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Article|20 Jun 2022|OPEN
Chromosome-scale genome assemblies of wild tomato relatives Solanum habrochaites and Solanum galapagense reveal structural variants associated with stress tolerance and terpene biosynthesis
Xiaofen Yu1,2 ,† , Minghao Qu1,3 ,† , Yanna Shi4 , Chenlu Hao1,3 , Sumin Guo1 , , Zhangjun Fei5,6 , , Lei Gao,1,2 ,
1CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan 430074, China
2Hubei Hongshan Laboratory, Wuhan 430070, China
3University of Chinese Academy of Sciences, Beijing 100049, China
4Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Hangzhou 310058, China
5Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA
6US Department of Agriculture-Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, NY 14853, USA
*Corresponding author. E-mail:,,
Both authors contributed equally to the study.

Horticulture Research 9,
Article number: uhac139 (2022)
Views: 203

Received: 29 Mar 2022
Accepted: 12 Jun 2022
Published online: 20 Jun 2022


Dear Editor,

Introducing beneficial genes/alleles from wild relatives into the cultivated tomato has been an important approach for tomato breeding. Solanum habrochaites and S. galapagense have been widely used as germplasm donors in modern breeding to improve biotic and abiotic stress tolerance of tomato. S. habrochaites grows in the Peruvian Andes at altitudes up to 3300 m and is notable for its tolerance of chilling and drought and resistance to many diseases and pests. S. galapagense is endemic to the Galápagos Islands, has extraordinary salt tolerance and insect resistance, and appears even more closely related to the cultivated tomato (Solanum lycopersicum) than Solanum pimpinellifolium, the wild progenitor of cultivated tomato [1]. Due to their importance, draft genomes of these two species have been assembled using Illumina short-read sequencing [2] or PacBio long-read sequencing [3]. However, high levels of fragmentation and/or the lack of chromosome-scale assemblies have limited their applications in tomato breeding and research.