Genome reconstruction in Cynara cardunculus taxa gains access to chromosome-scale DNA variation

Abstract The genome sequence of globe artichoke (Cynara cardunculus L. var. scolymus, 2n = 2x = 34) is now available for use. A survey of C. cardunculus genetic resources is essential for understanding the evolution of the species, carrying out genetic studies and for application of breeding strateg...

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Autores principales:	Alberto Acquadro, Lorenzo Barchi, Ezio Portis, Giulio Mangino, Danila Valentino, Giovanni Mauromicale, Sergio Lanteri
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2017
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/439871683f904366bc9e6415b76e2921
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spelling	oai:doaj.org-article:439871683f904366bc9e6415b76e29212021-12-02T12:32:16ZGenome reconstruction in Cynara cardunculus taxa gains access to chromosome-scale DNA variation10.1038/s41598-017-05085-72045-2322https://doaj.org/article/439871683f904366bc9e6415b76e29212017-07-01T00:00:00Zhttps://doi.org/10.1038/s41598-017-05085-7https://doaj.org/toc/2045-2322Abstract The genome sequence of globe artichoke (Cynara cardunculus L. var. scolymus, 2n = 2x = 34) is now available for use. A survey of C. cardunculus genetic resources is essential for understanding the evolution of the species, carrying out genetic studies and for application of breeding strategies. We report on the resequencing analyses (~35×) of four globe artichoke genotypes, representative of the core varietal types, as well as a genotype of the related taxa cultivated cardoon. The genomes were reconstructed at a chromosomal scale and structurally/functionally annotated. Gene prediction indicated a similar number of genes, while distinctive variations in miRNAs and resistance gene analogues (RGAs) were detected. Overall, 23,5 M SNP/indel were discovered (range 6,34 M –14,50 M). The impact of some missense SNPs on the biological functions of genes involved in the biosynthesis of phenylpropanoid and sesquiterpene lactone secondary metabolites was predicted. The identified variants contribute to infer on globe artichoke domestication of the different varietal types, and represent key tools for dissecting the path from sequence variation to phenotype. The new genomic sequences are fully searchable through independent Jbrowse interfaces (www.artichokegenome.unito.it), which allow the analysis of collinearity and the discovery of genomic variants, thus representing a one-stop resource for C. cardunculus genomics.Alberto AcquadroLorenzo BarchiEzio PortisGiulio ManginoDanila ValentinoGiovanni MauromicaleSergio LanteriNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 7, Iss 1, Pp 1-15 (2017)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Alberto Acquadro Lorenzo Barchi Ezio Portis Giulio Mangino Danila Valentino Giovanni Mauromicale Sergio Lanteri Genome reconstruction in Cynara cardunculus taxa gains access to chromosome-scale DNA variation
description	Abstract The genome sequence of globe artichoke (Cynara cardunculus L. var. scolymus, 2n = 2x = 34) is now available for use. A survey of C. cardunculus genetic resources is essential for understanding the evolution of the species, carrying out genetic studies and for application of breeding strategies. We report on the resequencing analyses (~35×) of four globe artichoke genotypes, representative of the core varietal types, as well as a genotype of the related taxa cultivated cardoon. The genomes were reconstructed at a chromosomal scale and structurally/functionally annotated. Gene prediction indicated a similar number of genes, while distinctive variations in miRNAs and resistance gene analogues (RGAs) were detected. Overall, 23,5 M SNP/indel were discovered (range 6,34 M –14,50 M). The impact of some missense SNPs on the biological functions of genes involved in the biosynthesis of phenylpropanoid and sesquiterpene lactone secondary metabolites was predicted. The identified variants contribute to infer on globe artichoke domestication of the different varietal types, and represent key tools for dissecting the path from sequence variation to phenotype. The new genomic sequences are fully searchable through independent Jbrowse interfaces (www.artichokegenome.unito.it), which allow the analysis of collinearity and the discovery of genomic variants, thus representing a one-stop resource for C. cardunculus genomics.
format	article
author	Alberto Acquadro Lorenzo Barchi Ezio Portis Giulio Mangino Danila Valentino Giovanni Mauromicale Sergio Lanteri
author_facet	Alberto Acquadro Lorenzo Barchi Ezio Portis Giulio Mangino Danila Valentino Giovanni Mauromicale Sergio Lanteri
author_sort	Alberto Acquadro
title	Genome reconstruction in Cynara cardunculus taxa gains access to chromosome-scale DNA variation
title_short	Genome reconstruction in Cynara cardunculus taxa gains access to chromosome-scale DNA variation
title_full	Genome reconstruction in Cynara cardunculus taxa gains access to chromosome-scale DNA variation
title_fullStr	Genome reconstruction in Cynara cardunculus taxa gains access to chromosome-scale DNA variation
title_full_unstemmed	Genome reconstruction in Cynara cardunculus taxa gains access to chromosome-scale DNA variation
title_sort	genome reconstruction in cynara cardunculus taxa gains access to chromosome-scale dna variation
publisher	Nature Portfolio
publishDate	2017
url	https://doaj.org/article/439871683f904366bc9e6415b76e2921
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Genome reconstruction in Cynara cardunculus taxa gains access to chromosome-scale DNA variation

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