Macroalgal genomics illuminate three paths to multicellularity - Supplementary Data - Tables - Data S4

Macroalgae are multicellular, aquatic autotrophs that play vital roles in global climate maintenance and have diverse applications in biotechnology and eco-engineering, which are directly linked to their multicellularity phenotypes. However, their genomic diversity and the evolutionary mechanisms underlying multicellularity in these organisms remain uncharacterized. Here, we sequenced 112 macroalgal genomes from diverse climates and phyla, identifying key genomic features that distinguish them from their microalgal relatives. We found that macroalgae have expanded gene families related to cellular adhesion, extracellular matrix formation, cytoskeletal organization and signaling pathways. We discovered that many of these genes have viral origins and are lineage-specific or conserved among the three major macroalgal phyla: Rhodophyta (red algae), Chlorophyta (green algae) and Ochrophyta (brown algae). Our work reveals genetic determinants of convergent and divergent evolutionary trajectories that have shaped morphological diversity in macroalgae and provides genome-wide frameworks to understand photosynthetic multicellular evolution in marine environments.

Table S1. Functional annotation and metadata for macroalgal species. This is a multi-sheet Excel workbook containing the PFAM count matrix for decontaminated assemblies and their strain metadata, contamination estimates, assembly metrics including BUSCO and N50 scores, and source data for the ternary analysis. Related to Figs. 2 and 3.

Table S2. GO enrichment in macroalgal-specific genes. This is a multi-sheet Excel workbook containing enriched GO terms in macroalgal-specific PFAMs conserved in Rhodophyta, Ochrophyta, and Chlorophyta and response screening results comparing means in PFAM counts between divisions. Related to Fig. 3.

Table S3. Comparative genomics of micro- and macroalgae. This is a multi-sheet Excel workbook containing response screening tables comparing PFAM and GO variation in micro- compared to macroalgae. Related to Fig. 4.

Table S4. Unraveling the macroalgal adhesome. This is a multi-sheet Excel workbook containing macroalgal adhesome atlas and response screens among macroalgal phyla and between micro- and macroalgae. Related to Fig. 4.

Table S5. Endogenous viral elements in macroalgae. This is a multi-sheet Excel workbook containing VFAM count matrix and response screening results for comparisons of macroalgal VFAM counts by climate and habitat. This table also includes the EVOP matrix and response screening results comparing EVOPs found in the macroalgal genomes among climates and macroalgal tORFs with EsV-1-7 domains and their codomains. Related to Fig. 5.