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Allotetraploidization event of Coptis chinensis shared by all Ranunculales

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Horticultural Plant Journal 2024年第1期10卷 288-303页

作者： Yan Zhang Weina Ge Jia Teng Yanmei Yang Jianyu Wang Zijian Yu Jiaqi Wang Qimeng Xiao Junxin Zhao Shaoqi Shen Yishan Feng Shoutong Bao Yu Li Yuxian Li Tianyu Lei Yuxin Pan Lan Zhang Jinpeng Wang Department of Bioinformatics School of Life SciencesNorth China University of Science and TechnologyTangshanHebei 063000China School of Life Sciences North China University of Science and TechnologyTangshanHebei 063000China State Key Laboratory of systematic and evolutionary botany Institute of BotanyChinese Academy of ScienceBeijing 100093China University of Chinese Academy of Sciences Beijing 100049China

Coptis chinensis Franch.,also named Chinese goldthread is a member of Ranunculaceae in the order Ranunculales and represents an important lineage of early eudicots with traditional medicinal value.In our study,by using syntenic analysis combined with phylogenomic analysis of C.chinensis and four other representative genomes from basal and core eudicots,we confirmed that the WGD event in C.chinensis was shared by Aquilegia coerulea and Papaver somniferum L.and quickly occurred after Ranunculales diverged from other eudicots,likely a Ranunculales common tetraploidization(RCT).The synonymous nucleotide substitutions at synonymous sites distribution of syntenic blocks across these genomes showed that the evolutionary rate of the P.somniferum genome is faster than that of the C.chinensis genome by approximately 13.7%,possibly due to Papaveraceaes having an additional special tetraploidization event(PST).After Ks correction,the RCT dated to 115—130 million years ago(MYA),which was close to the divergence of Ranunculaceaes and Papaveraceaes approximately115.45—130.51 MYA.Moreover,we identified homologous genes related to polyploidization and speciation and constructed multiple sequence alignments with different reference genomes.Notably,the event-related subgenomes in the basal genomes all showed genomic fractionation bias,suggesting a likely allopolyploid nature of the RCT,PST and T-Alpha and T-Beta events in Tetracentron sinense.In addition,we detected that the sixteen P450 subfamilies were markedly expanded in the genomes of Ranunculales,and most of them were related to the RCT and PST events.We constructed a new platform for Early Eudicot Comparative Genomic Research(http://www.***.top/index.html)to store more information.In summary,our findings support the WGD of C.chinensis shared by Ranunculales,which is likely an allotetraploidization event.This present effort offered new insights into the evolution of key polyploidization events and the genes related to secondary metabolites during the diversification of ea

关键词： Coptis chinensis Ranunculales Polyploidization Genomic fractionation P450 genes

A likely paleo-autotetraploidization event shaped the high conservation of Nyssaceae genome

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Horticultural Plant Journal 2024年第3期10卷 911-930页

作者： Yishan Feng Zhenyi Wang Qimeng Xiao Jia Teng Jianyu Wang Zijian Yu Jiaqi Wang Qiang Xu Yan Zhang Shaoqi Shen Shoutong Bao Yu Li Zimo Yan Yue Ding Zihan Liu Yuxian Li Tianyu Lei Min Yuan Xiu-Qing Li Jinpeng Wang Department of Bioinformatics School of Life SciencesNorth China University of Science and TechnologyTangshanHebei 063000China Fredericton Research and Development Centre Agriculture and Agri-Food CanadaFrederictonNew Brunswick E3B 4Z7Canada State Key Laboratory of systematic and evolutionary botany Institute of BotanyChinese Academy of ScienceBeijing 100093China University of Chinese Academy of Sciences Beijing 100049China

Scientific knowledge about the ancestral genome of core eudicot plant kingdom can potentially have profound impacts on both basic and applied research,including evolution,genetics,genomics,ecology,agriculture,forestry,and global climate.To investigate which plant conserves best the core eudicots common ancestor genome,we compared Arcto-Tertiary relict Nyssaceae and 30 other eudicot plant families.The genomes of Davidia involucrata(a known living fossil),Camptotheca acuminata and Nyssa sinensis,one per existent genus of Nyssaceae,were performed comparative genomic analysis.We found that Nyssaceae originated from a single Nyssaceae common tetraploidization event(NCT)-autotetraploidization 28-31 Mya after the core eudicot common hexaploidization(ECH).We identified Nyssaceae orthologous and paralogous genes,determined its chromosomal evolutionary trajectory,and reconstructed the Nyssaceae most recent ancestor genome.D.involucrata genome contained the entire seven paleochromosomes and 17 ECH-generated eudicot common ancestor chromosomes and was the slowest in mutation among the analyzed 42 species of 31 plant families.Combing both its high retention of paleochromosomes and its low mutation rate,D.involucrata provides the best case in conservation of the core eudicot paleogenome.

