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    Bioinformatic and Molecular Analysis of Satellite Repeat Diversity in Vaccinium Genomes
    (Mdpi, 2020) Sultana, Nusrat; Menzel, Gerhard; Heitkam, Tony; Kojima, Kenji K.; Bao, Weidong; Serce, Sedat
    Bioinformatic and molecular characterization of satellite repeats was performed to understand the impact of their diversification onVacciniumgenome evolution. Satellite repeat diversity was evaluated in four cultivated and wild species, including the diploid speciesVaccinium myrtillusandVaccinium uliginosum, as well as the tetraploid speciesVaccinium corymbosumandVaccinium arctostaphylos. We comparatively characterized six satellite repeat families using in total 76 clones with 180 monomers. We observed that the monomer units of VaccSat1, VaccSat2, VaccSat5, and VaccSat6 showed a higher order repeat (HOR) structure, likely originating from the organization of two adjacent subunits with differing similarity, length and size. Moreover, VaccSat1, VaccSat3, VaccSat6, and VaccSat7 were found to have sequence similarity to parts of transposable elements. We detected satellite-typical tandem organization for VaccSat1 and VaccSat2 in long arrays, while VaccSat5 and VaccSat6 distributed in multiple sites over all chromosomes of tetraploidV. corymbosum, presumably in long arrays. In contrast, very short arrays of VaccSat3 and VaccSat7 are dispersedly distributed over all chromosomes in the same species, likely as internal parts of transposable elements. We provide a comprehensive overview on satellite species specificity inVaccinium, which are potentially useful as molecular markers to address the taxonomic complexity of the genus, and provide information for genome studies of this genus.
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    Bioinformatics and molecular characterization of tandemly organized repetitive DNA family in highbush blueberry (Vaccinium corymbosum L.) cultivar 'Jubilee' genome
    (Niğde Ömer Halisdemir Üniversitesi / Fen Bilimleri Enstitüsü, 2018) Sultana, Nusrat; Serçe, Sedat
    Vaccinium is a taxonomically diverse genus. Subgenus and species are mostly prone to extensive polyploidization within intra and interspecies level. In this study, Vaccinium genome analysis has been performed through ploidy level estimation and repetitive DNA exploration using RepeatExplorer software. It is found that total percentage of repetitive sequences is 80 and 90% in blueberry (Vaccinium corymbosum L.) and cranberry genome (Vaccinium macrocarpon Ait.), respectively. The main portion of which belong to transposable elements, satellite repeats and rDNA sequences. A total of six different satellite families, 28 full-length Ty3/gypsy and 26 Ty1/copia LTR-retrotransposon are identified from the Vaccinium genome. Internal structural features of both satellite repeats and LTR retrotansposons are characterized. Cloning and molecular characterization of satellite repeats from five different sections (Cyanococcus, Oxycococcus, Myrtillus, Hemimyrtillus and Vaccinium) of the genus Vaccinium revealed that VaccSat1, 5 and 6 have some levels of species specificity, while VaccSat2, 3 and 7 are common satellite families in all studied species. The results from this investigation suggest VaccSat1, 5 and 6 can be used as markers for species identification. Overall, the results from this research expand the limited knowledge about Vaccinium genome structure and evolution.
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    Contribution to the knowledge of genome size evolution in edible blueberries (genus Vaccinium)
    (Ios Press, 2020) Sultana, Nusrat; Pascual-Diaz, Joan Pere; Gers, Ahsen; Ilga, Kubra; Serce, Sedat; Vitales, Daniel; Garcia, Sonia
    BACKGROUND: Vaccinium is one of the largest genera (ca. 500 species) of Ericaceae, well known for its edible and ornamental uses. Although there is certain karyological knowledge, information about genome size (GS) is scarce in the genus. OBJECTIVE: The main goal is providing GS data for several Vaccinium species with prevalence in Europe and Western Asia and analysing global GS variation in the genus, considering available data and phylogenetic context. METHODS: New GS assessments were obtained by flow cytometry and chromosome counts were verified. Phylogenetic analyses (using nuclear ITS, and chloroplastic matK and ndhF) were performed by Bayesian inference and reconstruction of ancestral GS by maximum parsimony. RESULTS: We obtained GS data for five Vaccinium species (13 populations). Three species are reported for the first time. Values (2C) ranged between 1.16-1.47 pg at the diploid (2n = 24) and between 3.13-3.16 pg at the tetraploid (2n = 48) levels. The five species here investigated have been placed and analysed in a reconstructed phylogenetic background (including 68 taxa). CONCLUSIONS: GS values of Vaccinium can be considered very small. The preliminary reconstruction of ancestral GS would point to a reduction in Vaccinium, although more data is needed to establish global GS evolutionary trend in the genus.
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    Genome size constancy in Antarctic populations ofColobanthus quitensisandDeschampsia antarctica
    (Springer, 2020) Pere Pascual-Diaz, Joan; Serce, Sedat; Hradecka, Ivana; Vanek, Martin; Ozdemir, Bahar Sogutmaz; Sultana, Nusrat; Vural, Mehtap
    Colobanthus quitensis(Kunth) Bartl. andDeschampsia antarcticaDesv., the only two native flowering plants in the Antarctica, are interesting study cases from the ecological, biogeographic, and evolutionary points of view. Here, we present the first genome size analysis focused in several populations from the Antarctic Peninsula and the surrounding islands for both species, with a broad sampling distributed along a distance of 800 km. We have used flow cytometry to estimate genome size, being the first time that this technique is used forD. antarctica.Average genome sizes forD. antarctica(2C = 10.63 pg) andC. quintesis(2C = 2.01 pg) are consistent with the scarce previous data available, and point to a diploid and tetraploid ploidy level, respectively, for the analysed taxa. Despite a certain deviating individual inD. antarctica, whose higher genome size could suggest the existence of B-chromosomes, no significant genome size differences were found amongst the populations studied, for both species, which might be related with the recent colonisation history of the Antarctic continent.
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    Genome-wide analysis of long terminal repeat retrotransposons from the cranberry Vaccinium macrocarpon
    (Ios Press, 2022) Sultana, Nusrat; Menzel, Gerhard; Seibt, Kathrin M.; Garcia, Sonia; Weber, Beatrice; Serce, Sedat; Heitkam, Tony
    BACKGROUND: 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.