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

Abstract

Macroalgal (seaweed) genomic resources are generally lacking as compared with other eukaryotic taxa, and this is particularly true in the red algae (Rhodophyta). Understanding red algal genomes is critical to understanding eukaryotic evolution given that red algal genes are spread across eukaryotic lineages from secondary endosymbiosis and red algae diverged early in the Archaeplastids. The Gracilariales is a highly diverse and widely distributed order including species that can serve as ecosystem engineers in intertidal habitats and several notorious introduced species. The genus Gracilaria is cultivated worldwide, in part for its production of agar and other bioactive compounds with downstream pharmaceutical and industrial applications. This genus is also emerging as a model for algal evolutionary ecology. Here, we report new whole-genome assemblies for two species (Gracilaria chilensis and Gracilaria gracilis), a draft genome assembly of Gracilaria caudata, and genome annotation of the previously published Gracilaria vermiculophylla genome. To facilitate accessibility and comparative analysis, we integrated these data in a newly created web-based portal dedicated to red algal genomics (https://rhodoexplorer.sb-roscoff.fr). These genomes will provide a resource for understanding algal biology and, more broadly, eukaryotic evolution.

Keywords: Rhodophyta; ecology; evolution; omics; ploidy.

Fig. 1.

(A) Genome assembly metrics of G. chilensis (top left), G. vermiculophylla (top right), G. caudata (bottom left), and G. gracilis (bottom right) (Challis 2017; https://github.com/rjchallis/assembly-stats). The inner radius of the circular plot represents the length of the longest scaffold in the assembly and the proportion of the assembly that it represents. The cumulative number of scaffolds within a given percentage of the genome is plotted in light purple originating at the center of the plot. The N50 and N90 scaffold lengths are indicated by dark and light orange, respectively. Genome scaffolds are plotted in gray from the circumference and the length of segment at a given percentage indicates the cumulative percentage of the assembly that is contained within scaffolds of at least that length. The guanine–cytosine (GC) content is marked by the dark blue outer circle. Complete, fragmented, and duplicated BUSCO genes are shown in green in the upper right corner. (B) Gracilaria chilensis (top left), G. vermiculophylla (top right), G. caudata (bottom left), and G. gracilis (bottom right). Photo credit in order: M.-L. Guillemin, S. Krueger-Hadfield, E. M. Plastino, C. Destombe.