Fig. S1 FISH analysis of BAC clone 004H08, which harbors the Cent-Dc tandem repeat, and carrot cot-1 DNA. Bar scale is 5 µm

004H08 Carrot cot-1 DNA Merge

068M03 GSSR-101

Chr. 1 LG 1

34.0

0.0

208.6

0.01DCOR

GSSR-17

067N21

025M09

032K14

238G06

Chr. 3 LG 8

31.4

0.0

0.271.8

103.3

0.56

0.66

0.88 A9P11

LCYB

Chr. 6 LG 3

0.0

110.3

57.5

0.83

Fig. S2 Relationship between pachytene chromosomes 1, 3, 4, 6, 7 and 9, and carrot (D. carota line B493)genetic linkage groups 1, 8, 6, 3, 5, and 7. For each chromosome, BAC clones are placed according to their relative distance from the end of the short arm. Dashed lines linking cytogenetic and genetic maps are drawn only between the map-anchored BAC clones and the corresponding genetic markers. Relative orientation between chromosome 4 and LG 6, chromosome 6 and LG3, and chromosome 9 and LG 7 is ambiguous

019A16

069N01

CRTISO

18S-25S rDNA

Chr4 LG6

0.0

38.9

139.6

0.0

0.37

0.82

113N07 SSR-W93

Chr. 9 LG 7

004J17

003E10

Y2mark

ZEP

Chr. 7 LG 5

154.2

0.0

121.5

97.50.81

0.98

143.5

0.0

63.80.34

Bac clone

Centromeric region

0.02112G15

238G06 18S-25S rDNA067N21032K14

032K14025M09

b ca

d

Fig. S3 FISH mapping of carrot chromosome 3-specific BACs on the somatic chromosomes of D. crinitus suggested the occurrence of at least one translocation and one inversion between these two species. (a) Somatic chromosomes of D. crinitus probed with BACs 067N21 (green) and 032K14 (red). (b) The same preparation reprobed with BAC 238G06 (red, arrowed) and (c) with 18S-25S rDNA (green). BAC 238G06 does not co-localized on the same chromosome as the former BACs (as in carrot), and it is located on the long arm of the chromosome pair bearing the 18S-25S rDNA. (d) Partial metaphase of D. crinitus probed with 032K14 (red) and 025M09 (green), indicating the inverted order of these BACs compared to carrot. Bar scale=5 µm

Fig. S4 Examples of comparative FISH mapping of carrot chromosome-specific BACs in D. crinitus and D. pusillus (both 2n=22). (a-b) Two carrot chromosome 5-specific BACs (red and green signals) hybridized to two different chromosome pairs in both D. crinitus and D. pusillus. (c-d) FISH mapping of carrot chromosome 7-specific BACs in D. crinitus indicated that the order of these clones is the same as in carrot. (c) D. crinitus chromosomes probed with BACs 003E10 (green signal) and 004J17 (red signal). (d) The same metaphase probed with BAC 112G15 (red signal). Bar scale=5 µm

A8N14A6F01

A8N14A6F01

D. pusillus D. crinitus a b

cD. crinitus D. crinitus

003E10004J17

112G15

d

a b c

5S rDNA064A04

124B06

5S rDNA

124B06

002B20

Fig. S5 FISH mapping of carrot chromosome 8-specific BACs on the somatic chromosomes of D. crinitus. (a) D. crinitus probed with 5S rDNA (green) and 064A04 (red). (b) The same preparation probed with 124B06 (red). (c) D. crinitus chromosomes probed with 5S rDNA (green), 002B20 (red) and 124B06 (green). Bar scale=5 µm