Wolfberry genomes and the evolution of Lycium (Solanaceae)

Communications Biology

Nobutaka Mitsuda¹  Chuan-Ming Yeh²  Shan-Ce Niu³  Takeshi Ishimizu⁴  You-Yi Chen⁵  Chieh-Kai Liang⁵  Zhen Li⁶  Yves Van de Peer⁷  Ning Wang⁸  Kun-Chan Tsai⁹  Toshihisa Kotake^1,10  Yu-Fu Lin^1,11  Wan-Lin Wu^1,11  Xiao-Kai Ma^1,12  Hsiang-Chai Lu^1,12  Ming-He Li^1,12  Si-Ren Lan^1,13  Xuedie Liu^1,13  Yu-Ting Jiang^1,13  Wei-Hong Sun^1,13  Diyang Zhang^1,13  Xing-Yu Liao^1,13  Xin-Yu Xu^1,13  Bin Liu^1,13  Shuang-Quan Zou^1,13  Yang Hao^1,13  Xia Yu^1,13  Jie-Yu Wang^1,14  Yan-long Li^1,15  Bo Zhang^1,15  Jun-Yi Wang^1,15  Yun-Fang Fan^1,15  Ya-Jun Wang^1,15  Yue Yin^1,15  Wei An^1,15  En-Ning Jiao^1,15  Jian-Hua Zhao^1,15  Jun He^1,15  Peng-Ju Wu^1,15  Ken Qin^1,15  Zhi-Gang Shi^1,15  You-Long Cao^1,15  Guo-Li Dai^1,15  Qing Luo^1,15  Zhong-Jian Liu^1,16  Yu-Yun Hsiao^1,17  Wen-Chieh Tsai^1,18  Zhi-Wen Wang^1,19  Wen-Ying Zhong^1,19  Xiang Zhao^1,19  Kouki Yoshida^2,20 

[1] Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 305-8562, Tsukuba, Ibaraki, Japan;Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 305-8562, Tsukuba, Ibaraki, Japan;Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, 338-8570, Sakura-ku, Saitama, Japan;Institute of Molecular Biology, National Chung Hsing University, 40227, Taichung, Taiwan, China;College of Horticulture, Hebei Agricultural University, 071000, Baoding, China;College of Life Sciences, Ritsumeikan University, Kusatsu, Japan;Department of Life Sciences, National Cheng Kung University, 701, Tainan, Taiwan, China;Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium;VIB Center for Plant Systems Biology, VIB, 9052, Ghent, Belgium;Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium;VIB Center for Plant Systems Biology, VIB, 9052, Ghent, Belgium;Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, 0028, Pretoria, South Africa;College of Horticulture, Nanjing Agricultural University, Nanjing, China;Faculty of Life and Environmental Sciences, University of Tsukuba, 305-8572, Tsukuba, Ibaraki, Japan;Food and Fertilizer Technology Center for the Asian and Pacific Region, 14 Wenchow St., 10648, Taipei, Taiwan, China;Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, 338-8570, Sakura-ku, Saitama, Japan;Institute of Tropical Plant Sciences and Microbiology, National Cheng Kung University, 701, Tainan, Taiwan, China;Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, 350002, Fuzhou, China;Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, 350002, Fuzhou, China;Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, 350002, Fuzhou, China;Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, 350002, Fuzhou, China;Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, 510650, Guangzhou, China;National Wolfberry Engineering Research Center, Ningxia Academy of Agriculture and Forestry Sciences, 750002, Yinchuan, China;Institute of Wolfberry Engineering Technology, Ningxia Academy of Agriculture and Forestry Sciences, 750002, Yinchuan, China;National Wolfberry Engineering Research Center, Ningxia Academy of Agriculture and Forestry Sciences, 750002, Yinchuan, China;Institute of Wolfberry Engineering Technology, Ningxia Academy of Agriculture and Forestry Sciences, 750002, Yinchuan, China;Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, 350002, Fuzhou, China;Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, 350002, Fuzhou, China;Orchid Research and Development Center, National Cheng Kung University, 701, Tainan, Taiwan, China;Orchid Research and Development Center, National Cheng Kung University, 701, Tainan, Taiwan, China;Institute of Tropical Plant Sciences and Microbiology, National Cheng Kung University, 701, Tainan, Taiwan, China;Department of Life Sciences, National Cheng Kung University, 701, Tainan, Taiwan, China;PubBio-Tech, 430070, Wuhan, China;Technology Center, Taisei Corporation, 245-0051, Yokohama, Kanagawa, Japan;

DOI  :  10.1038/s42003-021-02152-8

来源: Springer

【 摘 要 】

Wolfberry Lycium, an economically important genus of the Solanaceae family, contains approximately 80 species and shows a fragmented distribution pattern among the Northern and Southern Hemispheres. Although several herbaceous species of Solanaceae have been subjected to genome sequencing, thus far, no genome sequences of woody representatives have been available. Here, we sequenced the genomes of 13 perennial woody species of Lycium, with a focus on Lycium barbarum. Integration with other genomes provides clear evidence supporting a whole-genome triplication (WGT) event shared by all hitherto sequenced solanaceous plants, which occurred shortly after the divergence of Solanaceae and Convolvulaceae. We identified new gene families and gene family expansions and contractions that first appeared in Solanaceae. Based on the identification of self-incompatibility related-gene families, we inferred that hybridization hotspots are enriched for genes that might be functioning in gametophytic self-incompatibility pathways in wolfberry. Extremely low expression of LOCULE NUBER (LC) and COLORLESS NON-RIPENING (CNR) orthologous genes during Lycium fruit development and ripening processes suggests functional diversification of these two genes between Lycium and tomato. The existence of additional flowering locus C-like MADS-box genes might correlate with the perennial flowering cycle of Lycium. Differential gene expression involved in the lignin biosynthetic pathway between Lycium and tomato likely illustrates woody and herbaceous differentiation. We also provide evidence that Lycium migrated from Africa into Asia, and subsequently from Asia into North America. Our results provide functional insights into Solanaceae origins, evolution and diversification.

【 授权许可】

CC BY