title: Genome complexity of harmful microalgae.
abstract: During the past decade, next generation sequencing (NGS) technologies have provided new insights into the diversity, dynamics, and metabolic pathways of natural microbial communities. But, these new techniques face challenges related to the genome size and level of genome complexity of the species under investigation. Moreover, the coverage depth and the short-read length achieved by NGS based approaches also represent a major challenge for assembly. These factors could limit the use of these high-throughput sequencing methods for species lacking a reference genome and characterized by a high level of complexity. In the present work, the evolutionary history, mainly consisting of gene transfer events from bacteria and unicellular eukaryotes to microalgae, including harmful species, is discussed and reviewed as it relates to NGS application in microbial communities, with a particular focus on harmful algal bloom species and dinoflagellates. In the context of genetic population studies, genotyping-by-sequencing (GBS), an NGS based approach, could be used for the discovery and analysis of single nucleotide polymorphisms (SNPs). The NGS technologies are still relatively new and require further improvement. Specifically, there is a need to develop and standardize tools and approaches to handle large data sets, which have to be used for the majority of HAB species characterized by evolutionary highly dynamic genomes.
authors.affiliation: Department of Biomolecular Sciences, University of Urbino, Viale Trieste 296, 61121 Pesaro, Italy; CoNISMa, Italian Interuniversity Consortium on Marine Sciences, Piazzale Flaminio 9, 00196, Rome, Italy.
authors.forename: Silvia
authors.initials: S
authors.lastname: Casabianca
authors.affiliation: Institute for Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, Zurich, Switzerland.
authors.forename: Luca
authors.initials: L
authors.lastname: Cornetti
authors.affiliation: Department of Biomolecular Sciences, University of Urbino, Viale Trieste 296, 61121 Pesaro, Italy; CoNISMa, Italian Interuniversity Consortium on Marine Sciences, Piazzale Flaminio 9, 00196, Rome, Italy.
authors.forename: Samuela
authors.initials: S
authors.lastname: Capellacci
authors.affiliation: Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, San Michele all'Adige, 38010 Trento, Italy.
authors.forename: Cristiano
authors.initials: C
authors.lastname: Vernesi
authors.affiliation: Department of Biomolecular Sciences, University of Urbino, Viale Trieste 296, 61121 Pesaro, Italy; CoNISMa, Italian Interuniversity Consortium on Marine Sciences, Piazzale Flaminio 9, 00196, Rome, Italy. Electronic address: antonella.penna@uniurb.it.
authors.forename: Antonella
authors.initials: A
authors.lastname: Penna
mesh_terms: D000818:Animals; D018745:Genome, Plant / Q000235:genetics*; D005838:Genotype; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D058086:Microalgae / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods
keywords: Diatoms; Dinoflagellates; Genome size; Genotyping-by-sequencing (GBS); Harmful algal blooms (HABs); Single nucleotide polymorphisms (SNPs)