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

Longxin Wang; Lei-Lei Li; Li Chen; Ren-Gang Zhang; Shi-Wei Zhao; Han Yan; Jie Gao; Xue Chen; Yu-Jun Si; Zhe Chen; Haibo Liu; Xiao-Man Xie; Wei Zhao; Biao Han; Xiaochun Qin; Kai-Hua Jia

doi:10.3389/fpls.2023.1290913

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

Front Plant Sci. 2023 Nov 2:14:1290913. doi: 10.3389/fpls.2023.1290913. eCollection 2023.

Authors

Longxin Wang^#¹, Lei-Lei Li^#², Li Chen^#³, Ren-Gang Zhang⁴, Shi-Wei Zhao⁵, Han Yan⁶, Jie Gao⁷, Xue Chen⁸, Yu-Jun Si⁸, Zhe Chen⁹, Haibo Liu¹⁰, Xiao-Man Xie¹¹, Wei Zhao¹², Biao Han¹¹, Xiaochun Qin¹, Kai-Hua Jia²

Affiliations

¹ School of Biological Science and Technology, University of Jinan, Jinan, China.
² Key Laboratory of Crop Genetic Improvement & Ecology and Physiology, Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences, Jinan, China.
³ Shandong Saienfu Stem Cell Engineering Group Co., Ltd, Jinan, China.
⁴ 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, Kunming, Yunnan, China.
⁵ Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, Umeå, Sweden.
⁶ The Second Affiliated Hospital of Shandong First Medical University, Taian, China.
⁷ Chinese Academy of Sciences (CAS), Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, China.
⁸ Weifang Academy of Agricultural Sciences, Weifang, China.
⁹ InvoGenomics Biotechnology Co., Ltd., Jinan, China.
¹⁰ Jinan Academy of Landscape and Forestry Science, Jinan, China.
¹¹ 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.
¹² Department of Ecology and Environmental Science, Umeå Plant Science Centre, Umeå University, Umeå, Sweden.

^# Contributed equally.

Abstract

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.

Keywords: Quercus variabilis; gap-less; genome assembly; haplotype-resolved; telomere-to-telomere.

Associated data

figshare/10.6084/m9.figshare.22313569.v2

Grants and funding

The author(s) declare financial support was received for the research, authorship, and/or publication of this article. This research was supported by National Forestry and Grassland Administration Science and Technology Development Center Project “Resource Collection and Genetic Diversity Evaluation of Quercus variabilis” (KJZXSA202301); by the Taishan Scholars Project (tsqn201812079); by the Science and Technology Project of University of Jinan (XBS2003); by the Shandong Province Postdoctoral Innovation Project (SDCX-ZG-202203059).