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Wolfberry genomes and the evolution of Lycium (Solanaceae)

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Abstract
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. Cao, Li, et al. sequence 13 perennial woody plant species of Lycium, and specifically provide a draft assembly of L. ruthenicum and a chromosome-level assembly of L. barbarum, the wolfberry or Goji berry. From a phylogenetic tree the authors identify an ancient hexaploidization event, and report the evolution of gene families including fruit ripening, fruit coloration, polysaccharide synthesis and self-incompatibility within Solanaceae and the general biogeography of L. barbarum.
Keywords
GAMETOPHYTIC SELF-INCOMPATIBILITY, COENZYME-A SYNTHETASE, FRUIT-DEVELOPMENT, PHYSIOLOGICAL-RESPONSE, PHYLOGENETIC ANALYSIS, LIGNIN BIOSYNTHESIS, MAXIMUM-LIKELIHOOD, READ ALIGNMENT, DROUGHT STRESS, GENE FAMILY

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MLA
Cao, You-Long, et al. “Wolfberry Genomes and the Evolution of Lycium (Solanaceae).” COMMUNICATIONS BIOLOGY, vol. 4, no. 1, 2021, doi:10.1038/s42003-021-02152-8.
APA
Cao, Y.-L., Li, Y., Fan, Y.-F., Li, Z., Yoshida, K., Wang, J.-Y., … Liu, Z.-J. (2021). Wolfberry genomes and the evolution of Lycium (Solanaceae). COMMUNICATIONS BIOLOGY, 4(1). https://doi.org/10.1038/s42003-021-02152-8
Chicago author-date
Cao, You-Long, Yan-long Li, Yun-Fang Fan, Zhen Li, Kouki Yoshida, Jie-Yu Wang, Xiao-Kai Ma, et al. 2021. “Wolfberry Genomes and the Evolution of Lycium (Solanaceae).” COMMUNICATIONS BIOLOGY 4 (1). https://doi.org/10.1038/s42003-021-02152-8.
Chicago author-date (all authors)
Cao, You-Long, Yan-long Li, Yun-Fang Fan, Zhen Li, Kouki Yoshida, Jie-Yu Wang, Xiao-Kai Ma, Ning Wang, Nobutaka Mitsuda, Toshihisa Kotake, Takeshi Ishimizu, Kun-Chan Tsai, Shan-Ce Niu, Diyang Zhang, Wei-Hong Sun, Qing Luo, Jian-Hua Zhao, Yue Yin, Bo Zhang, Jun-Yi Wang, Ken Qin, Wei An, Jun He, Guo-Li Dai, Ya-Jun Wang, Zhi-Gang Shi, En-Ning Jiao, Peng-Ju Wu, Xuedie Liu, Bin Liu, Xing-Yu Liao, Yu-Ting Jiang, Xia Yu, Yang Hao, Xin-Yu Xu, Shuang-Quan Zou, Ming-He Li, Yu-Yun Hsiao, Yu-Fu Lin, Chieh-Kai Liang, You-Yi Chen, Wan-Lin Wu, Hsiang-Chai Lu, Si-Ren Lan, Zhi-Wen Wang, Xiang Zhao, Wen-Ying Zhong, Chuan-Ming Yeh, Wen-Chieh Tsai, Yves Van de Peer, and Zhong-Jian Liu. 2021. “Wolfberry Genomes and the Evolution of Lycium (Solanaceae).” COMMUNICATIONS BIOLOGY 4 (1). doi:10.1038/s42003-021-02152-8.
Vancouver
1.
Cao Y-L, Li Y, Fan Y-F, Li Z, Yoshida K, Wang J-Y, et al. Wolfberry genomes and the evolution of Lycium (Solanaceae). COMMUNICATIONS BIOLOGY. 2021;4(1).
IEEE
[1]
Y.-L. Cao et al., “Wolfberry genomes and the evolution of Lycium (Solanaceae),” COMMUNICATIONS BIOLOGY, vol. 4, no. 1, 2021.
@article{8710616,
  abstract     = {{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. Cao, Li, et al. sequence 13 perennial woody plant species of Lycium, and specifically provide a draft assembly of L. ruthenicum and a chromosome-level assembly of L. barbarum, the wolfberry or Goji berry. From a phylogenetic tree the authors identify an ancient hexaploidization event, and report the evolution of gene families including fruit ripening, fruit coloration, polysaccharide synthesis and self-incompatibility within Solanaceae and the general biogeography of L. barbarum.}},
  articleno    = {{671}},
  author       = {{Cao, You-Long and Li, Yan-long and Fan, Yun-Fang and Li, Zhen and Yoshida, Kouki and Wang, Jie-Yu and Ma, Xiao-Kai and Wang, Ning and Mitsuda, Nobutaka and Kotake, Toshihisa and Ishimizu, Takeshi and Tsai, Kun-Chan and Niu, Shan-Ce and Zhang, Diyang and Sun, Wei-Hong and Luo, Qing and Zhao, Jian-Hua and Yin, Yue and Zhang, Bo and Wang, Jun-Yi and Qin, Ken and An, Wei and He, Jun and Dai, Guo-Li and Wang, Ya-Jun and Shi, Zhi-Gang and Jiao, En-Ning and Wu, Peng-Ju and Liu, Xuedie and Liu, Bin and Liao, Xing-Yu and Jiang, Yu-Ting and Yu, Xia and Hao, Yang and Xu, Xin-Yu and Zou, Shuang-Quan and Li, Ming-He and Hsiao, Yu-Yun and Lin, Yu-Fu and Liang, Chieh-Kai and Chen, You-Yi and Wu, Wan-Lin and Lu, Hsiang-Chai and Lan, Si-Ren and Wang, Zhi-Wen and Zhao, Xiang and Zhong, Wen-Ying and Yeh, Chuan-Ming and Tsai, Wen-Chieh and Van de Peer, Yves and Liu, Zhong-Jian}},
  issn         = {{2399-3642}},
  journal      = {{COMMUNICATIONS BIOLOGY}},
  keywords     = {{GAMETOPHYTIC SELF-INCOMPATIBILITY,COENZYME-A SYNTHETASE,FRUIT-DEVELOPMENT,PHYSIOLOGICAL-RESPONSE,PHYLOGENETIC ANALYSIS,LIGNIN BIOSYNTHESIS,MAXIMUM-LIKELIHOOD,READ ALIGNMENT,DROUGHT STRESS,GENE FAMILY}},
  language     = {{eng}},
  number       = {{1}},
  pages        = {{13}},
  title        = {{Wolfberry genomes and the evolution of Lycium (Solanaceae)}},
  url          = {{http://dx.doi.org/10.1038/s42003-021-02152-8}},
  volume       = {{4}},
  year         = {{2021}},
}

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