Young, Intact And Nested Retrotransposons Are Abundant In The Onion And Asparagus Genomes

ASU Author/Contributor (non-ASU co-authors, if there are any, appear on document)
Matt Estep, Assistant Professor (Creator)
Appalachian State University (ASU )
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Abstract: Background and Aims Although monocotyledonous plants comprise one of the two major groups of angiosperms and include .65 000 species, comprehensive genome analysis has been focused mainly on the Poaceae (grass) family. Due to this bias, most of the conclusions that have been drawn for monocot genome evolution are based on grasses. It is not known whether these conclusions apply to many other monocots.† Methods To extend our understanding of genome evolution in the monocots, Asparagales genomic sequence data were acquired and the structural properties of asparagus and onion genomes were analysed. Speci?cally, several available onion and asparagus bacterial arti?cial chromosomes (BACs) with contig sizes .35 kb were annotated and analysed, with a particular focus on the characterization of long terminal repeat (LTR) retrotransposons.† Key Results The results reveal that LTR retrotransposons are the major components of the onion and garden aspara-gus genomes. These elements are mostly intact (i.e. with two LTRs), have mainly inserted within the past 6 million years and are piled up into nested structures. Analysis of shotgun genomic sequence data and the observation of two copies for some transposable elements (TEs) in annotated BACs indicates that some families have become particu-larly abundant, as high as 4–5 % (asparagus) or 3–4 % (onion) of the genome for the most abundant families, as also seen in large grass genomes such as wheat and maize.† Conclusions Although previous annotations of contiguous genomic sequences have suggested that LTR retrotran-sposons were highly fragmented in these two Asparagales genomes, the results presented here show that this was largely due to the methodology used. In contrast, this current work indicates an ensemble of genomic features similar to those observed in the Poaceae.

Additional Information

C. Vitte, M. C. Estep, J. Leebens-Mack and J. L. Bennetzen (2013) "Young, Intact And Nested Retrotransposons Are Abundant In The Onion And Asparagus Genomes."Annals of Botany. Version of Record Available At [doi:10.1093/aob/mct155]
Language: English
Date: 2013
Asparagus officinalis, Allium cepa, garden asparagus, onion, Asparagales, transposable elements, LTR retrotransposons, BAC annotation.

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