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引用本文:张军毅,孙蓓丽,朱冰川,石浚哲,周克茹,吕学研,葛芹玉,张咏,陆祖宏,张虎军.基于分子标记的藻类鉴定研究进展.湖泊科学,2021,33(6):1607-1625. DOI:10.18307/2021.0601
Zhang Junyi,Sun Beili,Zhu Bingchuan,Shi Junzhe,Zhou Keru,Lv Xueyan,Ge Qinyu,Zhang Yong,Lu Zuhong,Zhang Hujun.Research progress in the taxonomic identification of algae on the basis of molecular markers. J. Lake Sci.2021,33(6):1607-1625. DOI:10.18307/2021.0601
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基于分子标记的藻类鉴定研究进展
张军毅1, 孙蓓丽2,3, 朱冰川1, 石浚哲1, 周克茹3, 吕学研4, 葛芹玉2, 张咏4, 陆祖宏2, 张虎军1
1.江苏省无锡环境监测中心, 无锡 214121;2.东南大学无锡分校, 无锡市生物芯片重点实验室, 无锡 214135;3.江苏宏众百德生物科技有限公司, 无锡 214028;4.江苏省环境监测中心, 南京 210019
摘要:
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.
关键词:  藻类鉴定  分子标记  数据库  SSU  LSU  ITS  COI  rbcL
DOI:10.18307/2021.0601
分类号:
基金项目:江苏省无锡市科学技术局社发项目(N20201017)、国家水体污染控制与治理科技重大专项(2018ZX07208002-02)和国家自然科学基金项目(91951104)联合资助.
Research progress in the taxonomic identification of algae on the basis of molecular markers
Zhang Junyi1, Sun Beili2,3, Zhu Bingchuan1, Shi Junzhe1, Zhou Keru3, Lv Xueyan4, Ge Qinyu2, Zhang Yong4, Lu Zuhong2, Zhang Hujun1
1.Jiangsu Wuxi Environmental Monitoring Center, Wuxi 214121, P. R. China;2.Wuxi Key Laboratory of Biochip, Southeast University Wuxi Campus, Wuxi 214135, P. R. China;3.Jiangsu MetaBio Science & Technology Co., Ltd., Wuxi 214028, P. R. China;4.Jiangsu Environmental Monitoring Center, Nanjing 210019, P. R. China
Abstract:
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.
Key words:  Algae identification  molecular maker  database  SSU  LSU  ITS  COI  rbcL
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