Evolution of the large genome in Capsicum annuum occurred through accumulation of single‐type long terminal repeat retrotransposons and their derivatives

Abstract

SUMMARYAlthough plant genome sizes are extremely diverse, the mechanism underlying the expansion of huge genomes that did not experience whole-genome duplication has not been elucidated. The pepper, Capsicum annuum, is an excellent model for studies of genome expansion due to its large genome size (2700 Mb) and the absence of whole genome duplication. As most of the pepper genome structure has been identified as constitutive heterochromatin, we investigated the evolution of this region in detail. Our findings show that the constitutive heterochromatin in pepper was actively expanded 20.0-7.5 million years ago through a massive accumulation of single-type Ty3/Gypsy-like elements that belong to the Del subgroup. Interestingly, derivatives of the Del elements, such as non-autonomous long terminal repeat retrotransposons and longunit tandem repeats, played important roles in the expansion of constitutive heterochromatic regions. This expansion occurred not only in the existing heterochromatic regions but also into the euchromatic regions. Furthermore, our results revealed a repeat of unit length 18-24 kb. This repeat was found not only in the pepper genome but also in the other solanaceous species, such as potato and tomato. These results represent a characteristic mechanism for large genome evolution in plants.

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

“…Complex patterns of nested insertions of LTR-RTs have also been found in intergenic regions of other plant species with large genomes (SanMiguel et al, 1996;Wicker et al, 2001;Wicker et al, 2005;Park et al, 2012b). In this study, the two BACs containing no functional gene structure, BACs 8D23 and 6J17, are likely to be representative of intergenic or heterochromatic regions in the ginseng genome.…”

“…(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).…”

A Glimpse of Panax ginseng Genome Structure Revealed from Ten BAC Clone Sequences Obtained by SMRT Sequencing Platform

“…1). The results suggest that LTR-RTs might play a major role in the increase of the genome size such as many other plants with large genomes size (SanMiguel et al 1996;Park et al 2012b).…”

Plant diversity and transcriptional variability assessed by retrotransposon-based molecular markers

“…LTR amplification technique displays is also efficient in examine genome structure and evolution in Solanaceous crop species, and in chromosome structure and transmission (Manetti et al, 2007(Manetti et al, , 2009Novakova et al, 2009;Park et al, 2012;Michael, 2014;Na et al, 2014;Tang et al, 2014).…”