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A chromosome-scale and haplotype-resolved genome assembly of carnation (Dianthus caryophyllus) based on high-fidelity sequencing

Dianthus caryophyllus is an economic species often considered excellent cut flowers and is suitable for bouquets and gardens. Here, we assembled the haplotype-resolved genome of D. caryophyllus ‘Aili’ at the chromosome level for the first time. The total lengths of the two assembled haplotypes of ca...

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Autores principales: Jiang, Heling, Zhang, Xiaoni, Leng, Luhong, Gong, Desheng, Zhang, Xiaohui, Liu, Junyang, Peng, Dan, Wu, Zhiqiang, Yang, Yingxue
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10437072/
https://www.ncbi.nlm.nih.gov/pubmed/37600187
http://dx.doi.org/10.3389/fpls.2023.1230836
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author Jiang, Heling
Zhang, Xiaoni
Leng, Luhong
Gong, Desheng
Zhang, Xiaohui
Liu, Junyang
Peng, Dan
Wu, Zhiqiang
Yang, Yingxue
author_facet Jiang, Heling
Zhang, Xiaoni
Leng, Luhong
Gong, Desheng
Zhang, Xiaohui
Liu, Junyang
Peng, Dan
Wu, Zhiqiang
Yang, Yingxue
author_sort Jiang, Heling
collection PubMed
description Dianthus caryophyllus is an economic species often considered excellent cut flowers and is suitable for bouquets and gardens. Here, we assembled the haplotype-resolved genome of D. caryophyllus ‘Aili’ at the chromosome level for the first time. The total lengths of the two assembled haplotypes of carnation were 584.88 Mb for haplotype genome 1 (hap1) and 578.78 Mb for haplotype genome 2 (hap2), respectively. We predicted a total of 44,098 and 42,425 protein-coding genes, respectively. The remarkable structure variation was identified between two haplotypes. Moreover, we identified 403.80 Mb of transposable elements (TEs) in hap1, which accounted for 69.34% of the genome. In contrast, hap2 had 402.70 Mb of TEs, representing 69.61% of the genome. Long terminal repeats were the predominant transposable elements. Phylogenetic analysis showed that the species differentiation time between carnation and gypsophila was estimated to be ~54.43 MYA. The unique gene families of carnation genomes were identified in ‘Aili’ and previously published ‘Francesco’ and ‘Scarlet Queen’. The assembled and annotated haplotype-resolved D. caryophyllus genome not only promises to facilitate molecular biology studies but also contributes to genome-level evolutionary studies.
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spelling pubmed-104370722023-08-19 A chromosome-scale and haplotype-resolved genome assembly of carnation (Dianthus caryophyllus) based on high-fidelity sequencing Jiang, Heling Zhang, Xiaoni Leng, Luhong Gong, Desheng Zhang, Xiaohui Liu, Junyang Peng, Dan Wu, Zhiqiang Yang, Yingxue Front Plant Sci Plant Science Dianthus caryophyllus is an economic species often considered excellent cut flowers and is suitable for bouquets and gardens. Here, we assembled the haplotype-resolved genome of D. caryophyllus ‘Aili’ at the chromosome level for the first time. The total lengths of the two assembled haplotypes of carnation were 584.88 Mb for haplotype genome 1 (hap1) and 578.78 Mb for haplotype genome 2 (hap2), respectively. We predicted a total of 44,098 and 42,425 protein-coding genes, respectively. The remarkable structure variation was identified between two haplotypes. Moreover, we identified 403.80 Mb of transposable elements (TEs) in hap1, which accounted for 69.34% of the genome. In contrast, hap2 had 402.70 Mb of TEs, representing 69.61% of the genome. Long terminal repeats were the predominant transposable elements. Phylogenetic analysis showed that the species differentiation time between carnation and gypsophila was estimated to be ~54.43 MYA. The unique gene families of carnation genomes were identified in ‘Aili’ and previously published ‘Francesco’ and ‘Scarlet Queen’. The assembled and annotated haplotype-resolved D. caryophyllus genome not only promises to facilitate molecular biology studies but also contributes to genome-level evolutionary studies. Frontiers Media S.A. 2023-08-04 /pmc/articles/PMC10437072/ /pubmed/37600187 http://dx.doi.org/10.3389/fpls.2023.1230836 Text en Copyright © 2023 Jiang, Zhang, Leng, Gong, Zhang, Liu, Peng, Wu and Yang https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Plant Science
Jiang, Heling
Zhang, Xiaoni
Leng, Luhong
Gong, Desheng
Zhang, Xiaohui
Liu, Junyang
Peng, Dan
Wu, Zhiqiang
Yang, Yingxue
A chromosome-scale and haplotype-resolved genome assembly of carnation (Dianthus caryophyllus) based on high-fidelity sequencing
title A chromosome-scale and haplotype-resolved genome assembly of carnation (Dianthus caryophyllus) based on high-fidelity sequencing
title_full A chromosome-scale and haplotype-resolved genome assembly of carnation (Dianthus caryophyllus) based on high-fidelity sequencing
title_fullStr A chromosome-scale and haplotype-resolved genome assembly of carnation (Dianthus caryophyllus) based on high-fidelity sequencing
title_full_unstemmed A chromosome-scale and haplotype-resolved genome assembly of carnation (Dianthus caryophyllus) based on high-fidelity sequencing
title_short A chromosome-scale and haplotype-resolved genome assembly of carnation (Dianthus caryophyllus) based on high-fidelity sequencing
title_sort chromosome-scale and haplotype-resolved genome assembly of carnation (dianthus caryophyllus) based on high-fidelity sequencing
topic Plant Science
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10437072/
https://www.ncbi.nlm.nih.gov/pubmed/37600187
http://dx.doi.org/10.3389/fpls.2023.1230836
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