关键词： Nyssaceae Polyploidization Multigenome alignment evolutionary rate Autotetraploidization Karyotype evolution

Impacts of road on plant invasions in the Middle Mountain region of central Nepal

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Journal of Mountain Science 2024年第2期21卷 619-632页

作者： Ananda ADHIKARI Adarsha SUBEDI Achyut TIWARI Bharat Babu SHRESTHA Central Department of botany Tribhuvan UniversityKirtipur 44618Nepal

Biological invasion is triggered by human development activities such as the construction and expansion of road networks.Road verges serve as important habitats and corridors for the distribution of invasive alien plant species(IAPS)between geographically distant habitats.However,the trajectory of plant invasion and the data regarding the impact of roads on IAPS distribution are relatively poor in Nepal.Here,we surveyed two road types(main roads and feeder road)in the Middle Mountain region of central Nepal in order to investigate how different road types are driving the dispersal of IAPS along road verges and the adjacent natural habitats.systematic sampling was conducted at ca 2.5 km intervals along the roads.At each sampling site,paired plots(25 m×4 m)were sampled:one adjacent to and along the road,and another 20 m away and parallel to it in the interior habitat.Our results revealed that the main road verges had a higher cover(33%)and a larger number of IAPS(14 species)than the feeder road(25%;10 species).The IAPS cover and richness were significantly higher along verges than in the adjacent interior habitats for both road types,indicating that roads are contributing as corridors for the dispersal of IAPS in the Middle Mountain areas of central Nepal.Further,elevation,tree canopy,and disturbances(grazing/mowing/trampling)were found to be the key factors that determine spatial distribution of IAPS along road verges.We emphasize that regular monitoring of vegetation along the road verges can help with the early detection and control of potential IAPS in the region before they become problematic.

关键词： Biological invasions Dispersal corridor Invasive alien plants Transport infrastructure Himalayan mountains

A comprehensive review of genetic causes of obesity

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World Journal of Pediatrics 2024年第1期20卷 26-39页

作者： Marcio Jose Concepcion-Zavaleta Juan Eduardo Quiroz-Aldave Maria del Carmen Durand-Vasquez Elman Rolando Gamarra-Osorio Juan del Carmen Valencia de la Cruz Claudia Mercedes Barrueto-Callirgos Susan Luciana Puelles-Leon Elena de Jesus Alvarado-Leon Frans Leiva-Cabrera Francisca Elena Zavaleta-Gutierrez Luis Alberto Concepcion-Urteaga Jose Paz-Ibarra Universidad Cientifica del Sur Bolivar 2150 AvenuePueblo Libre15084LimaPeru division of Medicine Hospital de Apoyo ChepénChepenPeru division of Family Medicine Hospital de Apoyo ChepénChepenPeru division of Endocrinology Hospital Victor Lazarte EchegarayTrujilloPeru division of Pediatrics Hospital de Apoyo ChepenChepenPeru division of Internal Medicine Hospital de Apoyo ChepenChepenPeru division of Genetics Universidad Nacional de TrujilloTrujilloPeru division of Neonatology Hospital Belen de TrujilloTrujilloPeru division of Internal Medicine Universidad Nacional de TrujilloTrujilloPeru Department of Medicine School of MedicineUniversidad Nacional Mayor de San MarcosLimaPeru

Background Obesity is a multifactorial chronic disease with a high,increasing worldwide prevalence.Genetic causes account for 7%of the cases in children with extreme obesity.Data sources This narrative review was conducted by searching for papers published in the PubMed/MEDLINE,Embase and SciELO databases and included 161 articles.The search used the following search terms:"obesity","obesity and genetics","leptin","Prader-Willi syndrome",and"melanocortins".The types of studies included were systematic reviews,clinical trials,prospective cohort studies,cross-sectional and prospective studies,narrative reviews,and case reports.Results The leptin-melanocortin pathway is primarily responsible for the regulation of appetite and body weight.However,several important aspects of the pathophysiology of obesity remain unknown.Genetic causes of obesity can be grouped into syndromic,monogenic,and polygenic causes and should be assessed in children with extreme obesity before the age of 5 years,hyperphagia,or a family history of extreme obesity.A microarray study,an analysis of the melanocortin type 4 receptor gene mutations and leptin levels should be performed for this purpose.There are three therapeutic levels:lifestyle modifications,pharmacological treatment,and bariatric surgery.Conclusions Genetic study technologies are in constant development;however,we are still far from having a personalized approach to genetic causes of obesity.A significant proportion of the affected individuals are associated with genetic causes;however,there are still barriers to its approach,as it continues to be underdiagnosed.

