The Dynamics of Long Terminal Repeat Retrotransposon Proliferation and Decay Drive the Evolution of Genome Size Variation in Capsicum
<i>Capsicum</i> (pepper) is an economically vital genus in the <i>Solanaceae</i> family, with most species possessing about 3 Gb genomes. However, the recently sequenced <i>Capsicum rhomboideum</i> (~1.7 Gb) represents the first reported case of an extremely compa...
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| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2025-07-01
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| Series: | Plants |
| Subjects: | |
| Online Access: | https://www.mdpi.com/2223-7747/14/14/2136 |
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| Summary: | <i>Capsicum</i> (pepper) is an economically vital genus in the <i>Solanaceae</i> family, with most species possessing about 3 Gb genomes. However, the recently sequenced <i>Capsicum rhomboideum</i> (~1.7 Gb) represents the first reported case of an extremely compact genome in <i>Capsicum</i>, providing a unique and ideal model for studying genome size evolution. To elucidate the mechanisms driving this variation, we performed comparative genomic analyses between the compact <i>Capsicum rhomboideum</i> and the reference <i>Capsicum annuum</i> cv. CM334 (~2.9 Gb). Although their genome size differences initially suggested whole-genome duplication (WGD) as a potential driver, both species shared two ancient WGD events with identical timing, predating their divergence and thus ruling out WGD as a direct contributor to their size difference. Instead, transposable elements (TEs), particularly long terminal repeat retrotransposons (LTR-RTs), emerged as the dominant force shaping genome size variation. Genome size strongly correlated with LTR-RT abundance, and multiple LTR-RT burst events aligned with major phases of genome expansion. Notably, the integrity and transcriptional activity of LTR-RTs decline over evolutionary time; older insertions exhibit greater structural degradation and reduced activity, reflecting their dynamic nature. This study systematically delineated the evolutionary trajectory of LTR-RTs—from insertion and proliferation to decay–uncovering their pivotal role in driving <i>Capsicum</i> genome size evolution. Our findings advance the understanding of plant genome dynamics and provide a framework for studying genome size variation across diverse plant lineages. |
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| ISSN: | 2223-7747 |