Bioinformatic and Molecular Analysis of Satellite Repeat Diversity in Vaccinium Genomes

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dc.authoridSULTANA, NUSRAT/0000-0003-1373-1286
dc.authoridHeitkam, Tony/0000-0003-0168-8428
dc.contributor.authorSultana, Nusrat
dc.contributor.authorMenzel, Gerhard
dc.contributor.authorHeitkam, Tony
dc.contributor.authorKojima, Kenji K.
dc.contributor.authorBao, Weidong
dc.contributor.authorSerce, Sedat
dc.date.accessioned2024-11-07T13:32:36Z
dc.date.available2024-11-07T13:32:36Z
dc.date.issued2020
dc.departmentNiğde Ömer Halisdemir Üniversitesi
dc.description.abstractBioinformatic 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.
dc.description.sponsorshipScientific Research Projects Unit (BAP) of Nigde Omer Halisdemir University; Scientific and Technological Research Council of Turkey (TUBITAK) [TUBITAK-2215]
dc.description.sponsorshipThis research was funded by Scientific Research Projects Unit (BAP) of Ni.gde Omer Halisdemir University with BAP provided FEB 2017/18 DOKTEP project. N.S. was funded by the Scientific and Technological Research Council of Turkey (TUBITAK), which provided the TUBITAK-2215 graduate scholarship program and fellowship for Erasmus+ student traineeship program during her Ph.D. research work.
dc.identifier.doi10.3390/genes11050527
dc.identifier.issn2073-4425
dc.identifier.issue5
dc.identifier.pmid32397417
dc.identifier.scopus2-s2.0-85084503747
dc.identifier.scopusqualityQ2
dc.identifier.urihttps://doi.org/10.3390/genes11050527
dc.identifier.urihttps://hdl.handle.net/11480/15514
dc.identifier.volume11
dc.identifier.wosWOS:000542276700021
dc.identifier.wosqualityQ2
dc.indekslendigikaynakWeb of Science
dc.indekslendigikaynakScopus
dc.indekslendigikaynakPubMed
dc.language.isoen
dc.publisherMdpi
dc.relation.ispartofGenes
dc.relation.publicationcategoryMakale - Uluslararası Hakemli Dergi - Kurum Öğretim Elemanı
dc.rightsinfo:eu-repo/semantics/openAccess
dc.snmzKA_20241106
dc.subjectVaccinium
dc.subjecttandem repeat
dc.subjectsatellite DNA
dc.subjecthigher order repeat (HOR)
dc.subjecttransposable elements
dc.titleBioinformatic and Molecular Analysis of Satellite Repeat Diversity in Vaccinium Genomes
dc.typeArticle

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