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Open Access Open Badges Research article

Chromosomal evolution in the plant family Solanaceae

Feinan Wu1 and Steven D Tanksley12*

Author Affiliations

1 Department of Plant Breeding and Genetics, Cornell University, Ithaca, NY 14853, USA

2 Department of Plant Biology, Cornell University, Ithaca, NY 14853, USA

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BMC Genomics 2010, 11:182  doi:10.1186/1471-2164-11-182

Published: 17 March 2010

Additional files

Additional file 1:

Figure S1 - Molecular dating of divergence time for several solanaceous species. A previously published dataset [3] was used to reconstruct the maximum-likelihood tree, and the divergence time was estimated using the non-parametric rate smoothing method (see Methods). The calibration point was 86MYA for tomato-coffee split [15].

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Additional file 2:

Figure S2 - Chromosomal rearrangements in the genomes of eggplant, pepper and Nicotiana with respect to the tomato genome. Genetic maps are modified from published work [9-11] with kind permission from Springer Science+Business Media. E1-12 represents the 12 eggplant chromosomes, P1-12 for pepper, and N1-12 for the MRCA of N. tomentosiformis and N. acuminata. Each tomato chromosome is assigned a different color (see color codes in the figure) and the orthologous chromosome segment(s) in eggplant, pepper and Nicotiana are painted with the same color. Putative centromere positions of eggplant and pepper chromosomes are based on their synteny with tomato and indicated by a white dot. It was not possible to determine the centromere positions for the Nicotiana chromosomes due to complex syntenic relationships with tomato. An arrow beside a chromosome indicates an inversion relative to tomato. A black bar indicates the breakpoint region of a translocation, and the chromosome is divided into segments (a-c) accordingly to facilitate comparisons of multiple species. The marker pair used to define the breakpoint region (i.e. the two adjacent markers mapped to different tomato chromosomes) or to define the borders of an inversion is highlighted in red. The map of the MRCA of N. tomentosiformis and N. acuminata is deduced based on the comparative maps of N. tomentosiformis, N. acuminata and tomato, and is not presented directly. The actual N. tomentosiformis map is presented, and the four inversions relative to its MRCA are indicated by dash arrows and the border markers are underlined.

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Additional file 3:

Figure S3 - Comparative maps of several solanaceous species and the deduced genome arrangement of MRCAs (close-up of Figure 4). Designation of chromosome and chromosome segment (a-c) as well as color codes follow Additional File 2. Nomenclature of MRCAs (ATPt, ATE and ATP) follows Figure 1. Maps of non-tomato species are depicted in a comparative way to the tomato map as follows. A black arrow depicts an inversion relative to tomato (a grey arrow for an uncertain inversion). A black bar depicts the breakpoint region of a translocation relative to tomato (a grey bar for an uncertain translocation). Two black bars connected by a curve indicate that 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+") on a single arrow indicates that the region has experienced at least one (or two) inversions but the exact number remains to be determined. Markers displayed on the tomato map were used to define breakpoint regions of translocations and borders of inversions. The prefix (in parentheses) of a marker name specifies at which non-tomato maps the marker locates (E = eggplant, P = pepper, N = Nicotiana). Due to a different tomato map used for tomato-potato comparison, location and length of inversions on the potato map are approximate [3,8]. White dots indicate the approximate centromere location of the tomato chromosomes.

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