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Article|18 Jun 2021|OPEN
A chromosome-level genome assembly of rugged rose (Rosa rugosa) provides insights into its evolution, ecology, and floral characteristics
Fei Chen1, Liyao Su1, Shuaiya Hu1, Jia-Yu Xue1,2, Hui Liu1, Guanhua Liu1, Yifan Jiang1, Jianke Du1, Yushan Qiao1, Yannan Fan3,4, Qi Yang5, Wenjie Lu5, Zhu-Qing Shao6, Jian Zhang7, Liangsheng Zhang8, Feng Chen9 & Zong-Ming (Max) Cheng1,
1College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
2Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
3BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
4Department of Biology, University of Copenhagen, Copenhagen, Denmark
5Grandomics Biosciences Co., Ltd, Wuhan, China
6School of Life Sciences, Nanjing University, Nanjing, China
7College of life science, Nantong University, Nantong, China
8Genomics and Genetic Engineering Laboratory of Ornamental Plants, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
9Department of plant sciences, University of Tennessee, Knoxville, TN, USA

Horticulture Research 8,
Article number: 141 (2021)
doi: 10.1038/hortres.2021.141
Views: 232

Received: 18 Mar 2021
Revised: 12 Apr 2021
Accepted: 11 Mar 2021
Published online: 18 Jun 2021

Abstract

Rosa rugosa, commonly known as rugged rose, is a perennial ornamental shrub. It produces beautiful flowers with a mild fragrance and colorful seed pods. Unlike many other cultivated roses, R. rugosa adapts to a wide range of habitat types and harsh environmental conditions such as salinity, alkaline, shade, drought, high humidity, and frigid temperatures. Here, we produced and analyzed a high-quality genome sequence for R. rugosa to understand its ecology, floral characteristics and evolution. PacBio HiFi reads were initially used to construct the draft genome of R. rugosa, and then Hi-C sequencing was applied to assemble the contigs into 7 chromosomes. We obtained a 382.6 Mb genome encoding 39,704 protein-coding genes. The genome of R. rugosa appears to be conserved with no additional whole-genome duplication after the gamma whole-genome triplication (WGT), which occurred ~100 million years ago in the ancestor of core eudicots. Based on a comparative analysis of the high-quality genome assembly of R. rugosa and other high-quality Rosaceae genomes, we found a unique large inverted segment in the Chinese rose R. chinensis and a retroposition in strawberry caused by post-WGT events. We also found that floral development- and stress response signaling-related gene modules were retained after the WGT. Two MADS-box genes involved in floral development and the stress-related transcription factors DREB2A-INTERACTING PROTEIN 2 (DRIP2) and PEPTIDE TRANSPORTER 3 (PTR3) were found to be positively selected in evolution, which may have contributed to the unique ability of this plant to adapt to harsh environments. In summary, the high-quality genome sequence of R. rugosa provides a map for genetic studies and molecular breeding of this plant and enables comparative genomic studies of Rosa in the near future.