Wolfberry genomes and the evolution of Lycium (Solanaceae).

Africa Asia Chromosomes, Plant / genetics Evolution, Molecular Fruit / genetics Gene Expression Regulation, Plant Genome, Plant / genetics Geography Lycium / classification North America Phylogeny Polyploidy Polysaccharides / metabolism Solanaceae / classification Species Specificity Whole Genome Sequencing / methods

Journal

Communications biology
ISSN: 2399-3642
Titre abrégé: Commun Biol
Pays: England
ID NLM: 101719179

Informations de publication

Date de publication:
03 06 2021
Historique:
received: 03 12 2020
accepted: 26 04 2021
entrez: 4 6 2021
pubmed: 5 6 2021
medline: 17 8 2021
Statut: epublish

Résumé

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.

Identifiants

DOI: 10.1038/s42003-021-02152-8 PMID: 34083720 PMC: PMC8175696
pubmed: 34083720
doi: 10.1038/s42003-021-02152-8
pii: 10.1038/s42003-021-02152-8
pmc: PMC8175696
doi:

Substances chimiques

Polysaccharides 0

Types de publication

Journal Article Research Support, Non-U.S. Gov't

Langues

eng

Sous-ensembles de citation

IM

Pagination

671

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Auteurs

You-Long Cao (YL)

National Wolfberry Engineering Research Center, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, 750002, China. youlongchk@163.com.
Institute of Wolfberry Engineering Technology, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, 750002, China. youlongchk@163.com.
ORCID: 0000-0002-2283-292X

Yan-Long Li (YL)

National Wolfberry Engineering Research Center, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, 750002, China.
Institute of Wolfberry Engineering Technology, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, 750002, China.

Yun-Fang Fan (YF)

National Wolfberry Engineering Research Center, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, 750002, China.
Institute of Wolfberry Engineering Technology, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, 750002, China.

Zhen Li (Z)

Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium.
VIB Center for Plant Systems Biology, VIB, 9052, Ghent, Belgium.

Kouki Yoshida (K)

Technology Center, Taisei Corporation, Yokohama, Kanagawa, 245-0051, Japan.

Jie-Yu Wang (JY)

Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China.
ORCID: 0000-0003-4186-3761

Xiao-Kai Ma (XK)

Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.

Ning Wang (N)

Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8572, Japan.

Nobutaka Mitsuda (N)

Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, 305-8562, Japan.
ORCID: 0000-0001-5689-3678

Toshihisa Kotake (T)

Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama, 338-8570, Japan.
ORCID: 0000-0002-1110-5006

Takeshi Ishimizu (T)

College of Life Sciences, Ritsumeikan University, Kusatsu, Japan.
ORCID: 0000-0003-4910-6810

Kun-Chan Tsai (KC)

Food and Fertilizer Technology Center for the Asian and Pacific Region, 14 Wenchow St., Taipei, 10648, Taiwan, China.

Shan-Ce Niu (SC)

College of Horticulture, Hebei Agricultural University, Baoding, 071000, China.

Diyang Zhang (D)

Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
ORCID: 0000-0001-7548-4378

Wei-Hong Sun (WH)

Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.

Qing Luo (Q)

National Wolfberry Engineering Research Center, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, 750002, China.
Institute of Wolfberry Engineering Technology, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, 750002, China.

Jian-Hua Zhao (JH)

National Wolfberry Engineering Research Center, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, 750002, China.
Institute of Wolfberry Engineering Technology, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, 750002, China.

Yue Yin (Y)

National Wolfberry Engineering Research Center, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, 750002, China.
Institute of Wolfberry Engineering Technology, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, 750002, China.

Bo Zhang (B)

National Wolfberry Engineering Research Center, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, 750002, China.
Institute of Wolfberry Engineering Technology, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, 750002, China.

Jun-Yi Wang (JY)

National Wolfberry Engineering Research Center, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, 750002, China.
Institute of Wolfberry Engineering Technology, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, 750002, China.

Ken Qin (K)

National Wolfberry Engineering Research Center, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, 750002, China.
Institute of Wolfberry Engineering Technology, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, 750002, China.

Wei An (W)

National Wolfberry Engineering Research Center, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, 750002, China.
Institute of Wolfberry Engineering Technology, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, 750002, China.

Jun He (J)

National Wolfberry Engineering Research Center, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, 750002, China.
Institute of Wolfberry Engineering Technology, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, 750002, China.

Guo-Li Dai (GL)

National Wolfberry Engineering Research Center, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, 750002, China.
Institute of Wolfberry Engineering Technology, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, 750002, China.

Ya-Jun Wang (YJ)

National Wolfberry Engineering Research Center, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, 750002, China.
Institute of Wolfberry Engineering Technology, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, 750002, China.

Zhi-Gang Shi (ZG)

National Wolfberry Engineering Research Center, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, 750002, China.
Institute of Wolfberry Engineering Technology, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, 750002, China.

En-Ning Jiao (EN)

National Wolfberry Engineering Research Center, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, 750002, China.
Institute of Wolfberry Engineering Technology, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, 750002, China.

Peng-Ju Wu (PJ)

National Wolfberry Engineering Research Center, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, 750002, China.
Institute of Wolfberry Engineering Technology, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, 750002, China.

Xuedie Liu (X)

Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.

Bin Liu (B)

Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.

Xing-Yu Liao (XY)

Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.

Yu-Ting Jiang (YT)

Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.

Xia Yu (X)

Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.

Yang Hao (Y)

Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.

Xin-Yu Xu (XY)

Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.

