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Abstract
BackgroundOver the past decades, extensive comparative mapping research has been performed in the plant family Solanaceae. The recent identification of a large set of single-copy conserved orthologous (COSII) markers has greatly accelerated comparative mapping studies among major solanaceous species including tomato, potato, eggplant, pepper and diploid Nicotiana species (as well as tetraploid tobacco). The large amount of comparative data now available for these species provides the opportunity to describe the overall patterns of chromosomal evolution in this important plant family. The results of this investigation are described herein.ResultsWe combined data from multiple COSII studies, and other comparative mapping studies performed in tomato, potato, eggplant, pepper and diploid Nicotiana species, to deduce the features and outcomes of chromosomal evolution in the Solanaceae over the past 30 million years. This includes estimating the rates and timing of chromosomal changes (inversions and translocations) as well as deducing the age of ancestral progenitor species and predicting their genome configurations.ConclusionsThe Solanaceae has experienced chromosomal changes at a modest rate compared with other families and the rates are likely conserved across different lineages of the family. Chromosomal inversions occur at a consistently higher rate than do translocations. Further, we find evidences for non-random positioning of the chromosomal rearrangement breakpoints. This finding is consistent with the similar finding in mammals, where hot spots for chromosomal breakages have apparently played a significant role in shaping genome evolution. Finally, by utilizing multiple genome comparisons we were able to reconstruct the most likely genome configuration for a number of now-extinct progenitor species that gave rise to the extant solanaceous species used in this research. The results from this study provide the first broad overview of chromosomal evolution in the family Solanaceae, and one of the most detailed thus far for any family of plants.
Highlights
Over the past decades, extensive comparative mapping research has been performed in the plant family Solanaceae
We ran the program r8s [13] to estimate the age of internal nodes by the non-parametric rate smoothing (NPRS) method, which does not rely on the assumption of a molecular clock [14]
Among the solanaceous species included in the current study, tomato, potato and eggplant belong to the genus Solanum, with tomato and potato closer to each other than to eggplant
Summary
Extensive comparative mapping research has been performed in the plant family Solanaceae. The large amount of comparative data available for these species provides the opportunity to describe the overall patterns of chromosomal evolution in this important plant family. The results of this investigation are described . The Solanaceae is a large plant family comprised of over 3000 species including many important crops such as tomato, potato, eggplant, and pepper. It represents a group of dicotyledonous plants in the Euasterid clade, which is divergent from the model plant Arabidopsis [1,2]. The Solanaceae and related taxa present a unique opportunity to study genome/gene evolution in the absence of recent polyploidization events
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