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Nuclear phylogeny and insights into wholegenome duplications and reproductive development of solanaceae plants

Plant Communications 2023年第4期4卷 301-322页

作者： Jie Huang Weibin Xu Junwen Zhai Yi Hu Jing Guo Caifei Zhang Yiyong Zhao Lin Zhang Christopher Martine Hong Ma Chien-Hsun Huang State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development Ministry of Education Key Laboratory of Biodiversity and Ecological EngineeringInstitute of Plant BiologyCenter of Evolutionary BiologySchool of Life SciencesFudan UniversityShanghai 200438China Guangxi Key Laboratory of Plant Conservation and Restoration Ecology in Karst Terrain Guangxi Institute of BotanyGuangxi Zhuangzu Autonomous Region and Chinese Academy of SciencesGuilin 541006China Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization Fujian Agriculture and Forestry UniversityFuzhou 350002China Department of Biology the Huck Institutes of Life Sciencesthe Pennsylvania State UniversityUniversity ParkState CollegePA 16802USA Department of Biology Bucknell UniversityLewisburgPA 17837USA

solanaceae,the nightshade family,have2700 species,including the important crops potato and tomato,ornamentals,and medicinal plants.Several sequenced solanaceae genomes show evidence for wholegenome duplication(WGD),providing an excellent opportunity to investigate WGD and its impacts.Here,we generated 93 transcriptomes/genomes and combined them with 87 public datasets,for a total of 180 solanaceae species representing all four subfamilies and 14 of 15 tribes.Nearly 1700 nuclear genes from these transcriptomic/genomic datasets were used to reconstruct a highly resolved solanaceae phylogenetic tree with six major clades.The solanaceae tree supports four previously recognized subfamilies(Goetzeioideae,Cestroideae,Nicotianoideae,and Solanoideae)and the designation of three other subfamilies(Schizanthoideae,Schwenckioideae,and Petunioideae),with the placement of several previously unassigned genera.We placed a solanaceae-specific whole-genome triplication(WGT1)at81 million years ago(mya),before the divergence of Schizanthoideae from other solanaceae subfamilies at73 mya.In addition,we detected two gene duplication bursts(GDBs)supporting proposed WGD events and four other GDBs.An investigation of the evolutionary histories of homologs of carpel and fruit developmental genes in 14 gene(sub)families revealed that 21 gene clades have retained gene duplicates.These were likely generated by the solanaceae WGT1 and may have promoted fleshy fruit development.This study presents a well-resolved solanaceae phylogeny and a new perspective on retained gene duplicates and carpel/fruit development,providing an improved understanding of solanaceae evolution.

关键词： solanaceae phylogeny transcriptome carpel and fruit development whole-genome duplication

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Cardioactive properties of solanaceae plant extracts and pure glycoalkaloids on Zophobas atratus

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Insect Science 2015年第2期22卷 251-262页

作者： Emanuela Ventrella Pawel Marciniak Zbigniew Adamski Grzegorz Rosirnski Szymon Chowanski Patrizia Falabella Laura Scrano SabinoA. Bufo Department of Science University of Basilicata Potenza Italy Department of Animal Physiology and Development Adam Mickiewicz University Poznan Poland Electron and Confocal Microscope Laboratory Adam Mickiewicz University Poznan Poland Department of European and Mediterranean Cultures University of Basilicata Matera Italy