Shuang-Quan Zou (SQ)

Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.

Ming-He Li (MH)

Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.

Yu-Yun Hsiao (YY)

Orchid Research and Development Center, National Cheng Kung University, Tainan, 701, Taiwan, China.
ORCID: 0000-0003-4580-2114

Yu-Fu Lin (YF)

Institute of Tropical Plant Sciences and Microbiology, National Cheng Kung University, Tainan, 701, Taiwan, China.

Chieh-Kai Liang (CK)

Department of Life Sciences, National Cheng Kung University, Tainan, 701, Taiwan, China.
ORCID: 0000-0001-8581-5986

You-Yi Chen (YY)

Department of Life Sciences, National Cheng Kung University, Tainan, 701, Taiwan, China.

Wan-Lin Wu (WL)

Institute of Tropical Plant Sciences and Microbiology, National Cheng Kung University, Tainan, 701, Taiwan, China.

Hsiang-Chai Lu (HC)

Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
ORCID: 0000-0002-5683-9249

Si-Ren Lan (SR)

Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.

Zhi-Wen Wang (ZW)

PubBio-Tech, Wuhan, 430070, China.

Xiang Zhao (X)

PubBio-Tech, Wuhan, 430070, China.

Wen-Ying Zhong (WY)

PubBio-Tech, Wuhan, 430070, China.

Chuan-Ming Yeh (CM)

Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, 305-8562, Japan. chuanmingy@nchu.edu.tw.
Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama, 338-8570, Japan. chuanmingy@nchu.edu.tw.
Institute of Molecular Biology, National Chung Hsing University, Taichung, 40227, Taiwan, China. chuanmingy@nchu.edu.tw.
ORCID: 0000-0001-8456-0125

Wen-Chieh Tsai (WC)

Orchid Research and Development Center, National Cheng Kung University, Tainan, 701, Taiwan, China. tsaiwc@mail.ncku.edu.tw.
Institute of Tropical Plant Sciences and Microbiology, National Cheng Kung University, Tainan, 701, Taiwan, China. tsaiwc@mail.ncku.edu.tw.
Department of Life Sciences, National Cheng Kung University, Tainan, 701, Taiwan, China. tsaiwc@mail.ncku.edu.tw.
ORCID: 0000-0001-9389-168X

Yves Van de Peer (Y)

Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium. yves.vandepeer@psb.vib-ugent.be.
VIB Center for Plant Systems Biology, VIB, 9052, Ghent, Belgium. yves.vandepeer@psb.vib-ugent.be.
Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, 0028, South Africa. yves.vandepeer@psb.vib-ugent.be.
College of Horticulture, Nanjing Agricultural University, Nanjing, China. yves.vandepeer@psb.vib-ugent.be.
ORCID: 0000-0003-4327-3730

Zhong-Jian Liu (ZJ)

National Wolfberry Engineering Research Center, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, 750002, China. zjliu@fafu.edu.cn.
Institute of Wolfberry Engineering Technology, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, 750002, China. zjliu@fafu.edu.cn.
Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China. zjliu@fafu.edu.cn.
Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China. zjliu@fafu.edu.cn.
ORCID: 0000-0003-4390-3878

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Classifications MeSH

questionsmedicales.fr › Régions géographiques › Afrique › Wolfberry genomes and the evolution of Lycium...
questionsmedicales.fr › Régions géographiques › Asie › Wolfberry genomes and the evolution of Lycium...
questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Chromosomes › Chromosomes de plante › Wolfberry genomes and the evolution of Lycium...
questionsmedicales.fr › Phénomènes biologiques › Évolution biologique › Évolution moléculaire › Wolfberry genomes and the evolution of Lycium...
questionsmedicales.fr › Aliments et boissons › Aliments › Fruit › Wolfberry genomes and the evolution of Lycium...
questionsmedicales.fr › Phénomènes génétiques › Régulation de l'expression des gènes › Régulation de l'expression des gènes végétaux › Wolfberry genomes and the evolution of Lycium...
questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Génome › Génome végétal › Wolfberry genomes and the evolution of Lycium...
questionsmedicales.fr › Disciplines des sciences naturelles › Sciences de la Terre › Géographie › Wolfberry genomes and the evolution of Lycium...
questionsmedicales.fr › Eucaryotes › Viridiplantae › Streptophyta › Embryophyta › Tracheobionta › Magnoliopsida › Solanales › Solanaceae › Lycium › Wolfberry genomes and the evolution of Lycium...
questionsmedicales.fr › Régions géographiques › Amériques › Amérique du Nord › Wolfberry genomes and the evolution of Lycium...
questionsmedicales.fr › Sciences de l'information › Phylogenèse › Wolfberry genomes and the evolution of Lycium...
questionsmedicales.fr › Phénomènes génétiques › Ploïdies › Polyploïdie › Wolfberry genomes and the evolution of Lycium...
questionsmedicales.fr › Glucides › Polyosides › Wolfberry genomes and the evolution of Lycium...
questionsmedicales.fr › Eucaryotes › Viridiplantae › Streptophyta › Embryophyta › Tracheobionta › Magnoliopsida › Solanales › Solanaceae › Wolfberry genomes and the evolution of Lycium...
questionsmedicales.fr › Phénomènes biologiques › Spécificité d'espèce › Wolfberry genomes and the evolution of Lycium...
questionsmedicales.fr › Techniques d'investigation › Techniques génétiques › Analyse de séquence › Analyse de séquence d'ADN › Séquençage du génome entier › Wolfberry genomes and the evolution of Lycium...