Genome and transcriptome analyses provide insights into disease resistance of smoke tree (Cotinus coggygria) to Verticillium dahliae

The smoke tree ( Cotinus coggygria ) has significant ecological and economic values, yet its health is threatened by Verticillium wilt (VW). VW was caused by Verticillium dahliae , which infects herbaceous annuals as well as woody perennials, causing enormous losses. Compared with annuals, VW symptoms of C. coggygria appear later, suggesting the VW resistance mechanisms in forest trees, which have not been adequately studied. The genome of C. coggygria uncovered its genome characteristics and evolutionary history. The transcriptome data of VW development in C. coggygria elucidated the molecular mechanism of VW resistance in C. coggygria , which might be a prerequisite for developing green disease control strategies. A chromosome-level genome of C. coggygria of 310.93 Mb in size with high-quality was generated, revealing that it harbors 35,304 protein-encoding genes. We discovered the expansion of the NLR family in C. coggygria genome. Although V. dahliae attack depressed the transcription of genes involved in phenylpropanoid biosynthesis, it activated phenylalanine ammonia-lyase (PAL) activity and increased the content of lignin and sugars, which might possess a protective effect on C. coggygria . The transcription of genes related to the conversion of scopoletin and scopolin was up-regulated, and scopoletin and scopolin showed inhibitory activity toward V. dahliae . This work generated a chromosome-scale genome for C. coggygria with high-quality, elucidated the crucial roles of the metabolism pathways in enhancing VW tolerance, and found the positive roles of sugars in disease control. These resources and results provide a valuable framework for understanding pathogen-host interactions in trees and offer novel insights into the control of VW. This research constructed a high-quality chromosome-level genome for C. coggygria , found its NLR family expansion, elucidated the crucial roles of the second metabolism pathways in enhancing VW tolerance, and found the positive roles of sugars in disease control. These resources and results provide a valuable framework for understanding pathogen-host interactions in trees and offer novel insights into the control of VW. • This study reported the first high-quality, chromosome-scale genomes of Cotinus coggygria. • Comparative genomics elucidated the phylogenetic relationships, genome characteristics, and NLR family expansion of C. coggygria genome. • Provides insights in understanding the molecular mechanism of disease tolerance of C. coggygria .