Glycoalkaloids, the biologically active secondary metabolites produced by solanaceae plants, are natural defenses against animals, insects and fungi. In this paper, the effects of glycoalkaloids present in extracts of solanaceae plants （potato, tomato and black nightshade） or pure commercial glycoalkaloids on the coleopteran Zophobas atratus E were evaluated by in vitro and in vivo bioassays using heart experimental models. Each tested extract induced a dose-dependent cardioinhibitory effect. The perfusion of Zophobas atratus semi-isolated heart using the highest potato and tomato extract concentration （1 mmol/L） caused irreversible cardiac arrests, while extract from black nightshade pro- duced fast but reversible arrests. Pure commercial glycoalkaloids caused similar but less evident effects compared with extracts. Our results showed that the bioactivity of tested compounds depended on their structure and suggested the existence of synergistic interac- tions when combinations of the main glycoalkaloids of potato and black nightshade were used for trials. Surprisingly, injection of tomato and potato extracts in 1-day-old pupae of Zophobas atratus induced reversible positive chronotropic effects and decreased the duration of the both phases （anterograde and retrograde） of the heart contractile activity. Furthermore, these extracts affected the amplitude of the heart contractions.

关键词： cardioinhibitory effect glycoalkaloid heart perfusion solanaceae Zophobas atratus

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Plastid phylogenomics and biogeography of the medicinal plant lineage Hyoscyameae(solanaceae)

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Plant Diversity 2021年第3期43卷 192-197页

作者： Feng-Wei Lei Ling Tong Yi-Xuan Zhu Xian-Yun Mu Tie-Yao Tu Jun Wen Laboratory of Systematic Evolution and Biogeography of Woody Plants College of Ecology and Nature ConservationBeijing Forestry UniversityBeijing100083China Department of Botany National Museum of Natural HistoryMRC 166Smithsonian InstitutionWashingtonDC20013-7012USA Key Laboratory of Plant Resources Conservation and Sustainable Utilization South China Botanical GardenChinese Academy of SciencesGuangzhou510650China

The cosmopolitan family solanaceae,which originated and first diversified in South America,is economically important.The tribe Hyoscyameae is one of the three clades in solanaceae that occurs outside of the New World;Hyoscyameae genera are distributed mainly in Europe and Asia,and have centers of species diversity in the Qinghai-Tibet Plateau and adjacent regions.Although many phylogenetic studies have focused on solanaceae,the phylogenetic relationships within the tribe Hyoscyameae and its biogeographic history remain obscure.In this study,we reconstructed the phylogeny of Hyoscyameae based on whole chloroplast genome data,and estimated lineage divergence times according to the newly reported fruit fossil from the Eocene Patagonia,Physalis infinemundi,the earliest known fossil of solanaceae.We reconstructed a robust phylogeny of Hyoscyameae that reveals the berry fruit-type Atropa is sister to the six capsule-bearing genera(Hyoscyameae sensu stricto),Atropanthe is sister to the clade(Scopolia,Physochlaina,Przewalskia),and together they are sister to the robustly supported AnisoduseHyoscyamus clade.The stem age of Hyoscyameae was inferred to be in the Eocene(47.11 Ma,95%HPD:36.75e57.86 Ma),and the crown ages of Hyoscyameae sensu stricto were estimated as the early Miocene(22.52 Ma,95%HPD:15.19e30.53 Ma),which shows a close correlation with the rapid uplift of the Qinghai-Tibet Plateau at the Paleogene/Neogene boundary.Our results provide insights into the phylogenetic relationships and the history of the biogeographic diversification of the tribe Hyoscyameae,as well as plant diversification on the Qinghai-Tibet Plateau.

关键词： Biogeography Hyoscyameae Plastid phylogenomics Qinghai-Tibet Plateau Rapid radiation solanaceae

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Chemistry and bioactivities of natural steroidal alkaloids

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Natural Products and Bioprospecting 2022年第1期12卷 310-359页

作者： Mei-Ling Xiang Bin-Yuan Hu Zi-Heng Qi Xiao-Na Wang Tian-Zhen Xie Zhao-Jie Wang Dan-Yu Ma Qi Zeng Xiao-Dong Luo Key Laboratory of Medicinal Chemistry for Natural Resource Ministry of EducationYunnan Provincial Center for Research&Development of Natural ProductsSchool of Chemical Science and TechnologyYunnan UniversityKunming 650091People’s Republic of China State Key Laboratory of Phytochemistry and Plant Resources in West China Kunming Institute of BotanyChinese Academy of SciencesKunming 650201People’s Republic of China

