De novo assembly and characterization of the first draft genome of quince (Cydonia oblonga Mill.)

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dc.contributor.authorSoyturk, Aysenur
dc.contributor.authorSen, Fatima
dc.contributor.authorUncu, Ali Tevfik
dc.contributor.authorCelik, Ibrahim
dc.contributor.authorUncu, Ayse Ozgur
dc.date.accessioned2024-02-23T14:16:44Z
dc.date.available2024-02-23T14:16:44Z
dc.date.issued2021
dc.departmentNEÜen_US
dc.description.abstractQuince (Cydonia oblonga Mill.) is the sole member of the genus Cydonia in the Rosacea family and closely related to the major pome fruits, apple (Malus domestica Borkh.) and pear (Pyrus communis L.). In the present work, whole genome shotgun paired-end sequencing was employed in order to assemble the first draft genome of quince. A genome assembly that spans 488.4 Mb of sequence corresponding to 71.2% of the estimated genome size (686 Mb) was produced in the study. Gene predictions via ab initio and homology-based sequence annotation strategies resulted in the identification of 25,428 and 30,684 unique putative protein coding genes, respectively. 97.4 and 95.6% of putative homologs of Arabidopsis and rice transcription factors were identified in the ab initio predicted genic sequences. Different machine learning algorithms were tested for classifying pre-miRNA (precursor microRNA) coding sequences, identifying Support Vector Machine (SVM) as the best performing classifier. SVM classification predicted 600 putative pre-miRNA coding loci. Repetitive DNA content of the assembly was also characterized. The first draft assembly of the quince genome produced in this work would constitute a foundation for functional genomic research in quince toward dissecting the genetic basis of important traits and performing genomics-assisted breeding.en_US
dc.identifier.doi10.1038/s41598-021-83113-3
dc.identifier.issn2045-2322
dc.identifier.issue1en_US
dc.identifier.pmid33589687en_US
dc.identifier.scopus2-s2.0-85101431173en_US
dc.identifier.scopusqualityQ1en_US
dc.identifier.urihttps://doi.org/10.1038/s41598-021-83113-3
dc.identifier.urihttps://hdl.handle.net/20.500.12452/12769
dc.identifier.volume11en_US
dc.identifier.wosWOS:000623879500021en_US
dc.identifier.wosqualityQ2en_US
dc.indekslendigikaynakWeb of Scienceen_US
dc.indekslendigikaynakScopusen_US
dc.indekslendigikaynakPubMeden_US
dc.language.isoenen_US
dc.publisherNature Portfolioen_US
dc.relation.ispartofScientific Reportsen_US
dc.relation.publicationcategoryMakale - Uluslararası Hakemli Dergi - Kurum Öğretim Elemanıen_US
dc.rightsinfo:eu-repo/semantics/openAccessen_US
dc.subject[Keyword Not Available]en_US
dc.titleDe novo assembly and characterization of the first draft genome of quince (Cydonia oblonga Mill.)en_US
dc.typeArticleen_US

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