David_Supplemental Figure S8

1. David_Supplemental Figure S8

2. Supplemental Figure S8. Hypothetical model of evolution of the B4 and Co-2 resistance loci, from the Mt, Lj, Gm and Pv common ancestor to the current state. In the hypothetical Mt, Lj, Gm and Pv common ancestor, we positioned the ancestral Co-2 locus (the aCo-2 locus, green, containing at least one CNL) and the ancestral B4 locus (the aB4 locus, orange, with no CNL) on two nonhomologous chromosomes aX and aY, respectively, given that chromosome macrosynteny is observed between Pv11and Lj3as well as between Pv4 and Lj2along their whole length (Hougaard et al., 2008). We also propose a subtelomeric location of the aB4 and aCo-2 loci because of the subtelomeric location of the B4 locus on Pv4 and of its corresponding syntenic regions on Mt6 and Gm19, and because of the inferred subtelomeric location of the Co-2 locus on Pv11. On the right of the scheme is presented the current state of the B4 and Co-2 loci in Pv as well as their orthologous regions in Mt, Lj and Gm, drawn on the corresponding chromosome (chromosomes not drawn to scale). Synteny relationships are indicated by dotted gray lines. After the divergence from a common ancestor of Mt, Lj, Gm and Pv that occurred 54 Mya, we propose three evolutionary scenarios, referred to as A, B, and C. These three scenarios share the same chromosome rearrangements in Mt and Lj, deduced from the present study as well as from the macrosynteny analyses between Mt, Lj, and Pv described in Choi et al. (2004), Zhu et al. (2005), Hougaard et al. (2008). In the Mt ancestor, since extensive macrosynteny is found between Pv11 and Mt4, except for the end of the Pv11 which is syntenic to Mt8, we propose that the aCo-2 locus was located on the ancestral Mt4 and that an ectopic recombination event occurred between ancestral chromosomes Mt4 and Mt8, resulting in the transfer of the aCo-2 locus to Mt8 (A1/B1/C1). Given the extensive macrosynteny relationship between Mt6 and Pv4, we do not propose any rearrangement involving the B4 locus in Mt (A1/B1/C1). In Lj, extensive synteny is found between Pv11 and Lj3, but the syntenic region of the Co-2 locus is located in an interstitial region of Lj3. In an attempt to explain the movement of the aCo-2 locus from the subtelomeric to the interstitial region of Lj3, we arbitrarily proposed that in the Lj ancestor an ectopic recombination event occurred between subtelomeric region of an unknown chromosome (referred to as chromosome aW) and chromosome aX (containing the aCo-2 locus), resulting in the transfer of a chromosomal region to the end of the chromosome aX (A2/B2/C2). This event is arbitrary since the synteny relationship between the end of Lj3 and Pv are unknown. Extensive synteny is found between Pv4 and Lj2, but the overall synteny of Lj2 is split in Pv between Pv4 and Pv2. Consequently, we propose that in the Lj ancestor, a chromosome fusion event occurred between chromosome aY (containing the aB4 locus) and a chromosome aZ (ancestral chromosome syntenic with Pv2), resulting in an interstitial localization of the B4 syntenic locus in Lj2.

3. Scenario A. In the Gm and Pv common ancestor, an ectopic recombination event occurred between subtelomeric regions of chromosomes aX and aY. Consequently, the aB4 and aCo-2 loci were contiguous (A3). Subsequent to this event, local Co-2-CNL amplification occurred at the aCo-2 locus and one Co-2-CNL duplicated in the aB4 locus, potentially involving khipu tandem repeat(s) (A4). After the divergence between Gm and Pv (19 Mya), a second ectopic recombination occurred in Pv ancestor between chromosomes aX and aY, leading to the back transfer of the aB4 locus from chromosome aX to chromosome aY (A5). Indeed, the B4 locus in the current state is located on Pv4 which is overall syntenic over its full length with Lj2. Subsequent to this event, massive CNL amplification occurred at the aB4 locus, potentially involving khipu tandem repeats, leading to four CNL sub-clusters in the current B4 locus (A6). In Gm, the whole genome duplication event (WGD) generated two copies of chromosomes aX (containing the aCo-2 locus) and aY (containing the aB4 locus), referred to as aX* (containing the aCo-2* locus) and aY* (containing the aB4* locus), respectively (A7). Subsequent to Gm WGD, numerous chromosome rearrangements have occurred, leading to the current state (A8-A9). First, the part of the aB4 locus carrying the B4-CNL-like sequence migrated from chromosome aX to aGm5, and the whole aB4* locus migrated from chromosome aX* to the subtelomeric region of aGm19 (A8). Subsequent to these events, the block containing the whole aCo-2 locus and the remaining part of the aB4 locus migrated from the subtelomeric region of chromosome aX to chromosome aGm13, and the aCo2* locus migrated from chromosomes aX*, to aGm15 pericentromeric region (A9). Scenario B. In the Gm and Pv common ancestor, CNL amplification occurred at the aCo-2 locus and a Co-2-CNL transposed in the aB4 locus through an ectopic recombination between the aCo-2 and aB4 subtelomeric regions, potentially involving khipu tandem repeat(s) (B3/C3). After Gm and Pv divergence (19 Mya), massive CNL amplification occurred in Pv at the aB4 locus, potentially involving khipu tandem repeats, leading to four CNL sub-clusters in the current B4 locus (B4/C4). In Gm, the WGD generated two copies of chromosomes aX (containing the aCo-2 locus) and aY (containing the aB4 locus), referred to as aX* (containing the aCo-2* locus) and aY* (containing the aB4* locus), respectively (B5/C5). After Gm WGD, numerous chromosome rearrangements have occurred. The aCo2 and aCo-2* loci migrated from chromosomes aX and aX* to an aGm13 interstitial region and to the aGm15 pericentromeric region, respectively (B6). The part of the aB4 locus carrying the B4-CNL-like sequence migrated from chromosome aY to aGm5 resulting in the split of the aB4 locus (B6). We also propose that the aB4* locus migrated from chromosome aY* to the subtelomeric region of aGm19. Indeed, based on the synteny relationships between Gm and Lj described in Tsubokura et al. (2008), Gm19 consists of a mosaic of small segments syntenic with parts of the Lj genome (B6). Subsequent to these events, the remaining part of the aB4 locus from chromosome aY migrated to aGm13 in a region contiguous to the aCo-2 locus (B7). Scenario C. This scenario involves the same events as scenario B for the Pv ancestor, but differs slightly for Gm ancestor. After the Gm WGD, numerous chromosome rearrangements have occurred, one of them leading to the transfer of the aCo-2* locus from chromosome aX* to the aGm15 pericentromeric region (C6). Two ectopic recombinations led to the transfer of the whole aB4* locus and of the part of the aB4 locus containing a CNL sequence from subtelomeric regions of chromosomes aY* and aY to the aGm19 subtelomeric region and aGm5 interstitial region, respectively (C6). Subsequently, the other part of the aB4 (without any CNL) migrated from chromosome aY to the subtelomeric region of chromosome aX containing the aCo2 locus (C7). Finally, the block containing the complete aCo-2 locus and a part of the aB4 locus migrated from the subtelomeric region of chromosome aX to chromosome aGm13 (C8). These three scenarios imply massive rearrangements in Gm, subsequent to the WGD, consistent with the analyses described in Tsubokura et al. (2008) where the major parts of Gm linkage groups consisted of mosaics of small segments syntenic with the Lj genome.