Dataset Information

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

ABSTRACT:

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.

SUBMITTER: Liu Y

PROVIDER: S-EPMC6466647 | biostudies-literature | 2019 Apr

REPOSITORIES: biostudies-literature

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Publications

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

Liu Yan Y Tahir Ul Qamar Muhammad M Feng Jia-Wu JW Ding Yuduan Y Wang Shuo S Wu Guizhi G Ke Lingjun L Xu Qiang Q Chen Ling-Ling LL

BMC plant biology 20190415 1

<h4>Background</h4>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.<h4>Results</h4>To address this knowledge gap, we developed different computational pipelines to analyze, annotate and classify MITEs and LTR retrotransposons ...[more]

PMID: 30987586

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Project description:BackgroundCoxiella burnetii is a Gram-negative gammaproteobacterium and zoonotic agent of Q fever. C. burnetii's genome contains an abundance of pseudogenes and numerous selfish genetic elements. MITEs (miniature inverted-repeat transposable elements) are non-autonomous transposons that occur in all domains of life and are thought to be insertion sequences (ISs) that have lost their transposase function. Like most transposable elements (TEs), MITEs are thought to play an active role in evolution by altering gene function and expression through insertion and deletion activities. However, information regarding bacterial MITEs is limited.ResultsWe describe two MITE families discovered during research on small non-coding RNAs (sRNAs) of C. burnetii. Two sRNAs, Cbsr3 and Cbsr13, were found to originate from a novel MITE family, termed QMITE1. Another sRNA, CbsR16, was found to originate from a separate and novel MITE family, termed QMITE2. Members of each family occur ~ 50 times within the strains evaluated. QMITE1 is a typical MITE of 300-400 bp with short (2-3 nt) direct repeats (DRs) of variable sequence and is often found overlapping annotated open reading frames (ORFs). Additionally, QMITE1 elements possess sigma-70 promoters and are transcriptionally active at several loci, potentially influencing expression of nearby genes. QMITE2 is smaller (150-190 bps), but has longer (7-11 nt) DRs of variable sequences and is mainly found in the 3' untranslated region of annotated ORFs and intergenic regions. QMITE2 contains a GTAG repetitive extragenic palindrome (REP) that serves as a target for IS1111 TE insertion. Both QMITE1 and QMITE2 display inter-strain linkage and sequence conservation, suggesting that they are adaptive and existed before divergence of C. burnetii strains.ConclusionsWe have discovered two novel MITE families of C. burnetii. Our finding that MITEs serve as a source for sRNAs is novel. QMITE2 has a unique structure and occurs in large or small versions with unique DRs that display linkage and sequence conservation between strains, allowing for tracking of genomic rearrangements. QMITE1 and QMITE2 copies are hypothesized to influence expression of neighboring genes involved in DNA repair and virulence through transcriptional interference and ribonuclease processing.

Dataset Information

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

Background

Results

Conclusions

Publications

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

Similar Datasets

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