Chromosome-level genome assembly of Quercus variabilis provides insights into the molecular mechanism of cork thickness

Ermei Chang; Wei Guo; Jiahui Chen; Jin Zhang; Zirui Jia; Timothy J Tschaplinski; Xiaohan Yang; Zeping Jiang; Jianfeng Liu

doi:10.1016/j.plantsci.2023.111874

Chromosome-level genome assembly of Quercus variabilis provides insights into the molecular mechanism of cork thickness

Plant Sci. 2023 Sep 22:337:111874. doi: 10.1016/j.plantsci.2023.111874. Online ahead of print.

Authors

Ermei Chang¹, Wei Guo², Jiahui Chen³, Jin Zhang⁴, Zirui Jia¹, Timothy J Tschaplinski⁵, Xiaohan Yang⁵, Zeping Jiang⁶, Jianfeng Liu⁷

Affiliations

¹ State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 10091, China.
² Taishan Academy of Forestry Sciences, Taian, Shandong 271000, China.
³ CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China.
⁴ State Key Laboratory of Subtropical Silviculture, College of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, Zhejiang 311300, China.
⁵ Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.
⁶ Key Laboratory of Forest Ecology of National Forestry and Grassland Administration, Environment and Protection, Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing 100091, China. Electronic address: jiangzp@caf.ac.cn.
⁷ State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 10091, China. Electronic address: liujf@caf.ac.cn.

PMID: 37742724
DOI: 10.1016/j.plantsci.2023.111874

Abstract

Quercus variabilis is a deciduous woody species with high ecological and economic value, and is a major source of cork in East Asia. Cork from thick softwood sheets have higher commercial value than those from thin sheets. It is extremely difficult to genetically improve Q. variabilis to produce high quality softwood due to the lack of genomic information. Here, we present a high-quality chromosomal genome assembly for Q. variabilis with length of 791,89 Mb and 54,606 predicted genes. Comparative analysis of protein sequences of Q. variabilis with 11 other species revealed that specific and expanded gene families were significantly enriched in the "fatty acid biosynthesis" pathway in Q. variabilis, which may contribute to the formation of its unique cork. Based on weighted correlation network analysis of time-course (i.e., five important developmental ages) gene expression data in thick-cork versus thin-cork genotypes of Q. variabilis, we identified one co-expression gene module associated with the thick-cork trait. Within this co-expression gene module, 10 hub genes were associated with suberin biosynthesis. Furthermore, we identified a total of 198 suberin biosynthesis-related new candidate genes that were up-regulated in trees with a thick cork layer relative to those with a thin cork layer. Also, we found that some genes related to cell expansion and cell division were highly expressed in trees with a thick cork layer. Collectively, our results revealed that two metabolic pathways (i.e., suberin biosynthesis, fatty acid biosynthesis), along with other genes involved in cell expansion, cell division, and transcriptional regulation, were associated with the thick-cork trait in Q. variabilis, providing insights into the molecular basis of cork development and knowledge for informing genetic improvement of cork thickness in Q. variabilis and closely related species.

Keywords: Chromosome-level genome; Cork thickness; Quercus variabilis; Suberin biosynthesis.