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Telomere-to-telomere and haplotype-resolved genome assembly of the Chinese cork oak (Quercus variabilis)

Wang, Longxin (author)
School of Biological Science and Technology, University of Jinan, Jinan, China
Li, Lei-Lei (author)
Key Laboratory of Crop Genetic Improvement & Ecology and Physiology, Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences, Jinan, China
Chen, Li (author)
Shandong Saienfu Stem Cell Engineering Group Co., Ltd, Jinan, China
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Zhang, Ren-Gang (author)
Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Yunnan, Kunming, China
Zhao, Shi-Wei (author)
Umeå universitet,Institutionen för fysiologisk botanik
Yan, Han (author)
The Second Affiliated Hospital of Shandong First Medical University, Taian, China
Gao, Jie (author)
Chinese Academy of Sciences (CAS), Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, China
Chen, Xue (author)
Weifang Academy of Agricultural Sciences, Weifang, China
Si, Yu-Jun (author)
Weifang Academy of Agricultural Sciences, Weifang, China
Chen, Zhe (author)
InvoGenomics Biotechnology Co., Ltd., Jinan, China
Liu, Haibo (author)
Jinan Academy of Landscape and Forestry Science, Jinan, China
Xie, Xiao-Man (author)
Key Laboratory of State Forestry and Grassland Administration Conservation and Utilization of Warm Temperate Zone Forest and Grass Germplasm Resources, Shandong Provincial Center of Forest and Grass Germplasm Resources, Jinan, China
Zhao, Wei (author)
Umeå universitet,Institutionen för ekologi, miljö och geovetenskap,Umeå Plant Science Centre (UPSC)
Han, Biao (author)
Key Laboratory of State Forestry and Grassland Administration Conservation and Utilization of Warm Temperate Zone Forest and Grass Germplasm Resources, Shandong Provincial Center of Forest and Grass Germplasm Resources, Jinan, China
Qin, Xiaochun (author)
School of Biological Science and Technology, University of Jinan, Jinan, China
Jia, Kai-Hua (author)
Key Laboratory of Crop Genetic Improvement & Ecology and Physiology, Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences, Jinan, China
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 (creator_code:org_t)
Frontiers Media S.A. 2023
2023
English.
In: Frontiers in Plant Science. - : Frontiers Media S.A.. - 1664-462X. ; 14
Related links:
https://doi.org/10.3...
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https://umu.diva-por... (primary) (Raw object)
https://urn.kb.se/re...
https://doi.org/10.3...
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  • Journal article (peer-reviewed)
Abstract Subject headings
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  • The Quercus variabilis, a deciduous broadleaved tree species, holds significant ecological and economical value. While a chromosome-level genome for this species has been made available, it remains riddled with unanchored sequences and gaps. In this study, we present a nearly complete comprehensive telomere-to-telomere (T2T) and haplotype-resolved reference genome for Q. variabilis. This was achieved through the integration of ONT ultra-long reads, PacBio HiFi long reads, and Hi-C data. The resultant two haplotype genomes measure 789 Mb and 768 Mb in length, with a contig N50 of 65 Mb and 56 Mb, and were anchored to 12 allelic chromosomes. Within this T2T haplotype-resolved assembly, we predicted 36,830 and 36,370 protein-coding genes, with 95.9% and 96.0% functional annotation for each haplotype genome. The availability of the T2T and haplotype-resolved reference genome lays a solid foundation, not only for illustrating genome structure and functional genomics studies but also to inform and facilitate genetic breeding and improvement of cultivated Quercus species.

Subject headings

NATURVETENSKAP  -- Biologi -- Genetik (hsv//swe)
NATURAL SCIENCES  -- Biological Sciences -- Genetics (hsv//eng)
NATURVETENSKAP  -- Biologi -- Botanik (hsv//swe)
NATURAL SCIENCES  -- Biological Sciences -- Botany (hsv//eng)

Keyword

gap-less
genome assembly
haplotype-resolved
Quercus variabilis
telomere-to-telomere

Publication and Content Type

ref (subject category)
art (subject category)

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