Whole-genome sequencing of Tisochrysis lutea strains for the DynAlgue genome-wide association study, 2020
Recently, an inventory of genes in phytoplankton was conducted through expeditions such as TARA Oceans. Approximately 1.5 million genes were identified, of which at least three-quarters have no known function. Currently, several research programs were sequencing marine biodiversity, leading to a rapid daily expansion of genomic databases. Access to the genomic sequences of these organisms will soon be readily accessible to the scientific community. Although analysing this data is promising, the characterization of genes or genomes, on the other hand, is progressing very slowly and remains a major challenge for scientists. The aim of this study was to use GWAS approaches to decipher genomic loci without a priori assumptions. The microalga Tisochrysis lutea was selected as a case study due to its economic importance and the extensive knowledge accumulated over the years. Particular attention was paid to pigment and lipid metabolism due to their high commercial value. To implement the GWAS approach, a collection of algal lineages were established (100 lineages). The whole genome of each agal lineage has been sequenced from culture algae cultivated in the same conditions during six days (Conway-Walne medium, 21 C, constant light irradiance of 50 mol m 2.s  1 and bubbled with 0.22 mm filtered-air). The 50 ml of microalgae, or approximately 250 million cells, were centrifuged (1000g), and the algae pellet was stored at -80C. Then, the whole genome of each agal lineage has been sequenced. DNA extractions were conducted using the phenol-chloroform method described in Hu et al.(Hu et al., 2004). The sequencing was performed in paired-end (2x150b) by the genomic platform, GenoToul, INRAE Toulouse using Illumina NovaSeq technology. See https://gitlab.ifremer.fr/gc0ca62/dynalgue-project/.