Dataset Information

DcSto: carrot Stowaway-like elements are abundant, diverse, and polymorphic.

ABSTRACT: We investigated nine families of Stowaway-like miniature inverted-repeat transposable elements (MITEs) in the carrot genome, named DcSto1 to DcSto9. All of them were AT-rich and shared a highly conserved 6 bp-long TIR typical for Stowaways. The copy number of DcSto1 elements was estimated as ca. 5,000 per diploid genome. We observed preference for clustered insertions of DcSto and other MITEs. Distribution of DcSto1 hybridization signals revealed presence of DcSto1 clusters within euchromatic regions along all chromosomes. An arrangement of eight regions encompassing DcSto insertion sites, studied in detail, was highly variable among plants representing different populations of Daucus carota. All of these insertions were polymorphic which most likely suggests a very recent mobilization of those elements. Insertions of DcSto near carrot genes and presence of putative promoters, regulatory motifs, and polyA signals within their sequences might suggest a possible involvement of DcSto in the regulation of gene expression.

SUBMITTER: Macko-Podgorni A

PROVIDER: S-EPMC3695323 | biostudies-literature | 2013 Jun

REPOSITORIES: biostudies-literature

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DcSto: carrot Stowaway-like elements are abundant, diverse, and polymorphic.

Macko-Podgorni Alicja A Nowicka Anna A Grzebelus Ewa E Simon Philipp W PW Simon Philipp W PW Grzebelus Dariusz D

Genetica 20130618 4-6

We investigated nine families of Stowaway-like miniature inverted-repeat transposable elements (MITEs) in the carrot genome, named DcSto1 to DcSto9. All of them were AT-rich and shared a highly conserved 6 bp-long TIR typical for Stowaways. The copy number of DcSto1 elements was estimated as ca. 5,000 per diploid genome. We observed preference for clustered insertions of DcSto and other MITEs. Distribution of DcSto1 hybridization signals revealed presence of DcSto1 clusters within euchromatic re ...[more]

PMID: 23775534

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Project description:BackgroundMiniature inverted repeat transposable elements (MITEs) are small non-autonomous DNA transposons that are ubiquitous in plant genomes, and are mobilised by their autonomous relatives. Stowaway MITEs are derived from and mobilised by elements from the mariner superfamily. Those elements constitute a significant portion of the carrot genome; however the variation caused by Daucus carota Stowaway MITEs (DcStos), their association with genes and their putative impact on genome evolution has not been comprehensively analysed.ResultsFourteen families of Stowaway elements DcStos occupy about 0.5% of the carrot genome. We systematically analysed 31 genomes of wild and cultivated Daucus carota, yielding 18.5 thousand copies of these elements, showing remarkable insertion site polymorphism. DcSto element demography differed based on the origin of the host populations, and corresponded with the four major groups of D. carota, wild European, wild Asian, eastern cultivated and western cultivated. The DcStos elements were associated with genes, and most frequently occurred in 5' and 3' untranslated regions (UTRs). Individual families differed in their propensity to reside in particular segments of genes. Most importantly, DcSto copies in the 2 kb regions up- and downstream of genes were more frequently associated with open reading frames encoding transcription factors, suggesting their possible functional impact. More than 1.5% of all DcSto insertion sites in different host genomes contained different copies in exactly the same position, indicating the existence of insertional hotspots. The DcSto7b family was much more polymorphic than the other families in cultivated carrot. A line of evidence pointed at its activity in the course of carrot domestication, and identified Dcmar1 as an active carrot mariner element and a possible source of the transposition machinery for DcSto7b.ConclusionStowaway MITEs have made a substantial contribution to the structural and functional variability of the carrot genome.

Dataset Information

DcSto: carrot Stowaway-like elements are abundant, diverse, and polymorphic.

Publications

DcSto: carrot Stowaway-like elements are abundant, diverse, and polymorphic.

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