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

Abstract

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.

The Rhodoexplorer Platform for Red Algal Genomics and Whole Genome Assemblies for Several Gracilaria Species

“…In addition, we created a draft genome assembly based on the Illumina sequencing only for G. caudata (32 Mbp) and reassembled the genome of G. vermiculophylla (Flanagan et al 2021) to a final 47 Mbp after bacterial contamination removal. The above genome assemblies were comparable to the genomes of G. domingensis (78 Mbp, Nakamura-Gouvea et al 2022) and G. changii (36 Mbp, Ho et al 2017). PacBio assemblies of G. chilensis and G. gracilis produced in this study (< 300 contigs per genome) are the most contiguous red macroalgal genomes presently available in public databases, apart from G. vermiculophylla and P. yezoensis where the addition of a HiC library enabled scaffolding nearly at the chromosome level (Wang et al 2020, Flanagan et al 2021).…”

Identification, Characteristics and Function of Phosphoglucomutase (PGM) in the Agar Biosynthesis and Carbon Flux in the Agarophyte Gracilariopsis lemaneiformis (Rhodophyta)

“…The floridean starch was found in the cytoplasm, surrounding by the nucleus, which is different from the starch observed in the chloroplast in higher plants. The extra-plastidic starch synthesis in this alga proceeds via a UDP glucose-selective α-glucan synthase, in analogy with the cytosolic pathway of glycogen synthesis in other eukaryotes [ 12 , 24 ]. However, the similar expressional patterns of GlPGM1 with agar variations were found under different conditions.…”

“…In G. lemaneiformis , (iso)floridoside, starch and agar accumulations are the main carbon sinks in the cells. It is also important to know how carbon flow is regulated by the carbohydrate and lipid metabolism in Rhodophyta, which is important for biofuel manipulations [ 24 ].…”

Red macroalgae in the genomic era

“…The analysis of red algal genomes has also given insights into the physiology of red algae, including inorganic carbon uptake (Wang et al ., 2020), osmotic regulation (Chen et al ., 2022), carbohydrate metabolism (Manat et al ., 2022), and agar and secondary metabolites (Nakamura‐Gouvea et al ., 2022). The currently sequenced red algal genomes have been mostly species of economical relevance, such as Pyropia/Porphyra or nori (Brawley et al ., 2017) and Gracilaria spp.…”

“…In the other red algal groups, only branched or unbranched filaments and more simple sheet-like structures are found , reinforcing the idea that complex multicellularity is an evolutionarily rare trait. In recent years, insights into the evolution of complex multicellularity in the brown and red macroalgae have been obtained using genomic approaches, in particular through the analysis of the complete genome sequences for multicellular species in comparison with closely related unicellular species sister to these groups (Nakamura-Gouvea et al, 2022). Despite these endeavours, the molecular basis of developmental patterning in the red algae is not commensurate with what is known in all the other multicellular groups (Cock & Coll en, 2015).…”