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Background: The genus Rhododendron (Ericaceae), a species-rich and widely distributed genus of woody plants, is distinguished for the beautiful and diverse flowers. Rhododendron delavayi Franch. and Rhododendron irroratum Franch., are highly attractive species widely distributed in south-west China and abundant new varieties have been selected from their genetic resources. Methods: We constructed chromosome-scale genome assemblies for Rhododendron delavayi and Rhododendron irroratum. Phylogenetic and whole-genome duplication analyses were performed to elucidate the evolutionary history of Rhododendron. Further, different types of gene duplications were identified and their contributions to gene family expansion were investigated. Finally, comprehensive characterization and evolutionary analysis of R2R3-MYB and NBS-encoding genes were conducted to explore their evolutionary patterns. Results: The phylogenetic analysis classified Rhododendron species into two sister clades, 'rhododendrons' and 'azaleas'. Whole-genome duplication (WGD) analysis unveiled only one WGD event that occurred in Rhododendron after the ancestral g triplication. Gene duplication and gene family expansion analyses suggested that the younger tandem and proximal duplications contributed greatly to the expansion of gene families involved in secondary metabolite biosynthesis and stress response. The candidate R2R3-MYB genes likely regulating anthocyanin biosynthesis and stress tolerance in Rhododendron will facilitate the breeding for ornamental use. NBS-encoding genes had undergone significant expansion and experienced species-specific gain and loss events in Rhododendron plants. Conclusions: The reference genomes presented here will provide important genetic resources for molecular breeding and genetic improvement of plants in this economically important Rhododendron genus. [ABSTRACT FROM AUTHOR]

The most predominant type of resistance (R) genes contain nucleotide-binding sites and leucine-rich repeat (NBS-LRR) domains, characterization of which is helpful for plant resistance improvement. However, the NBS genes of Ipomoea trifida (H.B.K.) remain insufficient to date. In this study, a genome-wide analysis of the NBS-encoding gene in I. trifida (H.B.K.) was carried out. A total of 442 NBS encoding genes were identified, amounting to 1.37% of the total genes of I. trifida (H.B.K.). Based on the analysis of the domains, the identified ItfNBS genes were further classified into seven groups: CNL, NL, CN, N, TNL, TN, and RNL. Phylogenetic analysis showed that the I. trifida NBS genes clustered into three independent clades: RNL, TNL, and CNL. Chromosome location analysis revealed that the distribution of ItfNBS genes in chromosomes was uneven, with a number ranging from 3 to 45. Multiple stress-related regulatory elements were detected in the promoters of the NBS-encoding genes, and their expression profiles were obtained. The qRT-PCR analysis revealed that IbNBS10, IbNBS20, IbNBS258, and IbNBS88 responded to stem nematode infection. These results provide critical proof for further characterization and analysis of NBS-encoding genes with important functions.

Background: The genus Rhododendron (Ericaceae), a species-rich and widely distributed genus of woody plants, is distinguished for the beautiful and diverse flowers. Rhododendron delavayi Franch. and Rhododendron irroratum Franch., are highly attractive species widely distributed in south-west China and abundant new varieties have been selected from their genetic resources., Methods: We constructed chromosome-scale genome assemblies for Rhododendron delavayi and Rhododendron irroratum . Phylogenetic and whole-genome duplication analyses were performed to elucidate the evolutionary history of Rhododendron . Further, different types of gene duplications were identified and their contributions to gene family expansion were investigated. Finally, comprehensive characterization and evolutionary analysis of R2R3-MYB and NBS-encoding genes were conducted to explore their evolutionary patterns., Results: The phylogenetic analysis classified Rhododendron species into two sister clades, 'rhododendrons' and 'azaleas'. Whole-genome duplication (WGD) analysis unveiled only one WGD event that occurred in Rhododendron after the ancestral γ triplication. Gene duplication and gene family expansion analyses suggested that the younger tandem and proximal duplications contributed greatly to the expansion of gene families involved in secondary metabolite biosynthesis and stress response. The candidate R2R3-MYB genes likely regulating anthocyanin biosynthesis and stress tolerance in Rhododendron will facilitate the breeding for ornamental use. NBS-encoding genes had undergone significant expansion and experienced species-specific gain and loss events in Rhododendron plants., Conclusions: The reference genomes presented here will provide important genetic resources for molecular breeding and genetic improvement of plants in this economically important Rhododendron genus., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Wu, Zhang, Wang, Zhang, Jin, Hu, Yang, Wu, Ma, Zhang and Wang.)