J Syst Evol

• Research Article •    

A haplotype‐resolved genome for Rhododendron × pulchrum and the expression analysis of heat shock genes

Jian‐Shuang Shen1†, Lan Lan2,3,4†*, Sheng‐Long Kan2,4, He‐Feng Cheng1, Dan Peng2, Zi‐Yun Wan1, Yue Hu1, Xiao‐Ling Huang1, Xue‐Qin Li1, Yuan‐Jun Ye5, Luke R. Tembrock6, Zhi‐Qiang Wu2,4*, and Song‐Heng Jin1,7*   

  1. 1 Jiyang College, Zhejiang A&F University, Zhuji 311800, Zhejiang, China;
    2 Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen Branch, Shenzhen 518120, China;
    3 School of Medical, Molecular & Forensic Sciences, Murdoch University, 90 South St, Perth, WA, Australia;
    4 Kunpeng Institute of Modern Agriculture at Foshan, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Foshan 528200, Guangdong, China;
    5 Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China;
    6 Department of Agricultural Biology, Colorado State University, Fort Collins 80523, CO, USA;
    7 Department of life science and health, Huzhou College, Huzhou 313000, Zhejiang, China
    These authors contributed equally to this work.
    *Authors for correspondence. Lan Lan. E‐mail: lanlan@caas.cn; Zhi‐Qiang Wu. E‐mail: wuzhiqiang@caas.cn; Song‐Heng Jin. E‐mail: shjin@zafu.edu.cn
  • Received:2023-02-24 Accepted:2023-06-07 Online:2023-07-21

Abstract: Rhododendron is the largest genus in Ericaceae and is well known for its diversity and beauty of flowers present in different species, making it a much‐revered lineage of ornamental plants. Many species of Rhododendron are intolerant of high temperatures, which are becoming more common and intense in urban areas under global climate change. Therefore, the discovery and description of genes from heat‐tolerant Rhododendron lineages are essential in the development of new climate‐resilient cultivars. One such species known to be heat tolerant is Rhododendron × pulchrum Sweet. To better understand the genomics of heat tolerance in this species, we assembled a haplotype‐resolved and chromosome‐scale genome for R. × pulchrum, which had a genome size of 509 Mb; a scaffold N50 of 37 251 370 bp; and contained 35 610 genes. In addition, based on the same reannotation pipeline, we conducted pan‐genomic analyses for all seven available chromosome‐scale Rhododendron genomes and found 14 415 gene groups shared across all species and 18 018 gene groups distributed in the other species, including 1879 gene groups found in only a single species. Finally, we analyzed the transcriptomic data from heat‐treated and non‐heat‐treated R. × pulchrum plants to quantify the genes that are most important during heat stress in an effort to inform the development of climate‐resilient cultivars. This study provides insight into the genome diversity in Rhododendron and targets several genes related to agronomic traits that may help in further analysis.

Key words: Ericaceae, genome evolution, heat shock proteins, horticulture, pan‐genome