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Young, intact and nested retrotransposons are abundant in the onion and asparagus genomes.
Ann Bot. 2013 Sep; 112(5):881-9.AB

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. Specifically, several available onion and asparagus bacterial artificial 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 asparagus 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 particularly 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 retrotransposons 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.

Authors+Show Affiliations

CNRS, UMR de Génétique Végétale, Ferme du Moulon, F-91190 Gif sur Yvette, France. vitte@moulon.inra.frNo affiliation info availableNo affiliation info availableNo affiliation info available

Pub Type(s)

Journal Article
Research Support, U.S. Gov't, Non-P.H.S.

Language

eng

PubMed ID

23887091

Citation

Vitte, C, et al. "Young, Intact and Nested Retrotransposons Are Abundant in the Onion and Asparagus Genomes." Annals of Botany, vol. 112, no. 5, 2013, pp. 881-9.
Vitte C, Estep MC, Leebens-Mack J, et al. Young, intact and nested retrotransposons are abundant in the onion and asparagus genomes. Ann Bot. 2013;112(5):881-9.
Vitte, C., Estep, M. C., Leebens-Mack, J., & Bennetzen, J. L. (2013). Young, intact and nested retrotransposons are abundant in the onion and asparagus genomes. Annals of Botany, 112(5), 881-9. https://doi.org/10.1093/aob/mct155
Vitte C, et al. Young, Intact and Nested Retrotransposons Are Abundant in the Onion and Asparagus Genomes. Ann Bot. 2013;112(5):881-9. PubMed PMID: 23887091.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Young, intact and nested retrotransposons are abundant in the onion and asparagus genomes. AU - Vitte,C, AU - Estep,M C, AU - Leebens-Mack,J, AU - Bennetzen,J L, Y1 - 2013/07/25/ PY - 2013/7/27/entrez PY - 2013/7/28/pubmed PY - 2014/3/4/medline KW - Allium cepa KW - Asparagales KW - Asparagus officinalis KW - BAC annotation KW - LTR retrotransposons KW - garden asparagus KW - onion KW - transposable elements SP - 881 EP - 9 JF - Annals of botany JO - Ann Bot VL - 112 IS - 5 N2 - 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. Specifically, several available onion and asparagus bacterial artificial 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 asparagus 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 particularly 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 retrotransposons 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. SN - 1095-8290 UR - https://www.unboundmedicine.com/medline/citation/23887091/Young_intact_and_nested_retrotransposons_are_abundant_in_the_onion_and_asparagus_genomes_ L2 - https://academic.oup.com/aob/article-lookup/doi/10.1093/aob/mct155 DB - PRIME DP - Unbound Medicine ER -