Steroidal alkaloids possess the basic steroidal skeleton with a nitrogen atom in rings or side chains incorporated as an integral part of the molecule.They have demonstrated a wide range of biological activities,and some of them have even been developed as therapeutic drugs,such as abiraterone acetate(Zytiga®),a blockbuster drug,which has been used for the treatment of prostate cancer.Structurally diverse natural steroidal alkaloids present a wide spectrum of biological activities,which are attractive for natural product chemistry and medicinal chemistry communities.This review comprehensively covers the structural classification,isolation and various biological activities of 697 natural steroidal alkaloids discovered from 1926 to October 2021,with 363 references being cited.

关键词： Steroidal alkaloids Chemistry Bioactivities solanaceae Liliaceae Apocynaceae Buxaceae

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Biogeographic diversification in Nolana(solanaceae),a ubiquitous member of the Atacama and Peruvian Deserts along the western coast of South America

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Journal of Systematics and Evolution 2009年第5期47卷 457-476页

作者： Michael O.DILLON Victor QUIPUSCOA SILVESTRE Department of Botany The Field Museum1400 South Lake Shore DriveChicagoIL 60605USA Departamento de Botánica Universidad Nacional de San Agustín

The present paper reconstructs the biogeographic diversification for Nolana L.f.(solanaceae),a genus of 89 endemic species largely restricted to fog-dependent desert lomas formations of coastal Peru and Chile.Previous efforts have reconstructed a phylogenetic estimate for Nolana using a combination of molecular markers.Herein,we expand on those results to examine hypotheses of biogeographic origins and diversification patterns.Nolana occupies habitats within a continuous coastal desert and forms a terrestrial archipelago of discrete "islands" unique in size,topography,and species composition.Each locality contains at least one Nolana species and many contain multiple species in sympatry.The genus has a Chilean origin,with the basal clades confined to Chile with wide geographic and ecological distributions.Peru contains two strongly supported clades,suggesting two introductions with subsequent radiation.A Chilean clade of shrubby,small-flowered species appears to have had its origins from the same ancestors of the second line that radiated in Peru and northern Chile.Nolana galapagensis is endemic to the Islas Gala’pagos,with origins traced to Peruvian taxa with a divergence time of 0.35 mya.Rates of diversification over the past 4.02 mya in Nolana,in one of the driest habitats on Earth,suggest rapid adaptive radiation in several clades.Success in Nolana may be attributed to characters that confer a competitive advantage in unpredictable and water-dependent environments,such as succulent leaf anatomy and ecophysiology,and the reproductive mericarp unique to Nolana.The processes affecting or shaping the biota of western South America are discussed.

关键词： Atacama Desert biogeography chloroplast DNA LEAFY second intron Nolana Peruvian Desert solanaceae South America.

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Discovery,Identification and Comparative Analysis of Non-Specific Lipid Transfer Protein (nsLtp) Family in solanaceae

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Genomics, Proteomics & Bioinformatics 2010年第4期8卷 229-237页

作者： Wanfei Liu Dawei Huang Kan Liu Songnian Hu Jun Yu Gang Gao Shuhui Song Key Laboratory of Genome Sciences and Information Beijing Institute of Genomics Chinese Academy of Sciences Beijing 100029 China Graduate University of Chinese Academy of Sciences Beijing 100049 China 3College of Life Sciences Shanxi Normal University Linfen 041004 China College of Life Sciences Shanxi Normal University Linfen 041004 China

