蜂属植物基因组综合分析及数据库构建

IF 13 1区综合性期刊 Q1 MULTIDISCIPLINARY SCIENCES

Journal of Advanced Research Pub Date : 2025-10-04 DOI:10.1016/j.jare.2025.10.007

Yanhong Fu, Tong Yu, Xiao Ma, Zhuo Liu, Chunjin Li, Shaoqin Shen, Rong Zhou, Yingchao Zhang, Xiaoming Song

{"title":"蜂属植物基因组综合分析及数据库构建","authors":"Yanhong Fu, Tong Yu, Xiao Ma, Zhuo Liu, Chunjin Li, Shaoqin Shen, Rong Zhou, Yingchao Zhang, Xiaoming Song","doi":"10.1016/j.jare.2025.10.007","DOIUrl":null,"url":null,"abstract":"<h3>Introduction</h3>The Apiales order harbors a rich variety of species, including vegetables, spices, and medicinal herbs, that possess diverse morphological characteristics and are globally distributed. Apiaceae and Araliaceae, being the two principal families within the Apiales order, have been the focus of extensive attention and research efforts on account of their significant value.<h3>Objectives</h3>Although the species in Apiales are important and there is a large amount of genomic data available, there is currently a lack of large-scale genomic analysis and database platform at the Apiales order level. Therefore, this study aims to conduct a comprehensive genomic analysis and database construction for Apiales.<h3>Methods</h3>This study performed comprehensive comparative genomic analysis by bioinformatics methods. The database was constructed with MySQL database management, the Django framework, and multiple programming languages.<h3>Results</h3>The present study was designed to clarify the phylogenetic associations and the phenomenon of paleo-polyploidization within Apiales species. Subsequently, an in-depth exploration was carried out to determine the ancestral karyotypes and to analyze the evolutionary pathways of chromosomes. In this research endeavor, genomic and transcriptomic data were employed to execute a comprehensive bioinformatic analysis. Eventually, through the integration of genomic data and bioinformatics findings, this study established the Apiales Genome Resources Database (TAGR), which is freely accessible at <span><span>http://tagr.bio2db.com/index.html</span><svg aria-label=\"Opens in new window\" focusable=\"false\" height=\"20\" viewbox=\"0 0 8 8\"><path d=\"M1.12949 2.1072V1H7V6.85795H5.89111V2.90281L0.784057 8L0 7.21635L5.11902 2.1072H1.12949Z\"></path></svg></span>.<h3>Conclusion</h3>The research project carried out a profound investigation into the genomic evolution and chromosomal karyotypes of Apiales species, unraveling their evolutionary history from a genomic perspective. In addition, this study established the TAGR, which will offer researchers convenient access to and efficient utilization of these omics data resources, facilitating genomic analysis and molecular breeding initiatives.","PeriodicalId":14952,"journal":{"name":"Journal of Advanced Research","volume":"77 1","pages":""},"PeriodicalIF":13.0000,"publicationDate":"2025-10-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"Comprehensive genomic analysis and database construction for Apiales\",\"authors\":\"Yanhong Fu, Tong Yu, Xiao Ma, Zhuo Liu, Chunjin Li, Shaoqin Shen, Rong Zhou, Yingchao Zhang, Xiaoming Song\",\"doi\":\"10.1016/j.jare.2025.10.007\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<h3>Introduction</h3>The Apiales order harbors a rich variety of species, including vegetables, spices, and medicinal herbs, that possess diverse morphological characteristics and are globally distributed. Apiaceae and Araliaceae, being the two principal families within the Apiales order, have been the focus of extensive attention and research efforts on account of their significant value.<h3>Objectives</h3>Although the species in Apiales are important and there is a large amount of genomic data available, there is currently a lack of large-scale genomic analysis and database platform at the Apiales order level. Therefore, this study aims to conduct a comprehensive genomic analysis and database construction for Apiales.<h3>Methods</h3>This study performed comprehensive comparative genomic analysis by bioinformatics methods. The database was constructed with MySQL database management, the Django framework, and multiple programming languages.<h3>Results</h3>The present study was designed to clarify the phylogenetic associations and the phenomenon of paleo-polyploidization within Apiales species. Subsequently, an in-depth exploration was carried out to determine the ancestral karyotypes and to analyze the evolutionary pathways of chromosomes. In this research endeavor, genomic and transcriptomic data were employed to execute a comprehensive bioinformatic analysis. Eventually, through the integration of genomic data and bioinformatics findings, this study established the Apiales Genome Resources Database (TAGR), which is freely accessible at <span><span>http://tagr.bio2db.com/index.html</span><svg aria-label=\\\"Opens in new window\\\" focusable=\\\"false\\\" height=\\\"20\\\" viewbox=\\\"0 0 8 8\\\"><path d=\\\"M1.12949 2.1072V1H7V6.85795H5.89111V2.90281L0.784057 8L0 7.21635L5.11902 2.1072H1.12949Z\\\"></path></svg></span>.<h3>Conclusion</h3>The research project carried out a profound investigation into the genomic evolution and chromosomal karyotypes of Apiales species, unraveling their evolutionary history from a genomic perspective. In addition, this study established the TAGR, which will offer researchers convenient access to and efficient utilization of these omics data resources, facilitating genomic analysis and molecular breeding initiatives.\",\"PeriodicalId\":14952,\"journal\":{\"name\":\"Journal of Advanced Research\",\"volume\":\"77 1\",\"pages\":\"\"},\"PeriodicalIF\":13.0000,\"publicationDate\":\"2025-10-04\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Journal of Advanced Research\",\"FirstCategoryId\":\"103\",\"ListUrlMain\":\"https://doi.org/10.1016/j.jare.2025.10.007\",\"RegionNum\":1,\"RegionCategory\":\"综合性期刊\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q1\",\"JCRName\":\"MULTIDISCIPLINARY SCIENCES\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Journal of Advanced Research","FirstCategoryId":"103","ListUrlMain":"https://doi.org/10.1016/j.jare.2025.10.007","RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"MULTIDISCIPLINARY SCIENCES","Score":null,"Total":0}

