Comparative analysis of pepper and tomato reveals euchromatin expansion of pepper genome caused by differential accumulation of Ty3/Gypsy-like elements

Abstract

BackgroundAmong the Solanaceae plants, the pepper genome is three times larger than that of tomato. Although the gene repertoire and gene order of both species are well conserved, the cause of the genome-size difference is not known. To determine the causes for the expansion of pepper euchromatic regions, we compared the pepper genome to that of tomato.ResultsFor sequence-level analysis, we generated 35.6 Mb of pepper genomic sequences from euchromatin enriched 1,245 pepper BAC clones. The comparative analysis of orthologous gene-rich regions between both species revealed insertion of transposons exclusively in the pepper sequences, maintaining the gene order and content. The most common type of the transposon found was the LTR retrotransposon. Phylogenetic comparison of the LTR retrotransposons revealed that two groups of Ty3/Gypsy-like elements (Tat and Athila) were overly accumulated in the pepper genome. The FISH analysis of the pepper Tat elements showed a random distribution in heterochromatic and euchromatic regions, whereas the tomato Tat elements showed heterochromatin-preferential accumulation.ConclusionsCompared to tomato pepper euchromatin doubled its size by differential accumulation of a specific group of Ty3/Gypsy-like elements. Our results could provide an insight on the mechanism of genome evolution in the Solanaceae family.

Major repeat components covering one‐third of the ginseng (Panax ginseng C.A. Meyer) genome and evidence for allotetraploidy

“…(Suoniemi et al, 1996;Vicient et al, 1999), wheat (Charles et al, 2008;Salina et al, 2011) and pepper (Park et al, 2011(Park et al, , 2012b, have reported that the genomes expanded and were rearranged by accumulation of LTR-RTs. Our results suggest that LTR-RTs are also the main players in the enlargement and evolution of the ginseng genome.…”

“…The accumulation of LTR-RTs around genic regions has been reported in maize (SanMiguel et al, 1998;Kronmiller and Wise, 2009), wheat (Wicker et al, 2001;Salina et al, 2011), barley (Wicker et al, 2005) and pepper (Park et al, 2011(Park et al, , 2012b. In the pepper genome, accumulation of the Ty3/Gypsy elements such as Tat and Athila-like subgroups has resulted in expansion of euchromatic regions by random insertion (Park et al, 2011), while the Del-like subgroup has accumulated in constitutive heterochromatic regions such as pericentromeric regions (Park et al, 2012b). By contrast, the Del-like elements and their solo LTRs were found in the areas adjacent to the genic region of 5J07 (Figure 1c).…”

Whole-genome sequencing of cultivated and wild peppers provides insights into Capsicum domestication and specialization

“…Another primary reason for limited applied and basic research in pepper has been lack of a reference genome sequence of ∼3.3 Gb (11). Recent work comparing two members of the Solanaceae family (pepper and tomato) has begun to shed light on the processes that influence the dynamics of genome size in angiosperms (12,13).…”

Mapping of the ms8 male sterility gene in sweet pepper (Capsicum annuum L.) on the chromosome P4 using PCR-based markers useful for breeding programmes

“…Table 1 sums up the results of the analysis. Five sequences (Z05-760, V17-320B, W06-520, V01-1000, and Q07-1100) revealed extensive similarity to at least eight pepper BAC clones that are rich in LTR/Gypsy-like retrotransposons as reported by Park et al (2011). The N16-800 sequence showed significant similarity to the cDNA pepper clone KS24.…”