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

文献类型： 外文期刊

作者： Wang, Longxin 1 ; Li, Lei-Lei 2 ; Chen, Li 3 ; Zhang, Ren-Gang 4 ; Zhao, Shi-Wei 5 ; Yan, Han 6 ; Gao, Jie 7 ; Chen, Xue 8 ; Si, Yu-Jun 8 ; Chen, Zhe 9 ; Liu, Haibo 10 ; Xie, Xiao-Man 11 ; Zhao, Wei 12 ; Han, Biao 11 ; Qin, Xiaochun 1 ; Jia, Kai-Hua 2 ;

作者机构： 1.Univ Jinan, Sch Biol Sci & Technol, Jinan, Peoples R China

2.Shandong Acad Agr Sci, Inst Crop Germplasm Resources, Key Lab Crop Genet Improvement & Ecol & Physiol, Jinan, Peoples R China

3.Jinan Sijian Construct Grp Co Ltd, Jinan, Peoples R China

4.Chinese Acad Sci, Kunming Inst Bot, Yunnan Key Lab Integrat Conservat Plant Species Ex, Key Lab Plant Divers & Biogeog East Asia, Kunming, Yunnan, Peoples R China

5.Umea Univ, Umea Plant Sci Ctr, Dept Plant Physiol, Umea, Sweden

6.Shandong First Med Univ, Affiliated Hosp 2, Tai An, Peoples R China

7.Chinese Acad Sci, Chinese Acad Sci CAS, Key Lab Trop Forest Ecol, Xishuangbanna Trop Bot Garden, Menglun, Peoples R China

8.Weifang Acad Agr Sci, Weifang, Peoples R China

9.InvoGen Biotechnol Co Ltd, Jinan, Peoples R China

10.Jinan Acad Landscape & Forestry Sci, Jinan, Peoples R China

11.Shandong Prov Ctr Forest & Grass Germplasm Resourc, Key Lab State Forestry & Grassland Adm Conservat &, Jinan, Peoples R China

12.Umea Univ, Umea Plant Sci Ctr, Dept Ecol & Environm Sci, Umea, Sweden

关键词： Quercus variabilis; genome assembly; telomere-to-telomere; gap-less; haplotype-resolved

期刊名称：FRONTIERS IN PLANT SCIENCE （ 影响因子：5.6； 五年影响因子：6.8 ）

ISSN： 1664-462X

年卷期： 2023 年 14 卷

页码：

收录情况： SCI

摘要： 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.

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