Journal Article

Comparative analysis of miniature inverted–repeat transposable elements (MITEs) and long terminal repeat (LTR) retrotransposons in six Citrus species

Liu, Yan, Wang, Shuo, Ding, Yuduan, Xu, Qiang, Wu, Guizhi, Ke, Lingjun, Tahir ul Qamar, Muhammad, Feng, Jia-Wu, Chen, Ling-Ling

2019

Overview

Background Miniature inverted-repeat transposable elements (MITEs) and long terminal repeat (LTR) retrotransposons are ubiquitous in plants genomes, and highly important in their evolution and diversity. However, their mechanisms of insertion/amplification and roles in Citrus genome’s evolution/diversity are still poorly understood. Results To address this knowledge gap, we developed different computational pipelines to analyze, annotate and classify MITEs and LTR retrotransposons in six different sequenced Citrus species. We identified 62,010 full-length MITEs from 110 distinguished families. We observed MITEs tend to insert in gene related regions and enriched in promoters. We found that DTM63 is possibly an active Mutator -like MITE family in the traceable past and may still be active in Citrus . The insertion of MITEs resulted in massive polymorphisms and played an important role in Citrus genome diversity and gene structure variations. In addition, 6630 complete LTR retrotransposons and 13,371 solo-LTRs were identified. Among them, 12 LTR lineages separated before the differentiation of mono- and dicotyledonous plants. We observed insertion and deletion of LTR retrotransposons was accomplished with a dynamic balance, and their half-life in Citrus was ~ 1.8 million years. Conclusions These findings provide insights into MITEs and LTR retrotransposons and their roles in genome diversity in different Citrus genomes.

• Publisher: BioMed Central,Springer Nature B.V,BMC
• Subject: Active transposon families / Agriculture / Biomedical and Life Sciences / Citrinae / Citrus / Citrus - genetics / Citrus fruits / Comparative analysis / Computer applications / Deoxyribonucleic acid / DNA / DNA Transposable Elements - genetics / Evolution / family / Fruits / Gene expression / genes / Genetic Variation / Genome diversity / Genome, Plant - genetics / Genomes / Genomics / Genomics and evolution / half life / Insertion / Inverted Repeat Sequences - genetics / Life Sciences / Long terminal repeat / Long terminal repeat (LTR) / Miniature inverted–repeat transposable elements (MITEs) / Plant Sciences / Polymorphism / Proteins / Research Article / Retroelements - genetics / Retrotransposons / species / Studies / terminal repeat sequences / Terminal Repeat Sequences - genetics / Transfer RNA / Tree Biology