Plant non-specific lipid transfer proteins （nsLtps） have been reported to be involved in plant defense activity against bacterial and fungal pathogens. In this study, we identified 135 （122 putative and 13 previously identified） solanaceae nsLtps, which are clustered into 8 different groups. By comparing with Boutrot’s nsLtp classification, we classified these eight groups into five types （I, II, IV, IX and X）. We compared solanaceae nsLtps with Arabidopsis and Gramineae nsLtps and found that （1） Types I, II and IV are shared by solanaceae, Gramineae and Arabidopsis; （2） Types III, V, VI and VIII are shared by Gramineae and Arabidopsis but not detected in solanaceae so far; （3） Type VII is only found in Gramineae whereas type IX is present only in Arabidopsis and solanaceae; （4） Type X is a new type that accounts for 52.59% solanaceae nsLtps in our data, and has not been reported in any other plant so far. We further built and compared the three-dimensional structures of the eight groups, and found that the major functional diversification within the nsLtp family could be predated to the monocot/dicot divergence, and many gene duplications and sequence variations had happened in the nsLtp family after the monocot/dicot divergence, especially in solanaceae.

关键词： nsLtp family solanaceae phylogenetic analysis three-dimensional structure

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A snapshot of the Chinese SOL Project

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Journal of Genetics and Genomics 2008年第7期35卷 387-390页

作者： Changbao Li Jiuhai Zhao Hongling Jiang Yu Geng Yuanyuan Dai Huajie Fan Dongfen Zhang Jinfeng Chen Fei Lu Jinfeng Shi Shouhong Sun Jianjun Chen Xiaohua Yang Chen Lu Mingsheng Chen Zhukuan Cheng Hongqing Ling Ying Wang Yongbiao Xue Chuanyou Li Institute of Genetics and Developmental Biology Chinese Academy of Sciences Beijing 100101 China Graduate School of Chinese Academy of Sciences Beijing 100039 China State Key Laboratory of Crop Biology Agronomy College Shandong Agricultural University Taian 271018 China Wuhan Boianical Garden Chinese Academy of Sciences Wuhan 430074 China

In 2003, the International solanaceae Project （SOL） was initiated by an international consortium of ten countries including Korea, China, the United Kingdom, India, the Netherlands, France, Japan, Spain, Italy and the United States. The first major effort of the SOL aimed to produce a DNA sequence map for euchromatin regions of 12 chromosomes of tomato （Solanum lycopersicum） before 2010. Here we present an update on Chinese effort for sequencing the euchromatin region of chromosome 3.

关键词： tomato Solanum lycopersicum solanaceae SOL

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A Plant Immune Receptor Adopts a Two-Step Recognition Mechanism to Enhance Viral Effector Perception

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Molecular Plant 2019年第2期12卷 248-262页

作者： Jia Li Haining Huang Min Zhu Shen Huang Wenhua Zhang Savithramma P. Dinesh-Kumar Xiaorong Tao Department of Plant Pathology Nanjing Agricultural University Nanjing 210095 P. R. China College of Life Science Nanjing Agricultural University Nanjing 210095 P. R. China Department of Plant Biology and The Genome Center College of Biological Sciences University of California Davis CA USA

Plant intracellular nucleotide binding leucine-rich repeat (NLR) immune receptors play critical roles in pathoge n surveillance. Most plant NLRs characterized so far were found to use a single domain/sensor to recognize pathogen effectors. Here we report that the Sw-5b NLR immune receptor uses two distinct domains to detect the viral movement protein NSm encoded by tospovirus. In addition to its leucine-rich repeat (LRR) domain that has been previously reported, the N-terminal solanaceae domain (SD) of Sw- 5b also interacts with NSm and a conserved 21-amino-acid region of NSm (NSm^21). The specific interaction between Sw-5b SD and NSm is required for releasing the inhibitory effect of coiled-coil domain on the NBARC- LRR region. Furthermore, we found that the binding of NSm affects the nucleotide binding activity of the NB-ARC-LRR in vitro, while Sw-5b NB-ARC-LRR is activated only when NSm and NSm^21 levels are high. Interestingly, Sw-5b SD could significantly enhanee the ability of the NB-ARC-LRR to detect low levels of NSm effector and facilitate its activation and induction of defense response. An Sw-5b SD mutant that is disrupted in NSm recognition failed to enhance the ability of the NB-ARC-LRR to sense low levels of NSm and NSm^21 . Taken together, our results suggest that Sw-5b SD functions as an extra sensor and the NB-ARC-LRR as an activator, and that Sw-5b NLR adopts a two-step recog nition mechanism to enhance viral effector perception.

