4 | 35150000 | 35160000 | MGA4 | likely small duplication | part of this segment duplicated at around 35,828,000
4 | 73080000 | 73090000 | MGA4 | small interchromosomal translocation to about 156.60 Mb orthologous coord. on MGA1 | may be misplacement of Ctg13.1004 in seq or LINE-based translocation of a small segment, see also GGA1:156,600,000
5 | 1 | 270229 | MGA5 | local small inversion with respect to p arm which as a whole is inverted | local inversion with respect to p arm which as a whole is inverted
5 | 1 | 7248180 | MGA5 | inversion of p arm | p arm likely inverted based on genetic map of Nte0897, [NAME]
6 | 1576787 | 13080207 | [NAME] | multiple inversions:  predicted order is [10430381-11438238]-[7654280-4075907]-(10349000-10370000)-gap-(3919938-3930000)-gap-[3919764-1576787]-[10296511-7735050]-[11531176-12153164]-[13080207-12264632]-[13140570 --------] | can be explained by a series of 4-5 consecutive inversions, including possible unequal recombination between SLC16A9 or, less likely, protocadherin genes
7 | 1 | 7248180 | MGA7 | inversion of p arm
8 random | 64951 | 407592 | [NAME] | GGA8_random sequences likely telomeric on [NAME] (and probably [NAME])
8 | 44817 | 10199568 | [NAME] | inversion of p arm | possible unequal recombination between AMY genes
8 | 8992540 | 9170000 | [NAME] | local small inversion with respect to p arm which as a whole is inverted | probable inversion but might be mis-orientation of GGA sequence contigs
9 | 1528027 | 4372460 | MGA11 | inversion | telomeric inversion
10 | 1907125 | 3642461 | MGA12 | no internal centromere observed in turkey | centromere misplaced in chicken or moved to telomere in turkey
11 | 75337 | 3280000 | MGA13 | no internal centromere observed in turkey | inversion of GGA 11p, FISH CONFIRMED
12 | 95816 | 940546 | MGA14 | may be inverted, orientation uncertain | may be fused to a repeat of 2.15-2.3 Mb region of GGA12
12 | 1050000 | 1100000 | MGA14 | possible small intrachromosomal translocation to telomere | small segment may be now at MGA telomere
12 | 1128610 | 1134284 | MGA14 | possible very small intrachromosomal translocation | small segment now between about 2,632,117-2,703,753 in GGA coordinates on q arm
12 | 1164577 | 1399694 | MGA14 | inversion  (1164577 joined to 1599552) | centromere either misplaced in GGA or moved telomeric or between 940,546 and 1,399,694
13 | 8233861 | 8511782 | MGA15 | small inversion
14 | 14370000 | 15070000 | MGA16 | inversion | FISH CONFIRMED
18 | 5062096 | 9882412 | MGA20 | inversion | unequal recombination between NME paralogs, FISH confirmed
28 | 1550000 | 1620000 | MGA30 | apparent duplication with extra copy at about 1.05 Mb in MGA | unclear if these are rearrangements or assembly errors
*Based on nomenclature of Griffin et al., 2008 (Ref. #10)