Genome-wide analysis of long terminal repeat retrotransposons from the cranberry Vaccinium macrocarpon

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dc.authoridGarcia, Sonia/0000-0002-3143-0527
dc.contributor.authorSultana, Nusrat
dc.contributor.authorMenzel, Gerhard
dc.contributor.authorSeibt, Kathrin M.
dc.contributor.authorGarcia, Sonia
dc.contributor.authorWeber, Beatrice
dc.contributor.authorSerce, Sedat
dc.contributor.authorHeitkam, Tony
dc.date.accessioned2024-11-07T13:34:53Z
dc.date.available2024-11-07T13:34:53Z
dc.date.issued2022
dc.departmentNiğde Ömer Halisdemir Üniversitesi
dc.description.abstractBACKGROUND: Long terminal repeat (LTR) retrotransposons are widespread in plant genomes and play a large role in the generation of genomic variation. Despite this, their identification and characterization remains challenging, especially for non-model genomes. Hence, LTR retrotransposons remain undercharacterized in Vaccinium genomes, although they may be beneficial for current berry breeding efforts. OBJECTIVE: Exemplarily focusing on the genome of American cranberry (Vaccinium macrocarpon Aiton), we aim to generate an overview of the LTR retrotransposon landscape, highlighting the abundance, transcriptional activity, sequence, and structure of the major retrotransposon lineages. METHODS: Graph-based clustering of whole genome shotgun Illumina reads was performed to identify the most abundant LTR retrotransposons and to reconstruct representative in silico full-length elements. To generate insights into the LTR retrotransposon diversity in V. macrocarpon, we also queried the genome assembly for presence of reverse transcriptases (RTs), the key domain of LTR retrotransposons. Using transcriptomic data, transcriptional activity of retrotransposons corresponding to the consensuses was analyzed. RESULTS: We provide an in-depth characterization of the LTR retrotransposon landscape in the V. macrocarpon genome. Based on 475 RTs harvested from the genome assembly, we detect a high retrotransposon variety, with all major lineages present. To better understand their structural hallmarks, we reconstructed 26 Ty1-copia and 28 Ty3-gypsy in silico consensuses that capture the detected diversity. Accordingly, we frequently identify association with tandemly repeated motifs, extra open reading frames, and specialized, lineage-typical domains. Based on the overall high genomic abundance and transcriptional activity, we suggest that retrotransposons of the Ale and Athila lineages are most promising to monitor retrotransposon-derived polymorphisms across accessions. CONCLUSIONS: We conclude that LTR retrotransposons are major components of the V. macrocarpon genome. The representative consensuses provide an entry point for further Vaccinium genome analyses and may be applied to derive molecular markers for enhancing cranberry selection and breeding.
dc.description.sponsorshipJagannath University, Bangladesh; Georg Forster fellowship of the Alexander von Humboldt Foundation
dc.description.sponsorshipThis work also acknowledges the financial support by the Jagannath University, Bangladesh, in the form of study grants as well as the Georg Forster fellowship of the Alexander von Humboldt Foundation awarded to NS.
dc.identifier.doi10.3233/JBR-211515
dc.identifier.endpage185
dc.identifier.issn1878-5093
dc.identifier.issn1878-5123
dc.identifier.issue2
dc.identifier.scopus2-s2.0-85132372549
dc.identifier.scopusqualityQ2
dc.identifier.startpage165
dc.identifier.urihttps://doi.org/10.3233/JBR-211515
dc.identifier.urihttps://hdl.handle.net/11480/16231
dc.identifier.volume12
dc.identifier.wosWOS:000813467000002
dc.identifier.wosqualityQ3
dc.indekslendigikaynakWeb of Science
dc.indekslendigikaynakScopus
dc.language.isoen
dc.publisherIos Press
dc.relation.ispartofJournal of Berry Research
dc.relation.publicationcategoryMakale - Uluslararası Hakemli Dergi - Kurum Öğretim Elemanı
dc.rightsinfo:eu-repo/semantics/openAccess
dc.snmzKA_20241106
dc.subjectCranberry
dc.subjectVaccinium macrocarpon
dc.subjectrepetitive DNA
dc.subjectLTR retrotransposon
dc.subjectTy1-copia
dc.subjectTy3-gypsy
dc.titleGenome-wide analysis of long terminal repeat retrotransposons from the cranberry Vaccinium macrocarpon
dc.typeArticle

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