The diurnal transcriptional landscape of the microalga Tetradesmus obliquus

Carrères, Benoît M.; León-Saiki, G. Mitsue; Schaap, Peter J.; Remmers, Ilse M.; Veen, Douwe van der; Santos, Vítor A. P. Martins dos; Wijffels, René H.; Martens, Dirk E.; Suárez-Diez, María

doi:10.1016/j.algal.2019.101477

Cited by 10 publications

(20 citation statements)

References 60 publications

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“…The genome is likely diploid, as there is separation of alleles, with 1,606 alternate haplotype contigs and an approximate haploid assembly size of 103.4 Mbp. The predicted 17,399 genes in the primary haplotype are comparable in number to other Sphaeropleales genomes but fewer than in the Scenedesmus obliquus strains (19,873 in UTEX 3031 haplotype 28 and 19,723 in UTEX 393 24 , 29 ) (Fig. 3b and Supplementary Table 1 ).…”

Section: Resultsmentioning

confidence: 78%

“…NREL 46B-D3 genome and transcriptome provide further insight into the metabolic and transcriptional stress response. While our current understanding of the molecular pathways in Scenedesmus species is limited, it is growing due to the genomic sequencing of several Scenedesmus species with biofuel feedstock potential 24,28,38 and additional transcriptomics profiling experiments 29,39 . Differences in the number of ion transporter gene copies in the NREL 46B-D3 genome compared to the S. obliquus UTEX 393 and S. obliquus UTEX 3031 genomes may be related to its halotolerance, including the endosomal K +/H+ antiporter and a voltage-channel chloride channel.…”

Section: Discussionmentioning

confidence: 99%

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A multi-omic characterization of temperature stress in a halotolerant Scenedesmus strain for algal biotechnology

et al. 2021

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Microalgae efficiently convert sunlight into lipids and carbohydrates, offering bio-based alternatives for energy and chemical production. Improving algal productivity and robustness against abiotic stress requires a systems level characterization enabled by functional genomics. Here, we characterize a halotolerant microalga Scenedesmus sp. NREL 46B-D3 demonstrating peak growth near 25 °C that reaches 30 g/m2/day and the highest biomass accumulation capacity post cell division reported to date for a halotolerant strain. Functional genomics analysis revealed that genes involved in lipid production, ion channels and antiporters are expanded and expressed. Exposure to temperature stress shifts fatty acid metabolism and increases amino acids synthesis. Co-expression analysis shows that many fatty acid biosynthesis genes are overexpressed with specific transcription factors under cold stress. These and other genes involved in the metabolic and regulatory response to temperature stress can be further explored for strain improvement.

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Section: Resultsmentioning

confidence: 78%

Section: Discussionmentioning

confidence: 99%

A multi-omic characterization of temperature stress in a halotolerant Scenedesmus strain for algal biotechnology

et al. 2021

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“…chui under natural photoperiod. In this regard, genes exhibiting differential transcriptional regulation under light/dark cycles have been reported in a range of different microalgae such as Chlamydomonas [ 93 , 94 ], Ostreococcus [ 93 , 95 ], Nannochloropsis [ 96 ], Phaeodactylum [ 97 ], Tetradesmus [ 98 ], Bigelowiella [ 99 ], or Chrysochromulina [ 100 ]. More research will be needed to confirm if the transcriptional pattern of AGPL and AGPS is conserved in a diel cycle, as well as to analyze the effect of changing climate conditions on their expression.…”

Section: Discussionmentioning

confidence: 99%

Selection and validation of reference genes for quantitative real-time PCR in the green microalgae Tetraselmis chui

Torres¹,

Lama²,

Mantecón³

et al. 2021

PLoS ONE

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Quantitative real-time reverse transcription PCR (RT-qPCR) is a highly sensitive technique that can be applied to analyze how genes are modulated by culture conditions, but identification of appropriate reference genes for normalization is a critical factor to be considered. For this reason, the expression stability of 18 candidate reference genes was evaluated for the green microalgae Tetraselmis chui using the widely employed algorithms geNorm, NormFinder, BestKeeper, the comparative ΔCT method, and RefFinder. Microalgae samples were collected from large scale outdoor photobioreactors during the growing phase (OUT_GP), and during the semi-continuous phase at different times of the day (OUT_DC). Samples from standard indoor cultures under highly controlled conditions (IND) were also collected to complement the other data. Different rankings for the candidate reference genes were obtained depending on the culture conditions and the algorithm employed. After comparison of the achieved ranks with the different methods, the references genes selected for samples from specific culture conditions were ALD and EFL in OUT_GP, RPL32 and UBCE in OUT_DC, and cdkA and UBCE in IND. Moreover, the genes EFL and cdkA or EFL and UBCE appeared as appropriate combinations for pools generated from all samples (ALL). Examination in the OUT_DC cultures of genes encoding the large and small subunits of ADP-glucose pyrophosphorylase (AGPL and AGPS, respectively) confirmed the reliability of the identified reference genes, RPL32 and UBCE. The present study represents a useful contribution for studies of gene expression in T. chui, and also represents the first step to set-up an RT-qPCR platform for quality control of T. chui biomass production in industrial facilities.

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“…The comparison 80 mycoplasma genomes was also enabled by GBOL 41 and shed light on host specificity. GBOL can also hold eukaryotic genome data as illustrated in 42 . Currently the GBOL stack is being used in various collaborative projects to handle genomic data of organisms across all domains of life (DigiSal, INFECT, MycoSynVac, EmPowerPutida).…”

Section: Discussionmentioning

confidence: 99%

The Empusa code generator and its application to GBOL, an extendable ontology for genome annotation

et al. 2019

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The RDF data model facilitates integration of diverse data available in structured and semi-structured formats. To obtain a coherent RDF graph the chosen ontology must be consistently applied. However, addition of new diverse data causes the ontology to evolve, which could lead to accumulation of unintended erroneous composites. Thus, there is a need for a gate keeping system that compares the intended content described in the ontology with the actual content of the resource. The Empusa code generator facilitates creation of composite RDF resources from disparate sources. Empusa can convert a schema into an associated application programming interface (API), that can be used to perform data consistency checks and generates Markdown documentation to make persistent URLs resolvable. Using Empusa consistency is ensured within and between the ontology and the content of the resource. As an illustration of the potential of Empusa, we present the Genome Biology Ontology Language (GBOL). GBOL uses and extends current ontologies to provide a formal representation of genomic entities, along with their properties, relations and provenance.

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The diurnal transcriptional landscape of the microalga Tetradesmus obliquus

Cited by 10 publications

References 60 publications

A multi-omic characterization of temperature stress in a halotolerant Scenedesmus strain for algal biotechnology

A multi-omic characterization of temperature stress in a halotolerant Scenedesmus strain for algal biotechnology

Selection and validation of reference genes for quantitative real-time PCR in the green microalgae Tetraselmis chui

The Empusa code generator and its application to GBOL, an extendable ontology for genome annotation

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