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  • Wang, LongxinSchool of Biological Science and Technology, University of Jinan, Jinan, China (author)

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

  • Article/chapterEnglish2023

Publisher, publication year, extent ...

  • Frontiers Media S.A.2023
  • electronicrdacarrier

Numbers

  • LIBRIS-ID:oai:DiVA.org:umu-217215
  • https://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-217215URI
  • https://doi.org/10.3389/fpls.2023.1290913DOI

Supplementary language notes

  • Language:English
  • Summary in:English

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Classification

  • Subject category:ref swepub-contenttype
  • Subject category:art swepub-publicationtype

Notes

  • 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 and genre

Added entries (persons, corporate bodies, meetings, titles ...)

  • Li, Lei-LeiKey Laboratory of Crop Genetic Improvement & Ecology and Physiology, Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences, Jinan, China (author)
  • Chen, LiShandong Saienfu Stem Cell Engineering Group Co., Ltd, Jinan, China (author)
  • Zhang, Ren-GangYunnan 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 (author)
  • Zhao, Shi-WeiUmeå universitet,Institutionen för fysiologisk botanik (author)
  • Yan, HanThe Second Affiliated Hospital of Shandong First Medical University, Taian, China (author)
  • Gao, JieChinese Academy of Sciences (CAS), Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, China (author)
  • Chen, XueWeifang Academy of Agricultural Sciences, Weifang, China (author)
  • Si, Yu-JunWeifang Academy of Agricultural Sciences, Weifang, China (author)
  • Chen, ZheInvoGenomics Biotechnology Co., Ltd., Jinan, China (author)
  • Liu, HaiboJinan Academy of Landscape and Forestry Science, Jinan, China (author)
  • Xie, Xiao-ManKey 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 (author)
  • Zhao, WeiUmeå universitet,Institutionen för ekologi, miljö och geovetenskap,Umeå Plant Science Centre (UPSC)(Swepub:umu)zhwe0002 (author)
  • Han, BiaoKey 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 (author)
  • Qin, XiaochunSchool of Biological Science and Technology, University of Jinan, Jinan, China (author)
  • Jia, Kai-HuaKey Laboratory of Crop Genetic Improvement & Ecology and Physiology, Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences, Jinan, China (author)
  • School of Biological Science and Technology, University of Jinan, Jinan, ChinaKey Laboratory of Crop Genetic Improvement & Ecology and Physiology, Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences, Jinan, China (creator_code:org_t)

Related titles

  • In:Frontiers in Plant Science: Frontiers Media S.A.141664-462X

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