关键词： Leptin Melanocortin Obesity Prader-Willi syndrome Precision medicine

A new type of cell related to organ movement for selfing in plants

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National Science Review 2023年第9期10卷 190-203页

作者： Yin-Zheng Wang Yan-Xiang Lin Qi Liu Jing Liu Spencer C.H.Barrett State Key Laboratory of systematic and evolutionary botany Institute of BotanyChinese Academy of Sciences China National Botanical Garden College of Life Sciences University of Chinese Academy of Sciences College of Pharmacy Fujian University of Traditional Chinese Medicine Department of Ecology and evolutionary Biology University of Toronto

Many plants employ osmotic and hydrostatic pressure to generate movement for survival,but little is known about the cellular mechanisms involved.Here,we report a new cell type in angiosperms termed ’contractile cells’ in the stigmas of the flowering plant Chirita pumila with a much-expanded rough endoplasmic reticulum(RER).Cryo-scanning electron microscopy and transmission electron microscopy analyses revealed that the RER is continuously distributed throughout the entirety of cells,confirmed by endoplasmic reticulum(ER)-specific fluorescent labeling,and is distinct from the common feature of plant ER.The RER is water-sensitive and extremely elongated with water absorption.We show that the contractile cells drive circadian stigma closing-bending movements in response to day-to-night moisture changes.RNA-seq analyses demonstrated that contractile cells have distinct molecular components.Furthermore,multiple microstructural changes in stigma movements convert an anti-selfing structure into a device promoting selfing—a unique cellular mechanism of reproductive adaptation for uncertain pollination environments.

关键词： stigma movement rough endoplasmic reticulum contractile cells circadian moisture changes reproductive transition

The origin and evolution of carpels and fruits from an evo-devo perspective

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Journal of Integrative Plant Biology 2023年第2期65卷 283-298页

作者： Hongyan Liu Jun Li Pichang Gong Chaoying He State Key Laboratory of systematic and evolutionary botany Institute of BotanyChinese Academy of SciencesBeijing 100093China University of Chinese Academy of Sciences Beijing 100049China The Innovative Academy of Seed Design Chinese Academy of SciencesBeijing 100101China

The flower is an evolutionary innovation in angiosperms that drives the evolution of biodiversity.The carpel is integral to a flower and develops into fruits after fertilization,while the perianth,consisting of the calyx and corolla,is decorative to facilitate pollination and protect the internal organs,including the carpels and stamens.Therefore,the nature of flower origin is carpel and stamen origin,which represents one of the greatest and fundamental unresolved issues in plant evolutionary biology.Here,we briefly summarize the main progress and key genes identified for understanding floral development,focusing on the origin and development of the carpels.Floral ABC models have played pioneering roles in elucidating flower development,but remain insufficient for resolving flower and carpel origin.The genetic basis for carpel origin and subsequent diversification leading to fruit diversity also remains elusive.Based on current research progress and technological advances,simplified floral models and integrative evolutionary-developmental(evodevo)strategies are proposed for elucidating the genetics of carpel origin and fruit evolution.Stepwise birth of a few master regulatory genes and subsequent functional diversification might play a pivotal role in these evolutionary processes.Among the identified transcription factors,AGAMOUS(AG)and CRABS CLAW(CRC)may be the two core regulatory genes for carpel origin as they determine carpel organ identity,determinacy,and functionality.Therefore,a comparative identification of their protein-protein interactions and downstream target genes between flowering and non-flowering plants from an evo-devo perspective may be primary projects for elucidating carpel origin and development.

