Domestication of cranberry and blueberry began in the United States in the early 1800s and 1900s,respectively,and in part owing to their f lavors and health-promoting benefits are now cultivated and consumed worldwide...Domestication of cranberry and blueberry began in the United States in the early 1800s and 1900s,respectively,and in part owing to their f lavors and health-promoting benefits are now cultivated and consumed worldwide.The industry continues to face a wide variety of production challenges(e.g.disease pressures),as well as a demand for higher-yielding cultivars with improved fruit quality characteristics.Unfortunately,molecular tools to help guide breeding efforts for these species have been relatively limited compared with those for other high-value crops.Here,we describe the construction and analysis of the first pangenome for both blueberry and cranberry.Our analysis of these pangenomes revealed both crops exhibit great genetic diversity,including the presence-absence variation of 48.4%genes in highbush blueberry and 47.0%genes in cranberry.Auxiliary genes,those not shared by all cultivars,are significantly enriched with molecular functions associated with disease resistance and the biosynthesis of specialized metabolites,including compounds previously associated with improving fruit quality traits.The discovery of thousands of genes,not present in the previous reference genomes for blueberry and cranberry,will serve as the basis of future research and as potential targets for future breeding efforts.The pangenome,as a multiple-sequence alignment,as well as individual annotated genomes,are publicly available for analysis on the Genome Database for Vaccinium-a curated and integrated web-based relational database.Lastly,the core-gene predictions from the pangenomes will serve useful to develop a community genotyping platform to guide future molecular breeding efforts across the family.展开更多
Background Seasonal patterns of mycobacterial infections affecting humans and animals remain a complex and understudied aspect of infectious disease dynamics.These intra-annual patterns are increasingly relevant in th...Background Seasonal patterns of mycobacterial infections affecting humans and animals remain a complex and understudied aspect of infectious disease dynamics.These intra-annual patterns are increasingly relevant in the context of global climate change,which may influence the timing and geographic spread of these diseases.A better understanding of such patterns could improve surveillance,prevention,and control strategies.Methods We conducted a mixed-methods bibliometric review combining bibliographic searches and scoping analysis to synthesize decades of research on the seasonality of mycobacterial infections in humans and animals.We systematically searched three major scientific databases—Scopus,PubMed-MEDLINE,and Web of Science—for articles published between 1971 and April 2023.From an initial dataset of 1830 unique articles,we identified and analysed 122 studies that met predefined inclusion criteria.We extracted information on pathogen type,statistical methods,geographic location,and host species.In addition,we conducted a co-citation network analysis to identify key methodological influences and research clusters.Results The retained studies encompassed tuberculosis,Buruli ulcer,bovine tuberculosis,and other mycobacterial diseases such as leprosy and Johne’s disease.Most articles focused on tuberculosis in humans,followed by Buruli ulcer caused by Mycobacterium ulcerans.There was a marked increase in studies on seasonal trends in tuberculosis and Buruli ulcer over time,with notable variation in geographic and methodological coverage.Research was heavily concentrated in the northern hemisphere,especially in China,while southern regions remained underrepresented.Advanced statistical tools,including generalized linear models and time-series analyses,were instrumental in detecting seasonality,particularly for tuberculosis and Buruli ulcer.Conclusion Seasonality appears to be a common yet understudied feature of many mycobacterial infections.Greater interdisciplinary collaboration and the use of appropriate analytical tools are essential to better understand these patterns,especially in underrepresented regions.Addressing methodological and geographic gaps will be crucial to improve responses to these diseases in a changing global environment.展开更多
基金supported by Michigan State University AgBioResearch,Michigan State University Institute for Cyber-Enabled Research,NIH 5T32GM110523-10,NSF NRT-HDR 1828149 USDANIFA HATCH MICL02742,USDA-NIFA AFRI 1015241,and USDANIFA SCRI award 2019-51181-30015supported in part by the National Science Foundation Research Traineeship Program(DGE-1828149)to M.J.
文摘Domestication of cranberry and blueberry began in the United States in the early 1800s and 1900s,respectively,and in part owing to their f lavors and health-promoting benefits are now cultivated and consumed worldwide.The industry continues to face a wide variety of production challenges(e.g.disease pressures),as well as a demand for higher-yielding cultivars with improved fruit quality characteristics.Unfortunately,molecular tools to help guide breeding efforts for these species have been relatively limited compared with those for other high-value crops.Here,we describe the construction and analysis of the first pangenome for both blueberry and cranberry.Our analysis of these pangenomes revealed both crops exhibit great genetic diversity,including the presence-absence variation of 48.4%genes in highbush blueberry and 47.0%genes in cranberry.Auxiliary genes,those not shared by all cultivars,are significantly enriched with molecular functions associated with disease resistance and the biosynthesis of specialized metabolites,including compounds previously associated with improving fruit quality traits.The discovery of thousands of genes,not present in the previous reference genomes for blueberry and cranberry,will serve as the basis of future research and as potential targets for future breeding efforts.The pangenome,as a multiple-sequence alignment,as well as individual annotated genomes,are publicly available for analysis on the Genome Database for Vaccinium-a curated and integrated web-based relational database.Lastly,the core-gene predictions from the pangenomes will serve useful to develop a community genotyping platform to guide future molecular breeding efforts across the family.
基金supported by the joint NSF-NIH-NIFA Ecology and Evolution of Infectious Disease program(DEB#1911457)CC and J-FG benefited from an‘Investissement d’Avenir’grant managed by Agence Nationale de la Recherche(LABEX CEBA:ANR-10-LABX-25-01)+1 种基金CAVC received a Master degree fellowship from DEB#1911457MEB received an award from an‘Investissement d’Avenir’grant managed by Agence Nationale de la Recherche(LABEX CEMEB:ANR-10-LABX-04-01).
文摘Background Seasonal patterns of mycobacterial infections affecting humans and animals remain a complex and understudied aspect of infectious disease dynamics.These intra-annual patterns are increasingly relevant in the context of global climate change,which may influence the timing and geographic spread of these diseases.A better understanding of such patterns could improve surveillance,prevention,and control strategies.Methods We conducted a mixed-methods bibliometric review combining bibliographic searches and scoping analysis to synthesize decades of research on the seasonality of mycobacterial infections in humans and animals.We systematically searched three major scientific databases—Scopus,PubMed-MEDLINE,and Web of Science—for articles published between 1971 and April 2023.From an initial dataset of 1830 unique articles,we identified and analysed 122 studies that met predefined inclusion criteria.We extracted information on pathogen type,statistical methods,geographic location,and host species.In addition,we conducted a co-citation network analysis to identify key methodological influences and research clusters.Results The retained studies encompassed tuberculosis,Buruli ulcer,bovine tuberculosis,and other mycobacterial diseases such as leprosy and Johne’s disease.Most articles focused on tuberculosis in humans,followed by Buruli ulcer caused by Mycobacterium ulcerans.There was a marked increase in studies on seasonal trends in tuberculosis and Buruli ulcer over time,with notable variation in geographic and methodological coverage.Research was heavily concentrated in the northern hemisphere,especially in China,while southern regions remained underrepresented.Advanced statistical tools,including generalized linear models and time-series analyses,were instrumental in detecting seasonality,particularly for tuberculosis and Buruli ulcer.Conclusion Seasonality appears to be a common yet understudied feature of many mycobacterial infections.Greater interdisciplinary collaboration and the use of appropriate analytical tools are essential to better understand these patterns,especially in underrepresented regions.Addressing methodological and geographic gaps will be crucial to improve responses to these diseases in a changing global environment.
