Insights into agar and secondary metabolite pathways from the genome of the red alga Gracilaria domingensis (Rhodophyta, Gracilariales)

Gracilariales is a clade of florideophycean red macroalgae known for being the main source of agar. We present a de novo genome assembly and annotation of Gracilaria domingensis, an agarophyte alga with flattened thallus widely distributed along Central and South American Atlantic intertidal zones. In addition to structural analysis, an organizational comparison was done with other Rhodophyta genomes. The nuclear genome has 78 Mbp, with 11,437 predicted coding genes, 4,075 of which did not have hits in sequence databases. We also predicted 1,567 noncoding RNAs, distributed in 14 classes. The plastid and mitochondrion genome structures were also obtained. Genes related to agar synthesis were identified. Genes for type II galactose sulfurylases could not be found. Genes related to ascorbate synthesis were found. These results suggest an intricate connection of cell wall polysaccharide synthesis and the redox systems through the use of L-galactose in Rhodophyta. The genome of G. domingensis should be valuable to phycological and aquacultural research, as it is the first tropical and Western Atlantic red macroalgal genome to be sequenced.

Automated summary

This study presents the de novo genome assembly and annotation of Gracilaria domingensis, a red macroalgae known for agar production. The nuclear genome has 78 Mbp with a total of 11,437 predicted coding genes, including 4,075 novel genes. Noncoding RNAs were also predicted, and the genome structures of plastid and mitochondrion were obtained. Genes related to agar synthesis and ascorbate synthesis were identified. This genome sequence of G. domingensis is the first of its kind in the tropical and Western Atlantic region, making it valuable for phycological and aquacultural research.