Genetic and phenotypic characterization of Phaeodactylum tricornutum (Bacillariophyceae) accessions¹

Abstract

In the last few years, genome-based studies in diatoms have received a major boost following the genome sequencing of the centric species Thalassiosira pseudonana Hasle et Heimdal and the pleiomorphic raphid pennate diatom Phaeodactylum tricornutum Bohlin. In addition, molecular tools, such as genetic transformation, have been developed for both species. Despite these molecular advances, relatively little is known regarding the genetic diversity of the available strains of these diatoms. In this study, we have compiled a historical summary of the known P. tricornutum species resources and have provided a genetic and phenotypic overview of 10 different axenic strains. Examination of intraspecies genetic diversity based on internal transcribed spacer 2 (ITS2) sequence and amplified fragment length polymorphism (AFLP) analyses indicate four different genotypes. Seven strains are predominantly fusiform, whereas one strain is predominantly oval, and another is predominantly triradiate. Another is defined as a tropical strain because it appears better acclimated to growth at higher temperatures. Observations in the natural environment indicate that P. tricornutum is a coastal marine diatom that is able to adapt to unstable environments, such as estuaries and rock pools. Because it has rarely been noted in nature, we have developed specific primers to amplify ITS2 sequences and have successfully identified it in environmental samples. These resources should become useful tools for the diatom community when combined with the whole genome sequence and will open up a range of new possibilities for experimental investigations that can exploit the genotypic and phenotypic characteristics described.

Insights into the role of DNA methylation in diatoms by genome-wide profiling in Phaeodactylum tricornutum

“…Furthermore, P. tricornutum has the peculiarity to be pleiomorphic as it can be found in the form of four different morphotypes: fusiform, oval, round and triradiate 44 . Significantly, morphotype transition occurs in response to specific environmental conditions such as salinity stress, temperature stress and nutrient limitation 44,45 . Therefore, P. tricornutum also constitutes an excellent model to study the basis of epigenomic reprogramming events that lead to morphological variations in response to external stimuli, for example, to assess the influence on adaptive evolutionary processes of the increased susceptibility of methylated genes to mutation.…”

Evolutionary genomics of the cold-adapted diatom Fragilariopsis cylindrus

“…We compared the F. cylindrus genome with those of Thalassiosira pseudonana 16 and Phaeodactylum tricornutum 17 (Extended Data Table 1), both of which live in temperate and neritic marine environments 18,19 characterized by higher water temperatures, turbidity and concentrations of dissolved iron. The haploid gene content of F. cylindrus is enriched for two conserved metal-binding protein families (structural classification of proteins (SCOP) fold families; Supplementary Information 6).…”

Linking phytoplankton community composition to seasonal changes in f-ratio

“…P. tricornutum occurs in three shapes, the tricornered hat, the spindle and a small (3-8 mm diameter) oval (Allen et al, 2008). The oval dominates most isolates when subjected to stress (De Martino et al, 2007). Using a PCR assay designed to be specific for the intergenic transcribed spacer region of the P. tricornutum 18S rRNA genes, De Martino et al (2007) detected P. tricornutum in the DNA extracts from April and July from which the array targets were prepared.…”

“…The oval dominates most isolates when subjected to stress (De Martino et al, 2007). Using a PCR assay designed to be specific for the intergenic transcribed spacer region of the P. tricornutum 18S rRNA genes, De Martino et al (2007) detected P. tricornutum in the DNA extracts from April and July from which the array targets were prepared. In fact, one of the first isolations of a culture of P. tricornutum, then called Nitzschia closterium var.…”