The Genome of the Diatom Thalassiosira Pseudonana : Ecology, Evolution, and Metabolism

Abstract

Diatoms are unicellular algae with plastids acquired by secondary endosymbiosis. They are responsible for approximately 20% of global carbon fixation. We report the 34 million-base pair draft nuclear genome of the marine diatom Thalassiosira pseudonana and its 129 thousand-base pair plastid and 44 thousand-base pair mitochondrial genomes. Sequence and optical restriction mapping revealed 24 diploid nuclear chromosomes. We identified novel genes for silicic acid transport and formation of silica-based cell walls, high-affinity iron uptake, biosynthetic enzymes for several types of polyunsaturated fatty acids, use of a range of nitrogenous compounds, and a complete urea cycle, all attributes that allow diatoms to prosper in aquatic environments.

Transcript level coordination of carbon pathways during silicon starvation‐induced lipid accumulation in the diatom Thalassiosira pseudonana

“…S4). De novo biosynthesis of fatty acids occurs in the chloroplast of diatoms via a type II fatty acid synthase (Armbrust et al ., 2004) and the first committed step of fatty acid synthesis is catalyzed by acetyl‐coA carboxylase (ACCase). All components of this fatty acid synthesis machinery, including both chloroplast‐ and cytosol‐localized copies of ACCase (ACCase chl , Thaps3_6770 and ACCase cyt , Thaps3_12234, respectively), and nearly all of the enzymes catalyzing the subsequent steps of the fatty acid synthase pathway are up‐regulated (FASII; Fig.…”

“…8a). This gene is in the process of being transferred from the chloroplast to the nuclear genome, and though the function of this protein is unknown, it is thought to stabilize the PSII protein complex (Armbrust et al ., 2004; García‐Cerdán et al ., 2011). The decoupling of its expression from all other components of PSII in the microarray experiment suggests it may have a unique role in light harvesting or photoprotection.…”

Finding a partner in the ocean: molecular and evolutionary bases of the response to sexual cues in a planktonic diatom

“…The genome size, N50 value and GC content were taken from the respective publications (Armbrust et al ., 2004; Bowler et al ., 2008; Cock et al ., 2010; Lévesque et al ., 2010; Lommer et al ., 2012; Tanaka et al ., 2015; Mock et al ., 2017). …”

Algal genomes reveal evolutionary mosaicism and the fate of nucleomorphs

“…Compared to the genomes of other secondary plastid-bearing algae, such as the diatoms Phaeodactylum tricornutum 5 and Thalassiosira pseudonana 6 , and the filamentous brown alga Ectocarpus siliculosus 7 , the B. natans and G. theta genomes are gene rich (.21,000 predicted protein genes each, .85% of which are supported by RNA-seq data). Of the inferred proteins, 51% in G. theta and 47% in B. natans are unique, that is, have no detectable homologues in any other organism.…”