The Solanaceae is an unusually divergent family consisting of approximately 90 genera and 3,000-4,000 species . Members of the Solanaceae have evolved into extremely divergent forms, ranging from trees to annual herbs, and they occupy diverse habitats ranging from deserts to aquatic areas . Such hyper-diversity in one family makes it useful to study plant adaptation and diversification. Despite this diversity, all Solanaceous species evolved during the last 40 million years . Furthermore, almost all members share the same chromosome number (x = 12) .
To date, diversity within the Solanaceae has been studied by comparative genome analyses using common genetic markers. As a result, we know that the Solanaceae genomes have undergone relatively small numbers of chromosomal rearrangements (e.g., about 5 rearrangements between potato and tomato and about 30 rearrangements between pepper and tomato), maintaining well-conserved gene content and order [3–8]. The conservation of the Solanaceae genic region was also identified by the comparison of a syntenic segment in eggplant, pepper, petunia and tomato .
Despite such conservation, the genome sizes of the Solanaceae family members are diverse. For example, the genome size of the Solanum tuberosum (potato) is 840 Mb, S. lycopersicum (tomato) 950 Mb, Petunia hybrida (petunia) 1200 Mb, and Capsicum annuum (pepper) 2700 Mb. However, the genetic analyses conducted to date were not successful at explaining genome size diversity due to limitations in the genetic markers. Hence, a sequence-level analysis to investigate the cause of the genome size diversity is required.
Among the Solanaceous species, pepper and tomato show strong advantages for the study of genome size difference because of following reasons. First, the genome size of pepper is three times larger than that of tomato. Second, the duplication of the whole genome did not occur during the evolution of both species . Third, although pepper and tomato show large size differences in their genomes, their speciation is estimated to have occurred recently (approximately 16.2-22.2 million years ago) , which makes them not as closely related as potato and tomato, but more closely related than tobacco and tomato within the Solanaceae family . Therefore, the investigation of genome diversity between pepper and tomato can represent the general trend of genome diversification among Solanaceous members that have not undergone the whole genome duplication.
To date, most studies related to the pepper genome have been carried out by generating genetic maps [6, 10–14]. In contrast, the structure of the tomato euchromatic and heterochromatic regions has been the subject of several studies through the analyses of tomato BAC sequences [15–17]. Furthermore, the tomato genome sequencing project is currently underway, with the goal of generating a reference genome in the Solanaceae [18–21].
As a first study concerning the expansion of the pepper genome, the present work addresses the causes behind the expansion of pepper euchromatic regions. For this purpose, 35.6 Mb of pepper sequences from 1,245 BAC clones selected from euchromatin-enriched regions were generated. Using information from the tomato genome project, 39.9 Mb BAC sequences of tomato were chosen for comparing orthologous gene-rich sequences and the constitution of repetitive elements between the pepper and tomato genomes. We used fluorescence in situ hybridization (FISH) to support the results. This study presents an example of the Solanaceae genome diversity revealing how the pepper euchromatic region was expanded.