Comparative maps of potato, eggplant, pepper and Nicotiana with respect to the tomato genome

1. Comparative maps of potato, eggplant, pepper and Nicotiana with respect to the tomato genome Silvana Grandillo CNR-IGV, Portici (Naples), Italy March 4, 2010 Main References • Tanksley SD, Ganal MW, Prince JP, de Vicente MC, Bonierbale MW, Broun P, Fulton TM, Giovannoni JJ, Grandillo S, Martin GB et al. (1992) High density molecular linkage maps of the tomato and potato genomes. Genetics 132:1141-1160. • Gebhardt C: MPI for Plant Breeding Research, Köln, Germany, personal communication. • Wu FN, Eannetta NT, Xu YM, Tanksley SD (2009a) A detailed synteny map of the eggplant genome based on conserved ortholog set II (COSII) markers. Theor Appl Genet 118:927-935. • Wu FN, Eannetta NT, Xu YM, Durrett R, Mazourek M, Jahn MM, Tanksley SD (2009b) A COSII genetic map of the pepper genome provides a detailed picture of synteny with tomato and new insights into recent chromosome evolution in the genus Capsicum. Theor Appl Genet 118:1279-1293. • Wu FN, Eannetta NT, Xu Y, Plieske J, Ganal M, Pozzi C, Bakaher N, Tanksley SD (2009c) COSII genetic maps of two diploid Nicotiana species provide a detailed picture of synteny with tomato and insights into chromosome evolution in tetraploid N. tabacum. Theor Appl Genet Theor Appl Genet (2010) 120:809–827 . • Wu FN, Tanksley SD (2010) Chromosomal Evolution in the Plant Family Solanaceae. BMC (in press)

2. Main chromosomal rearrangements in the genomes of potato, eggplant, pepper and Nicotiana with respect to the tomato genome (modified from Wu and Tanksley 2010; BMC, in press) T1-12: tomato chromosomes Pt1-12: potato chromosomes P1-12: pepper chromosomes N1-12: Nicotiana chromosomes Maps of the other species are depicted in a comparative way to the tomato map as follows: Inversion relative to tomato Breakpoint region of a translocation relative to tomato Designation of chromosome segments (a-c) is detailed in Aditional Figure S1. The segment in between is excised in a translocation while the remained parts stay together, e.g. E10a is embedded in E3b. (1+) or (2+) The region has experienced at least one (or two) inversions but the exact number remains to be determined. Approximate centromere location of the tomato chromosomes. Position and length of arrows and bars are approximate. See the close-up figure in Additional Figure S1.

3. Comparative maps of potato, eggplant with respect to the tomato genome Potato-Tomato (Tanksley et al 1992; Gebhardt C, personal communication) Tomato and potato differ by 6 inversions (paracentric) on chormosomes: 2 (new), 5, 9, 10, 11, 12 Eggplant-Tomato(Wu et al. 2009a) Deductions concerning the syntenic relationships of the eggplant and tomato genomes were based on 110 COSII markers and 179 tomato-derived markers. These 289 orthologous markers are referred to as “synteny markers”. Since divergence from their last common ancestor approximately 12 million years ago, the eggplant and tomato genomes have become differentiated by a minimum number of 24 inversions and 5 chromosomal translocations, as well as a number of single gene transpositions possibly triggered by transposable elements The two genomes share 37 conserved syntenic segments (CSSs) within which gene/marker order is well preserved. The CSSs ranged in size from 3 to 105 cM with an average size of 34 cM (cM value based on the eggplant map) They covered from 57% (E11) to 98% (E9) of different eggplant linkage groups and totaled 1,241 cM corresponding to 81% of the eggplant map.

4. Comparative maps of pepper with respect to the tomato genome Pepper-Tomato(Wu et al. 2009b) Deductions concerning the syntenic relationships of the pepper and tomato genomes were based on 299 orthologous markers including 263 COSII markers, which are referred to as “synteny markers”. Since divergence from their last common ancestor is approximately 20 million years ago, the two genomes have become differentiated by a minimum number of 19 inversions (1.6 per chromosome on average, of these, only two (P1) are likely to be pericentric inversions.) and 6 chromosome translocations (especially with break points at or near the centromeres), as well as numerous putative single gene transpositions. The two genomes share 35 conserved syntenic segments (CSSs)--defining majority of the pepper and tomato genomes within which gene/ marker order have been well preserved. The CSSs ranged in size from 6 to 117 cM with an average size of 32 cM (cM value based on the pepper map) They covered from 52% (P1) to 97% (P7) of different pepper linkage groups and totaled 1,117 cM corresponding to 69% of the pepper map.

5. Comparative maps of Nicotiana with respect to the tomato genome Nicotiana-Tomato(Wu et al. 2009b; Wu and Tanksley 2010, BMC in press) Using single-copy conserved ortholog set (COSII) and simple sequence repeat (SSR) markers, two genetic maps for diploid Nicotiana species, N. tomentosiformis and N. acuminata, respectively were constructed. N. acuminata is phylogenetically closer to N. sylvestris than to N. tomentosiformis, the latter two of which are thought to contribute the S-genome and T-genome, respectively, to the allotetraploid tobacco (N. tabacum L., 2n = 48). Mapped COSII markers permitted the investigation of Nicotiana–tomato syntenic relationships. A minimum of 3 (and up to 10) inversions and 11 reciprocal translocations differentiate the tomato genome from that of the last common ancestor of N. tomentosiformis and N. acuminata. Nevertheless, the marker/gene order is well preserved in 25 conserved syntenic segments.