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

• Published in: The Plant journal : for cell and molecular biology Vol. 69; no. 6; pp. 1018 - 1029
• Main Authors: Park, Minkyu, Park, Jongsun, Kim, Seungill, Kwon, Jin‐Kyung, Park, Hye Mi, Bae, Ik Hyun, Yang, Tae‐Jin, Lee, Yong‐Hwan, Kang, Byoung‐Cheorl, Choi, Doil
• Format: Journal Article
• Language: English
• Published: Oxford, UK Blackwell Publishing Ltd 01.03.2012; Blackwell
• Subjects: Biological and medical sciences; Capsicum - classification; Capsicum - genetics; Capsicum - metabolism; Capsicum annuum; Chromosomes, Artificial, Bacterial - genetics; Chromosomes, Artificial, Bacterial - metabolism; Euchromatin - genetics; Euchromatin - metabolism; Evolution; Evolution & development; Evolution, Molecular; Flowers & plants; Fundamental and applied biological sciences. Psychology; Genic rearrangement. Recombination. Transposable element; genome expansion; Genome Size; Genome, Plant; Genomes; Heterochromatin; Heterochromatin - genetics; Heterochromatin - metabolism; In Situ Hybridization, Fluorescence; Long terminal repeat; LTR retrotransposon; Lycopersicon esculentum; Molecular and cellular biology; Molecular genetics; Phylogeny; Plant biology; Plant physiology and development; Plant Proteins - classification; Plant Proteins - genetics; Plant Proteins - metabolism; Retroelements; Retrotransposons; Solanum tuberosum; tandem repeat; Tandem Repeat Sequences; Terminal Repeat Sequences; Retrotransposon; tandem repeat; Transposable element; Tandemly repeated sequence; genome expansion; Accumulation; Molecular evolution; Heterochromatin; Dicotyledones; Angiospermae; Capsicum annuum; Spermatophyta; Solanaceae; Genome; Expansion; LTR retrotransposon
• ISSN: 0960-7412; 1365-313X
• DOI: 10.1111/j.1365-313X.2011.04851.x

Summary Although 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 long‐unit 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.