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

doi:10.1016/j.plantsci.2023.111874

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	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
	2023
发表期刊	PLANT SCIENCE
ISSN	1873-2259
卷号	337
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.
关键词	Quercus variabilis Chromosome-level genome Cork thickness Suberin biosynthesis SUBERIN BIOSYNTHESIS GENE PROGRAM TRANSCRIPTOME ACCURATE ENCODES TOOL WAX
DOI	10.1016/j.plantsci.2023.111874
收录类别	SCI
WOS记录号	WOS:001171345700001
引用统计
文献类型	期刊论文
条目标识符	http://ir.kib.ac.cn/handle/151853/75406
专题	中国科学院昆明植物研究所
推荐引用方式 GB/T 7714	Chang,Ermei,Guo,Wei,Chen,Jiahui,et al. Chromosome-level genome assembly of Quercus variabilis provides insights into the molecular mechanism of cork thickness[J]. PLANT SCIENCE,2023,337.
APA	Chang,Ermei.,Guo,Wei.,Chen,Jiahui.,Zhang,Jin.,Jia,Zirui.,...&Liu,Jianfeng.(2023).Chromosome-level genome assembly of Quercus variabilis provides insights into the molecular mechanism of cork thickness.PLANT SCIENCE,337.
MLA	Chang,Ermei,et al."Chromosome-level genome assembly of Quercus variabilis provides insights into the molecular mechanism of cork thickness".PLANT SCIENCE 337(2023).

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