High-throughput sequencing for algal systematics

Abstract

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 data sets 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.

Phylogenomic study and organellar genomic characterization of gracilarioids seaweeds (Gracilariaceae, Rhodophyta)

“…Illumina is the dominant system in the HTS market (Reuter et al 2015;Oliveira et al 2018), which possess different types of sequencing instruments with a large range of output quantity, from low-throughput to very large output (up to 900 Gb in Illumina HiSeq X) (Goodwin et al 2016). Error rates are very low for all these platforms, compared with other technologies.…”

“…Error rates are very low for all these platforms, compared with other technologies. PacBio and MinION technologies can produce long sequence reads but produce a lower yield and generally have a higher error rate than Illumina (Goodwin et al 2016, Oliveira et al 2018. They are typically used to complement the more accurate and higher-throughput Illumina methods for assembly and genome finishing (Oliveira et al 2018).…”

“…For example, a whole-genome sequencing (WGS) including the total genomic DNA of the organism, which include organelle DNA, plasmid DNA, nuclear DNA, and genomes from endosymbionts. It is also possible to sequence a set of different organisms in the same run, using the multiplexing approach, in which the DNA fragments of each sample is ligated to a short sequence tag (called index or barcode) and the reads of each sample are latter identified by bioinformatic tools (Oliveira et al 2018). The biggest challenge about HTS technologies is the high demand for bioinformatic tools capable of sorting, analyzing and managing large amounts of data (Dijk et al 2014a;Oliveira et al 2018).…”

“…It is also possible to sequence a set of different organisms in the same run, using the multiplexing approach, in which the DNA fragments of each sample is ligated to a short sequence tag (called index or barcode) and the reads of each sample are latter identified by bioinformatic tools (Oliveira et al 2018). The biggest challenge about HTS technologies is the high demand for bioinformatic tools capable of sorting, analyzing and managing large amounts of data (Dijk et al 2014a;Oliveira et al 2018). Each HTS run produce millions of sequences reads that require specific computational analysis workflows to produce interpretable results.…”

“…Each HTS run produce millions of sequences reads that require specific computational analysis workflows to produce interpretable results. Individual steps in a workflow can be carried out by different programs, with customizable sets of features (Oliveira et al 2018).…”