引用次数: 0

摘要

Apiales目包含丰富多样的物种，包括蔬菜、香料和草药，它们具有不同的形态特征，分布于全球。蜂科和五加科作为蜂科的两个主要科，因其重要的价值而受到广泛的关注和研究。目的虽然蜜蜂属重要物种，且基因组数据丰富，但目前尚缺乏大规模的蜜蜂目基因组分析和数据库平台。因此，本研究旨在对阿蜂属植物进行全面的基因组分析和数据库建设。方法采用生物信息学方法进行全面的比较基因组分析。该数据库是使用MySQL数据库管理、Django框架和多种编程语言构建的。结果本研究旨在阐明蜜蜂种间的系统发育关系和古多倍体化现象。随后，进行了深入的探索，确定了祖先的核型，并分析了染色体的进化途径。在这项研究中，基因组学和转录组学数据被用于进行全面的生物信息学分析。最终，本研究通过整合基因组数据和生物信息学发现，建立了蜜蜂基因组资源数据库（TAGR），该数据库可在http://tagr.bio2db.com/index.html.ConclusionThe上免费获取，研究项目对蜜蜂物种的基因组进化和染色体核型进行了深入的研究，从基因组的角度揭示了它们的进化史。此外，本研究还建立了TAGR，为研究人员方便地访问和有效利用这些组学数据资源，促进基因组分析和分子育种计划提供了便利。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

Comprehensive genomic analysis and database construction for Apiales

查看原文本刊更多论文

Comprehensive genomic analysis and database construction for Apiales

Introduction

The Apiales order harbors a rich variety of species, including vegetables, spices, and medicinal herbs, that possess diverse morphological characteristics and are globally distributed. Apiaceae and Araliaceae, being the two principal families within the Apiales order, have been the focus of extensive attention and research efforts on account of their significant value.

Objectives

Although the species in Apiales are important and there is a large amount of genomic data available, there is currently a lack of large-scale genomic analysis and database platform at the Apiales order level. Therefore, this study aims to conduct a comprehensive genomic analysis and database construction for Apiales.

Methods

This study performed comprehensive comparative genomic analysis by bioinformatics methods. The database was constructed with MySQL database management, the Django framework, and multiple programming languages.

Results

The present study was designed to clarify the phylogenetic associations and the phenomenon of paleo-polyploidization within Apiales species. Subsequently, an in-depth exploration was carried out to determine the ancestral karyotypes and to analyze the evolutionary pathways of chromosomes. In this research endeavor, genomic and transcriptomic data were employed to execute a comprehensive bioinformatic analysis. Eventually, through the integration of genomic data and bioinformatics findings, this study established the Apiales Genome Resources Database (TAGR), which is freely accessible at http://tagr.bio2db.com/index.html.

Conclusion

The research project carried out a profound investigation into the genomic evolution and chromosomal karyotypes of Apiales species, unraveling their evolutionary history from a genomic perspective. In addition, this study established the TAGR, which will offer researchers convenient access to and efficient utilization of these omics data resources, facilitating genomic analysis and molecular breeding initiatives.

求助全文

通过发布文献求助，成功后即可免费获取论文全文。去求助

来源期刊

Journal of Advanced Research Multidisciplinary-Multidisciplinary

CiteScore

21.60

自引率

0.90%

发文量

280

审稿时长

12 weeks

期刊介绍： Journal of Advanced Research (J. Adv. Res.) is an applied/natural sciences, peer-reviewed journal that focuses on interdisciplinary research. The journal aims to contribute to applied research and knowledge worldwide through the publication of original and high-quality research articles in the fields of Medicine, Pharmaceutical Sciences, Dentistry, Physical Therapy, Veterinary Medicine, and Basic and Biological Sciences. The following abstracting and indexing services cover the Journal of Advanced Research: PubMed/Medline, Essential Science Indicators, Web of Science, Scopus, PubMed Central, PubMed, Science Citation Index Expanded, Directory of Open Access Journals (DOAJ), and INSPEC.