High-throughput sequencing for algal systematics

被引：36

作者：

Oliveira, Mariana C. ^{[1
]}

Repetti, Sonja I. ^{[2
]}

Iha, Cintia ^{[2
]}

Jackson, Christopher J. ^{[2
]}

Diaz-Tapia, Pilar ^{[2
,3
,4
]}

Lubiana, Karoline Magalhaes Ferreira ^{[1
]}

Cassano, Valeria ^{[1
]}

Costa, Joana F. ^{[2
]}

Cremen, Ma Chiela M. ^{[2
]}

Marcelino, Vanessa R. ^{[2
,5
,6
,7
]}

Verbruggen, Heroen ^{[2
]}

机构：

[1] Univ Sao Paulo, Biosci Inst, Dept Bot, BR-05508090 Sao Paulo, Brazil

[2] Univ Melbourne, Sch Biosci, Melbourne, Vic 3010, Australia

[3] Univ A Coruna, Coastal Biol Res Grp, Fac Sci, La Coruna 15071, Spain

[4] Univ A Coruna, Ctr Adv Sci Res CICA, La Coruna 15071, Spain

[5] Univ Sydney, Marie Bashir Inst Infect Dis & Biosecur, Sydney, NSW 2006, Australia

[6] Univ Sydney, Sydney Med Sch, Sydney, NSW 2006, Australia

[7] Westmead Inst Med Res, Westmead, NSW 2145, Australia

来源：

EUROPEAN JOURNAL OF PHYCOLOGY | 2018年 / 53卷 / 03期

基金：

澳大利亚研究理事会; 巴西圣保罗研究基金会;

关键词：

bioinformatic workflows; classification; high-throughput sequencing; molecular data; multiplexing; nomenclature; species boundaries; species discovery; systematics; COMPLETE MITOCHONDRIAL GENOME; DEEP-LEVEL RELATIONSHIPS; APPLYING AVAILABLE NAMES; SPECIES DELIMITATION; RED ALGAE; CHLOROPLAST GENOMES; ANCIENT DNA; DIVERSITY; SPECIMENS; RHODOPHYTA;

D O I：

10.1080/09670262.2018.1441446

中图分类号：

Q94 [植物学];

学科分类号：

071001 ;

摘要：

In recent years, the use of molecular data in algal systematics has increased as high-throughput sequencing (HTS) has become more accessible, generating very large datasets at a reasonable cost. In this perspectives paper, our goal is to describe how HTS technologies can advance algal systematics. Following an introduction to some common HTS technologies, we discuss how metabarcoding can accelerate algal species discovery. We show how various HTS methods can be applied to generate datasets for accurate species delimitation, and how HTS can be applied to historical type specimens to assist the nomenclature process. Finally, we discuss how HTS data such as organellar genomes and transcriptomes can be used to construct well-resolved phylogenies, leading to a stable and natural classification of algal groups. We include examples of bioinformatic workflows that may be applied to process data for each purpose, along with common programs used to achieve each step. We also discuss possible strategies and the new skill set that will be required to fully embrace HTS as a part of algal systematics, along with considerations of cost and experimental design. HTS technology has revolutionized many fields in biology, and will certainly do the same in algal systematics.

引用

页码：256 / 272

页数：17

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