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

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

doi:10.1016/j.plantsci.2023.111874

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

Journal Article · Fri Sep 22 00:00:00 EDT 2023 · Plant Science

DOI:https://doi.org/10.1016/j.plantsci.2023.111874· OSTI ID:2076179

Chang, Ermei ^[1]; Guo, Wei ^[2]; Chen, Jiahui ^[3]; Zhang, Jin ^[4]; Jia, Zirui ^[1]; Tschaplinski, Timothy J. ^[5]; Yang, Xiaohan ^[5]; Jiang, Zeping ^[1]; Liu, Jianfeng ^[1]

Chinese Academy of Forestry (CAF), Beijing (China)
Taishan Academy of Forestry Sciences (China)
Chinese Academy of Sciences (CAS), Kunming (China)
Zhejiang A & F University (ZAFU), Hangzhou (China)
Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)

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. Additionally, 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.

View Accepted Manuscript (DOE)

Research Organization:: Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)

Sponsoring Organization:: Chinese Academy of Forestry (CAF); National Natural Science Foundation of China (NSFC); USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: AC05-00OR22725

OSTI ID:: 2076179

Alternate ID(s):: OSTI ID: 2369803

Journal Information:: Plant Science, Journal Name: Plant Science Vol. 337; ISSN 0168-9452

Publisher:: ElsevierCopyright Statement

Country of Publication:: United States

Language:: English

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59 BASIC BIOLOGICAL SCIENCES
Chromosome-level genome
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Quercus variabilis
Suberin biosynthesis

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

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