Table 3.

Typical transcriptomic approaches according to the investigation of how gene expression in macroalgae can be influenced by abiotic stress.

Macroalgae	Planning and Data Generation	Transcriptome Assembly	Expression Quantification	Differential Expression	Reference
Saccharina japonica (brown algae)	Copper treatments were conducted by transferring the juvenile sporophytes to fresh seawater with final Cu2+ concentrations of 10, 100, and 200 μg L−1. Illumina Hiseq sequencing.	De novo transcriptome assembly with Trinity. Functional annotation using the basic local alignment search tool and a translated nucleotide query (BLASTX) against the non-redundant protein and non-redundant nucleotide databases of the NCBI, Protein family, SwissProt, eukaryotic Ortholog Groups (KOG), and the KEGG databases. Functional annotation by Gene Ontology (GO) was performed using Blast2GO software.	Transcript quantification with RSEM. Validation of the differentially expressed genes (DEGs) by RT-qPCR.	Compared with the control, the number of DEGs was 11,350 (4944 up- and 6406 downregulated) in the 200 μg L−1 treatment group and 2868 (1075 up- and 1793 downregulated) in the 100 μg L−1 treatment group, whereas much fewer DEGs were detected in the 10 μg L−1 treatment group.	[77]
Laurencia dendroidea (red algae)	Three specimens of L. dendroidea collected in the intertidal zone during high tide. The EST sequences deposited for the class. Florideophyceae in the NCBI were downloaded and the reads were assembled using the TGICL software from TIGR.	The assembly was aligned against the Florideophyceae. EST NCBI database. Taxonomic and functional analysis performed on assembled sequences using the Newbler software, and annotated, using the MG-RAST server, through BLAST, against the GenBank, COG, KEGG and Subsystems databases.	PCR amplification.	A total of 6 transcriptomes were obtained from specimens of L. dendroidea sampled in three different coastal locations of Rio de Janeiro state.	[78]
Ectocarpus siliculosus (brown algae)	Three different stresses: (hyposaline, hypersaline, oxidative). 90,637 EST sequences used for the microarray design.	Sequences were annotated with KEGG orthology (KO) numbers using KOBAS and with GO terms using GOPET. Protein sequences corresponding to the assembled EST sequences were predicted using ORF predictor.	RT-qPCR validation of the microarray.	70% of the expressed genes are regulated in response to at least one of these stressors.	[79]