叶绿体基因组是研究植物分类、进化和异源生产次生代谢产物以及蛋白药物的重要工具.随着测序技术的发展和测序成本的下降,叶绿体基因组数据得到了快速积累.但已发布的叶绿体基因组相关数据库存在数据不全面、不完整和管理不足以及叶绿体基因组相关信息不准确、不统一等问题,给叶绿体基因组的开发利用带来更多挑战,亟须建立一个能提供全面且可靠信息的叶绿体基因组数据库.该文对全球物种数量最多的叶绿体基因组综合数据库(Chloroplast Genome Information Resource,CGIR)进行简要介绍.该数据库包含了基因组(genomes)、基因(genes)、微卫星序列(SSRs)、DNA条形码(bar-codes),DNA特征序列(DSSs)5个模块,目前已收录了16717个物种的34923条叶绿体基因组.基于数据库模块功能,文章还系统总结了该数据库在植物系统发育分析、物种鉴定和叶绿体基因工程的应用进展.未来将对该叶绿体基因组数据库进行持续更新,以期为叶绿体基因组研究提供坚实可靠的数据基础,并进一步推动中药鉴定、资源保护、种质创新等研究.
Establishment and application of chloroplast genome database with the largest number of species in world
The chloroplast genome is an important tool for studying plant classification,evolution,and the heterologous production of secondary metabolites and protein drugs.With advancements in sequencing technology and reductions in sequencing costs,chloroplast genome data have rapidly accumulated.However,existing chloroplast genome databases suffer from issues such as incomplete data,inadequate management,and inconsistent,inaccurate information,posing significant challenges for the development and utilization of the chloroplast genome.Therefore,it is urgently necessary to establish a database that provides comprehensive and reliable chloroplast genome information.This article provides a brief introduction to the Chloroplast Genome Information Resource (CGIR),the most comprehensive chloroplast genome database globally in terms of species coverage.The database,consisting of five modules,i.e.,① genomes,② genes,③ simple sequence repeats (SSRs),④ DNA barcodes,and ⑤ DNA signature sequences (DSSs),currently includes 34923 chloroplast genome assemblies from 16717 species.Based on the functionalities of these modules,the article systematically summarizes the progress in the application of the database in plant phylogenetic analysis,species identification,and chloroplast genetic engineering.The chloroplast genome database will be continuously updated in the future to provide a solid and reliable data foundation for chloroplast genome research,further promoting studies on traditional Chinese medicine (TCM)identification,resource conservation,and germplasm innovation.
万方数据
维普
