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A chromosome-level genome assembly of the Chinese cork oak (Quercus variabilis)

文献类型： 外文期刊

作者： Han, Biao 1 ; Wang, Longxin 2 ; Xian, Yang 1 ; Xie, Xiao-Man 1 ; Li, Wen-Qing 1 ; Zhao, Ye 3 ; Zhang, Ren-Gang 4 ; Qin, Xiaochun 2 ; Li, De-Zhu 5 ; Jia, Kai-Hua 6 ;

作者机构： 1.Shandong Prov Ctr Forest & Grass Germplasm Resour, Key Lab State Forestry & Grassland Adm Conservat, Jinan, Peoples R China

2.Univ Jinan, Sch Biol Sci & Technol, Jinan, Peoples R China

3.Beijing Forestry Univ, Key Lab Genet & Breeding Forest Trees & Ornamenta, Beijing Adv Innovat Ctr Tree Breeding Mol Design, Minist Educ,Coll Biol Sci & Technol,Natl Engn Lab, Beijing, Peoples R China

4.Ori Shandong Gene Sci & Technol Co Ltd, Dept Bioinformat, Weifang, Peoples R China

5.Chinese Acad Sci, Kunming Inst Bot, Germplasm Bank Wild Species, Kunming, Yunnan, Peoples R China

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

关键词： Quercus variabilis; genome assembly; PacBio HiFi sequencing; Hi-C sequencing; comparative genomics

期刊名称：FRONTIERS IN PLANT SCIENCE （ 影响因子：6.627； 五年影响因子：7.255 ）

ISSN： 1664-462X

年卷期： 2022 年 13 卷

页码：

收录情况： SCI

摘要： Quercus variabilis (Fagaceae) is an ecologically and economically important deciduous broadleaved tree species native to and widespread in East Asia. It is a valuable woody species and an indicator of local forest health, and occupies a dominant position in forest ecosystems in East Asia. However, genomic resources from Q. variabilis are still lacking. Here, we present a high-quality Q. variabilis genome generated by PacBio HiFi and Hi-C sequencing. The assembled genome size is 787 Mb, with a contig N50 of 26.04 Mb and scaffold N50 of 64.86 Mb, comprising 12 pseudo-chromosomes. The repetitive sequences constitute 67.6% of the genome, of which the majority are long terminal repeats, accounting for 46.62% of the genome. We used ab initio, RNA sequence-based and homology-based predictions to identify protein-coding genes. A total of 32,466 protein-coding genes were identified, of which 95.11% could be functionally annotated. Evolutionary analysis showed that Q. variabilis was more closely related to Q. suber than to Q. lobata or Q. robur. We found no evidence for species-specific whole genome duplications in Quercus after the species had diverged. This study provides the first genome assembly and the first gene annotation data for Q. variabilis. These resources will inform the design of further breeding strategies, and will be valuable in the study of genome editing and comparative genomics in oak species.

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