古树基因组数据库开发与应用  

Development and application of ancient tree genome database

作　　者：张辉 冯一健 韦上校 李华 彭海旭 吴邵元 马晓燕[3] 李玮瑜 王森[1,2] 郑轶 ZHANG Hui;FENG Yijian;WEI Shangxiao;LI Hua;PENG Haixu;WU Shaoyuan;MA Xiaoyan;LI Weiyu;WANG Sen;ZHENG Yi(Beijing Key Laboratory of New Technology in Agricultural Application/College of Plant Science and Technology,Beijing University of Agriculture,Beijing 102206,China;Bioinformatics Center,Beijing University of Agriculture,Beijing 102206,China;National Forestry Grassland Ancient Tree Health and Ancient Tree Culture Engineering Technology Research Center,Beijing 102206,China)

机构地区：[1]北京农学院,植物科学技术学院/农业应用新技术北京市重点实验室,北京102206 [2]北京农学院生物信息中心,北京102206 [3]北京农学院,国家林业草原古树健康与古树文化工程技术研究中心,北京102206

出　　处：《北京农学院学报》2024年第3期109-115,共7页Journal of Beijing University of Agriculture

基　　金：2023年北京农学院揭榜挂帅项目;北京农学院青年教师科研创新能力提升计划(QJKC2022044)。

摘　　要：【目的】建立古树基因组数据库存储古树名木及相关物种的基因组遗传信息数据,实现基因组数据的浏览、查询、在线分析。【方法】依据《古树名木普查技术规范》的相关规定,树龄在100年以上的树木为古树。参照记录在册的古树品种,从相关数据库收集国内外已公开发表的同种古树基因组等遗传信息,同时对收集的古树基因组进行整理与校正、基因功能注释,遗传数据进行整理与分析,将其标准化的数据上传到开发的古树基因组数据库。【结果】开发了古树基因组数据库并完成上线,实现了对古树基因组等遗传数据存储、查询、浏览。目前共收录了等89种古树名木及相关物种的基因组及比较基因组数据,为研究古树在复杂环境胁迫下长寿的分子机制提供数据支持。开发了在线数据挖掘工具,实现了遗传信息基于BLAST的序列比对、序列批量提取、GO和KEGG的富集分析、共线性分析等功能,为研究古树优良基因提供数据分析平台。【结论】古树及相关物种基因组遗传信息的整理归纳,古树基因组数据库的开发应用为古树科研用户提供了极大的便利,为有效地保护古树资源提供新的见解。[Objective]To establish an ancient tree genome database for storing genetic information data of ancient tree and related species,and to achieve browsing,querying,and online analysis of genome data.[Methods]According to the relevant provisions of the"Technical Specifications for the Survey of Ancient Trees and Famous Trees",trees aged 100 years or older are considered ancient trees.In this study,registered ancient tree species were referenced to collect genetic information of the same species of ancient trees published worldwide from relevant databases.The collected ancient tree genomes were organized,corrected,and annotated for gene function,and genetic data were organized and analyzed.The standardized data were uploaded to the developed ancient tree genome database.[Results]The ancient tree genome database was developed and launched online,enabling storage,querying,and browsing of genetic data such as ancient tree genomes.Currently,genetic and comparative genomic data of 89 species of ancient trees and related species have been collected,providing data support for studying the molecular mechanisms of longevity under complex environmental stresses in ancient trees.Online data mining tools have been developed,realizing functions such as sequence alignment based on BLAST,batch sequence extraction,enrichment analysis of GO and KEGG,and collinearity analysis,providing a data analysis platform for studying excellent genes in ancient trees.[Conclusion]The compilation and summarization of genetic information of ancient tree and related species genomes,and the development and application of the ancient tree genome database,have greatly facilitated scientific researchers in ancient tree research,providing new insights for effectively conserving ancient tree resources.

关 键 词：古树 基因组 数据库 数据挖掘 

分 类 号：Q811.4[生物学—生物工程]