关键词： plant innate immunity nucleotide binding leucine-rich repeat (NLR) immune receptors solanaceae domain (SD) pathogen perception two-step recognition defense response

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Effect of aqueous extract of Solanum xanthocarpum Schrad. & Wendl. on postmenopausal syndrome in ovariectomized rats

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Journal of Integrative Medicine 2014年第5期12卷 439-446页

作者： Urmila Aswar Mayuri Gurav Ganesh More Khaled Rashed Manoj Aswar Department of Pharmacology Sinhgad Institute of Pharmacy Narhe Pune 411041 India Department of Pharmacognosy National Research CentreDokki Giza 12411 Egypt

OBJECTIVE： Solanum xanthocarpum Schrad. ＆ Wendl. （solanaceae） is present in many Ayurveda compound formulations including Chavanaprasha and Dasamoolarishta. The whole plant is used in conditions such as inflammation, constipation and promoting conception in females. In the present study, we carried out different tests to evaluate the effect of aqueous extract of Solanum xanthocarpum （SXE） in postmenopausal syndrome. METHODS： The study was carried out in bilaterally ovariectomized one-month-old Wistar rats （40-50 g）. Bilaterally ovariectomized （OVX） Wistar rats were divided into four groups （n=6） receiving different treatments, consisting of a vehicle （distilled water）, aqueous extract of Solanum xanthocarpum at two different doses （200 and 400 mg/kg） administered orally daily for 90 d and standard drug β estradiol at a dose of 1 mg/kg administered subcutaneously biweekly for 90 d. Estrogenic activity was assessed by vaginal cornification, sexual behavior, serum estradiol and uterine weight to body weight ratio. Antiosteoporotic activity was assessed on the basis of biomechanical and biochemical parameters followed by histopathological studies, and antidepressant activity was assessed by forced swim test. RESULTS： SXE showed presence of steroids. At the dose of 200 mg/kg, it significantly improved all the parameters of sexual behavior （P〈0.01）, caused vaginal cornification, and increased serum estradiol and uterine weight （P〈0.01）. It also significantly improved all the parameters of bone strength as well as depression （P〈0.01）. Histopathology of bones confirmed the above findings. CONCLUSION： The study indicated that SXE may provide an effective treatment in the prevention of postmenopausal symptoms.

关键词： antidepressant herbal drugs solanaceae postmenopausal syndrome ovariectomy rats

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Tomato Genome Gets Fully Decoded—Paves Way to Tastier and Healthier Fruits

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Journal of Genetics and Genomics 2012年第7期39卷 303-305页

作者： Jianfeng Ren Changbao Li Chuanyou Li State Key Laboratory of Plant Genomics National Centre for Plant GeneResearchInstitute of Genetics and Developmental BiologyChinese Academy of SciencesNo.1 West Beichen RoadBeijing 100101China Vegetable Research Center Beijing Academy of Agriculture and Forestry SciencesBeijing 100097China

Thanks to the nearly eight year＇s hard work of the Tomato Genome Consortium （TGC） including more than 300 scien- tists from 14 countries, the genomes of the cultivated tomato Solanum lycopersicum and its closest wild relative, Solanum pimpinellifolium have been decoded and the corresponding findings were published in the journal Nature （The Tomato Genome Consortium, 2012）. The sequences will help researchers find the links between certain tomato genes and the characteristics they determine. Scientists will be able to focus more accurately on beneficial traits and deliver new tomato varieties more quickly and efficiently. New varieties could include tomatoes with improved taste, color and higher nutrient concentrations, or those better equipped for combating disease and drought.

关键词： solanaceae PROJECT SOL

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