基于分子标记的藻类鉴定研究进展

Research progress in the taxonomic identification of algae on the basis of molecular markers

藻类鉴定被广泛应用于藻类遗传学、生理学、生态学和应用藻类学,尤其是藻类调查和评估.然而,基于形态学的鉴定往往因为分类特征未出现或不典型、设备限制和人员经验欠缺等原因带来较大误差.随着测序技术的不断发展,分子标记已成为藻类鉴定的一个通用工具.由于藻类类群众多且差异很大,分子标记的选择成为藻类鉴定的关键.本文综述了蓝藻、硅藻、绿藻、甲藻、裸藻、隐藻、金藻、黄藻、红藻和褐藻等主要门类分子标记的选择及应用进展,包括分子标记选择原则、常用标记和相应序列数据库,以及各个分子标记在不同类群应用中的优缺点等.藻类分子鉴定源于编码核糖体RNA的基因(rDNA),发展于细胞核、线粒体、叶绿体DNA等.然而,当前藻类分子鉴定逐渐细化和完善,单一的核糖体DNA、内转录间隔区(ITS)和保守蛋白编码基因等短序列分子标记已经很难满足藻类鉴定的需求,多标记组合成为一种必然选择.同时,线粒体基因组、叶绿体基因组、核基因组、转录组和宏基因组等提供了更多遗传进化信息,弥补了短序列分子标记在系统分类应用中的不足.对于藻类鉴定,单纯依赖分子标记或形态学都不足以保证鉴定的准确性,采用将分子生物学、形态学、生理生化学等结合的多相学方法,才能准确地完成鉴定工作.此外,藻类分子数据库的建立和完善是未来分子鉴定的重要工作,快速鉴定方法也必将在未来获得广泛的应用和发展.

Taxonomic identification of algae is widely used in algal genetics,physiology,ecology,applied phycology,and particularly bioassessment.Errors in identification have been caused by the inherent problems of atypical or absent taxonomic features,research-grade microscopes,and inadequate taxonomic expertise.In recent years,as longer,cheaper,and faster DNA sequencing technologies have become more accessible,molecular markers have increasingly become universal tools in algae identification.The selection of molecular markers is critical for the molecular identification of algae because there are obvious differences among various phyla.We reviewed the progress in selecting and applying molecular markers in Cyanophyta,Bacillariophyta,Chlorophyta,Pyrrophyta,Euglenophyta,Cryptophyta,Chrysophyta,Xanthophyta,Rhodophyta,and Phaeophyta,and examined the principles governing selection,common molecular markers,improvements in the sequence database,and the advantages and disadvantages of the application in different phyla.Identifying species using nucleic,mitochondrial,and chloroplast DNA has become commonplace in recent years.To date,it has been considered that combining multiple markers of ribosomal DNA(rDNA),internal transcribed spacers(ITS),and conserved protein coding genes is much more effective than using a single marker for algae molecular identification.In addition,the mitochondrial,chloroplast,and nuclear genome,transcriptome,and metagenome contain large amounts of phylogenetic information,and their use is becoming significant for phylogenetic analysis as well as in the classification of algae.Potentially,they represent giant molecular markers for use in future research into algae systematics.Phylogenetic analysis on the basis of molecular markers,together with morphological features,is insufficient for exact identification.A polyphasic approach-combining features from molecular biology,morphology,physiology,and biochemistry-has been applied in algae classification and will become the strategy of choice for accurate and systematic algae classification and identification.Databases are essential for the application of algae molecular identification,and much work needs to be done to perfect the databases for the molecular marker for each alga.The rapid identification approach on the basis of molecular markers will be widely applied in future.