文献类型：期刊文献

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

作者：Chang, Ermei[1] Guo, Wei[2] Chen, Jiahui[3] Zhang, Jin[4] Jia, Zirui[1] Tschaplinski, Timothy J.[5,6] Yang, Xiaohan[5,6] Jiang, Zeping[7] Liu, Jianfeng[1]

第一作者：常二梅

通信作者：Liu, JF[1];Jiang, ZP[2]

机构：[1]Chinese Acad Forestry, Res Inst Forestry, Natl Forestry & Grassland Adm, State Key Lab Tree Genet & Breeding,Key Lab Tree, Beijing 10091, Peoples R China;[2]Taishan Acad Forestry Sci, Tai An 271000, Shandong, Peoples R China;[3]Chinese Acad Sci, Kunming Inst Bot, CAS Key Lab Plant Divers & Biogeog East Asia, Kunming 650201, Yunnan, Peoples R China;[4]Zhejiang A&F Univ, Coll Forestry & Biotechnol, State Key Lab Subtrop Silviculture, Hangzhou 311300, Zhejiang, Peoples R China;[5]Oak Ridge Natl Lab, Biosci Div, Oak Ridge, TN 37831 USA;[6]Oak Ridge Natl Lab, Ctr Bioenergy Innovat, Oak Ridge, TN 37831 USA;[7]Chinese Acad Forestry, Res Inst Forest Ecol Environm & Protect, Natl Forestry & Grassland Adm, Key Lab Forest Ecol,Environm & Protect, Beijing 100091, Peoples R China

年份：2023

卷号：337

外文期刊名：PLANT SCIENCE

收录：;Scopus(收录号：2-s2.0-85173166943);WOS:【SCI-EXPANDED(收录号:WOS:001171345700001)】；

基金：This work was supported by the National Non-Profit Research Institutions of the Chinese Academy of Forestry [Grant numbers: CAFYBB2022ZA001, CAFYBB2018ZB001] and the National Natural Science Foundation of China [Grant number 42071065]. Timothy J. Tschaplinski and Xiaohan Yang were supported by the Center for Bio-energy Innovation (CBI), which is a U.S. Department of Energy (DOE) Bioenergy Research Center supported by the Biological and Environmental Research program in the DOE Office of Science. The genome sequencing, assembly and annotation were performed with the help of Biomarker Technologies. We are particularly thankful to Dr. Quanzi Li, Dr. Yunhui Xie, and Dr. Guodong Rao for their helpful suggestions on our work.

语种：英文

外文关键词：Quercus variabilis; Chromosome-level genome; Cork thickness; Suberin biosynthesis

摘要：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.