Abstract Detail

Comparative Genomics/Transcriptomics

Ou, Shujun [1], Jiang, Ning [2].

Dynamic of LTR Retrotransposons in Plant Genome Evolution.

Plant genome varies more than three magnitudes in size. The vastly different DNA content but the similar evolutionary complexity of plant genomes result in the well-known C-value paradox, which could be largely explained by the varying amount of transposable elements, especially the long terminal repeat (LTR) retrotransposons. LTR retrotransposons are prevalent in plant genomes, the identification of which is efficient based on its well-conserved structure. Out of many available programs, we developed a much more accurate but also sensitive program, LTR_retriever, to achieve high-quality LTR annotation. In addition to finding canonical LTR-RTs with 5'-TG…CA-3' termini, LTR_retriever also identifies non-canonical LTR-RTs (non-TGCA), which have been largely ignored in genome-wide studies. We identified seven types of non-canonical LTRs from 50 plant genomes. The majority of non-canonical LTRs are Copia elements, with which the LTR is four times shorter than that of canonical Copia elements, which may be a result of their target specificity. Strikingly, non-TGCA Copia elements are often located in genic regions and preferentially insert nearby or within genes, indicating their impact on the evolution of genes and potential as mutagenesis tools. Further, we show that small genomes may be able to remove LTR retrotransposons efficiently, providing insights about mechanisms guard against genome obesity.

Related Links:
The paper published in Plant Physiology
Link to the software download (GitHub)

1 - Michigan State University, 1066 Bogue St, Room A326, East Lansing, MI, 48823, United States
2 - Michigan State University, 1066 Bogue St, Room A330, East Lansing, MI, 48823, United States

LTR retrotransposon
genome size
genome evolution.

Presentation Type: Oral Paper
Number: 0002
Abstract ID:647
Candidate for Awards:Margaret Menzel Award

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