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

Abstract Quince (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 as...

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Autores principales:	Aysenur Soyturk, Fatima Sen, Ali Tevfik Uncu, Ibrahim Celik, Ayse Ozgur Uncu
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/9c31467d14774bfebe9d07d95d114fb8
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spelling	oai:doaj.org-article:9c31467d14774bfebe9d07d95d114fb82021-12-02T14:21:51ZDe novo assembly and characterization of the first draft genome of quince (Cydonia oblonga Mill.)10.1038/s41598-021-83113-32045-2322https://doaj.org/article/9c31467d14774bfebe9d07d95d114fb82021-02-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-83113-3https://doaj.org/toc/2045-2322Abstract Quince (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.Aysenur SoyturkFatima SenAli Tevfik UncuIbrahim CelikAyse Ozgur UncuNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-11 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Aysenur Soyturk Fatima Sen Ali Tevfik Uncu Ibrahim Celik Ayse Ozgur Uncu De novo assembly and characterization of the first draft genome of quince (Cydonia oblonga Mill.)
description	Abstract Quince (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.
format	article
author	Aysenur Soyturk Fatima Sen Ali Tevfik Uncu Ibrahim Celik Ayse Ozgur Uncu
author_facet	Aysenur Soyturk Fatima Sen Ali Tevfik Uncu Ibrahim Celik Ayse Ozgur Uncu
author_sort	Aysenur Soyturk
title	De novo assembly and characterization of the first draft genome of quince (Cydonia oblonga Mill.)
title_short	De novo assembly and characterization of the first draft genome of quince (Cydonia oblonga Mill.)
title_full	De novo assembly and characterization of the first draft genome of quince (Cydonia oblonga Mill.)
title_fullStr	De novo assembly and characterization of the first draft genome of quince (Cydonia oblonga Mill.)
title_full_unstemmed	De novo assembly and characterization of the first draft genome of quince (Cydonia oblonga Mill.)
title_sort	de novo assembly and characterization of the first draft genome of quince (cydonia oblonga mill.)
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/9c31467d14774bfebe9d07d95d114fb8
work_keys_str_mv	AT aysenursoyturk denovoassemblyandcharacterizationofthefirstdraftgenomeofquincecydoniaoblongamill AT fatimasen denovoassemblyandcharacterizationofthefirstdraftgenomeofquincecydoniaoblongamill AT alitevfikuncu denovoassemblyandcharacterizationofthefirstdraftgenomeofquincecydoniaoblongamill AT ibrahimcelik denovoassemblyandcharacterizationofthefirstdraftgenomeofquincecydoniaoblongamill AT ayseozguruncu denovoassemblyandcharacterizationofthefirstdraftgenomeofquincecydoniaoblongamill
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De novo assembly and characterization of the first draft genome of quince (Cydonia oblonga Mill.)

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