Table 1

Deletions with skipping and blocking

Event

i

a

-7

-6

-5

-4

-3

-2

-1

0

1

2

3

4

5

6

7

8

r


Start

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

-1

3

1

1

1

1

1

1

    0

    0

    0

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

2

1

1

1

1

1

1

0

0

0

1

1

1

1

1

1

1

1

-4

1

1

1

1

    0

1

1

1

1

1

1

1

1

1

1

1

1

1

3

5

1

1

1

1

1

1

1

0

0

0

1

1

1

    0

1

1

1

1,1

1

1

1

0

1

1

1

1

1

1

1

1

1

1

1

1

1

4

4

3

1

1

1

1

1

1

0

0

0

1

1

    0

0

    0

    0

1

1,2

1

1

1

0

1

1

1

1

1

1

1

1

1

1

1

1

1

5

1

1

1

1

1

1

0

0

0

1

1

0

0

0

0

1

2

-5

4

1

1

    0

0

    0

    0

1

1

1

1

1

1

1

1

1

1

3


Five deletion events affecting two homeologous chromosomes, leading to two runs of single-copy genes. The fourth step illustrates the "skip" process, at i = 5 where the pre-existing deletion is incorporated into a longer run with r = 2. The fifth step shows how further deletion (at i = -1) and the "skip" process (to i = 2) are blocked when a single-copy gene is encountered (i = -1) on the homeologous chromosome. This creates a single-copy run with length l = 7 and r = 3, part on one chromosome, part on the other. Note that r is not observable from the genome data.

Sankoff et al. BMC Genomics 2012 13(Suppl 1):S8   doi:10.1186/1471-2164-13-S1-S8

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