Stowaway miniature inverted repeat transposable elements are important agents driving recent genomic diversity in wild and cultivated carrot

Alicja Macko-Podgórni , Katarzyna Stelmach , Kornelia Kwolek , Dariusz Grzebelus

Abstract

Background: Miniature 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. Results: Fourteen 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. Conclusion: Stowaway MITEs have made a substantial contribution to the structural and functional variability of the carrot genome.
Author Alicja Macko-Podgórni (FoBaH / IoPBaB)
Alicja Macko-Podgórni,,
- Institute of Plant Biology and Biotechnology
, Katarzyna Stelmach (FoBaH / IoPBaB)
Katarzyna Stelmach,,
- Institute of Plant Biology and Biotechnology
, Kornelia Kwolek (FoBaH / IoPBaB)
Kornelia Kwolek,,
- Institute of Plant Biology and Biotechnology
, Dariusz Grzebelus (FoBaH / IoPBaB)
Dariusz Grzebelus,,
- Institute of Plant Biology and Biotechnology
Journal seriesMobile DNA, ISSN 1759-8753, (N/A 140 pkt)
Issue year2019
No10
Pages1-17
Publication size in sheets0.8
Article number47
Keywords in EnglishTransposable elements, Insertional polymorphism, TE-gene association, Mariner, DcSto, Daucus carota
ASJC Classification1312 Molecular Biology
DOIDOI:10.1186/s13100-019-0190-3
URL https://mobilednajournal.biomedcentral.com/track/pdf/10.1186/s13100-019-0190-3
Languageen angielski
LicenseJournal (articles only); author's original; Uznanie Autorstwa (CC-BY); after publication
Score (nominal)140
Score sourcejournalList
Publication indicators WoS Citations = 0; Scopus SNIP (Source Normalised Impact per Paper): 2016 = 0.809; WoS Impact Factor: 2018 = 3.63 (2) - 2018=4.405 (5)
Citation count*
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FinansowanieThe research was financed from (1) funds for basic research on crop improvement granted by the Polish Ministry of Agriculture and Rural Development, (2) MINIATURA1 (grant number 2017/01/X/NZ9/00930) granted by the Polish National Science Center, and (3) funds for the statutory activity of the Faculty of Biotechnology and Horticulture, University Macko-Podgórni et al. Mobile DNA (2019) 10:47 Page 14 of 17 of Agriculture in Krakow, granted by the Polish Ministry of Science and Higher Education.
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* presented citation count is obtained through Internet information analysis and it is close to the number calculated by the Publish or Perish system.
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