TABLE 1

Example of genome distance computation

EggplantTomato
    E3. 1 2 3 4 5 6    T3. 1 -5 2 6
    E4. 7 8    T4. 21 -22 -20 8
    E5. 9 10    T5. -4 14 11 -15 3 9
    E10. 11 12 13 14 15 16 17 18    T10. 7 16 -18 17
    E11. 19 20 21 22    T11. -19 24 -26 27 25
    E12. 23 24 25 26 27    T12. -12 23 13 10
Eggplant doubled, ends added
    1000, 1 2, 3 4, 5 6, 7 8, 9 10, 11 12, 1001
    1002, 13 14, 15 16, 1003
    1004, 17 18, 19 20, 1005
    1006, 21 22, 23 24, 25 26, 27 28, 29 30, 31 32, 33 34, 35 36, 1007
    1008, 37 38, 39 40, 41 42, 43 44, 1009
    1010, 45 46, 47 48, 49 50, 51 52, 53 54, 1011
Tomato doubled, ends added
    2000, 1 2, 10 9, 3 4, 11 12, 2001
    2002, 41 42, 44 43, 40 39, 15 16, 2003
    2004, 8 7, 27 28, 21 22, 30 29, 5 6, 17 18, 2005
    2006, 13 14, 31 32, 36 35, 33 34, 2007
    2008, 38 37, 47 48, 52 51, 53 54, 49 50, 2009
    2010, 24 23, 45 46, 25 26, 19 20, 2011
Short paths in breakpoint graph = 5 (one for each end that agrees)
    1000-1-2000, 1001-12-2001, 1003-16-2003, 1002-13-2002, and 1005-20-2011
Long paths in breakpoint graph = 7
    1004 17 6 7 27 26 19 18 2005
    1006 21 28 29 5 4 11 10 2 3 9 8 2004
    1007 36 32 33 35 34 2007
    1008 37 47 46 25 24 2010
    1009 44 42 43 40 41 2002
    1010 45 23 22 30 31 14 15 39 38 2008
    1011 54 49 48 52 53 51 50 2009