关键词： AGAMOUS CRABS CLAW carpel origin evo-devo floral development fruit evolution

Impact of exercise on markers of B cell-related immunity:A systematic review

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Journal of Sport and Health Science 2024年第3期13卷 339-352,I0002页

作者： David Walzik Sergen Belen Karen Wilisch Marie Kupjetz Silvana Kirschke Tobias Esser Niklas Joisten Alexander Schenk Sebastian Proschinger Philipp Zimmer division of Performance and Health(Sports Medicine) Institute for Sport and Sport ScienceTU Dortmund UniversityDortmund 44227Germany

Background:B cells represent a crucial component of adaptive immunity that ensures long-term protection from infection by generating pathogen-specific immunoglobulins.Exercise alters B cell counts and immunoglobulin levels,but evidence-based conclusions on potential benefits for adaptive immunity are lacking.This systematic review assessed current literatures on the impact of acute exercise and exercise training on B cells,immunoglobulins,and markers of secretory immunity in human biofluids.Methods:According to the Preferred Reporting Items for systematic Reviews and Meta-Analyses(PRISMA)guidelines,MEDLINE,Web of Science,and Embase were searched on March 8,2023.Non-randomized controlled trials and crossover trials investigating the impact of acute exercise or exercise training on B cell counts and proportions,immunoglobulin levels,salivary flow rate,or secretory immunoglobulin A secretion rate were included.Quality and reporting of exercise training studies were assessed using the Tool for the Assessment of Study Quality and reporting in Exercise.Study characteristics,outcome measures,and statistically significant changes were summarized tabularly.Results:Of the 67 eligible studies,22 applied acute exercise and 45 applied exercise training.All included outcomes revealed significant alterations over time in acute exercise and exercise training context,but only a few investigations showed significant differences compared to control conditions.Secretory and plasma immunoglobulin A levels were most consistently increased in response to exercise training.Conclusion:B cell-related outcomes are altered by acute exercise and exercise training,but evidence-based conclusions cannot be drawn with high confidence due to the large heterogeneity in populations and exercise modalities.Well-designed trials with large sample sizes are needed to clarify how exercise shapes B cell-related immunity.

关键词： Antibody B-lymphocyte Exercise Humoral immunity Immune system

Pollen Morphology of the Platycodonoid Group (Campanulaceae s.str.) and Its systematic Implications

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Journal of Integrative Plant Biology 2012年第10期54卷 773-789页

作者： HONG De-Yuan PAN Kai-Yu State Key Laboratory of systematic&evolutionary botany Institute of BotanyThe Chinese Academy of SciencesChina

In this study, we examined the pollen morphology of the platycodonoid group in Campanulaceae s. str. using a scanning electronic microscope. We used pollen grains of 25 accessions representing 24 species of the Codonopsis complex （including Campanumoea, Cyclocodon, Leptocodon, and all three subgenera of Codonopsis）, which is extremely controversial among authors for taxonomic treatment. Pollen morphology of all the other genera in the group observed by previous authors is taken into account in our discussion. A total of nine pollen types with two subtypes in the group were recognized and named for the first time. Molecular and morphological data imply that each pollen type corresponds to a natural group at generic level, and thus the mergence of Leptocodon with Codonopsis and the restoration of Cyclocodon as a separate genus are justifiable, and Codonopsis subg. Pseudocodonopsis, subg. Obconicicapsula, and two species of Codonopsis subg. Codonopsis （C. purpurea and C. chimiliensis） may be better classified as three independent genera separate from the core Codonopsis.

关键词： Campanulaceae s. str. platycodonoid group Codonopsis complex pollen morphology pollen type taxonomy systematics.

Deciphering gastric inflammation-induced tumorigenesis through multi-omics data and AI methods

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Cancer Biology & Medicine 2024年第4期21卷 312-330页

作者： Qian Zhang Mingran Yang Peng Zhang Bowen Wu Xiaosen Wei Shao Li Institute for TCM-X MOE Key Laboratory of BioinformaticsBioinformatics DivisionBNRISTDepartment of AutomationTsinghua UniversityBeijing 100084China

Gastric cancer(GC), the fifth most common cancer globally, remains the leading cause of cancer deaths worldwide. Inflammation-induced tumorigenesis is the predominant process in GC development;therefore, systematic research in this area should improve understanding of the biological mechanisms that initiate GC development and promote cancer hallmarks. Here, we summarize biological knowledge regarding gastric inflammation-induced tumorigenesis, and characterize the multi-omics data and systems biology methods for investigating GC development. Of note, we highlight pioneering studies in multi-omics data and state-of-the-art network-based algorithms used for dissecting the features of gastric inflammation-induced tumorigenesis, and we propose translational applications in early GC warning biomarkers and precise treatment strategies. This review offers integrative insights for GC research, with the goal of paving the way to novel paradigms for GC precision oncology and prevention.

关键词： Gastric cancer inflammation-induced tumorigenesis multi-omics artificial intelligence network-based methods