Nucleomorph phylogenomics suggests a deep and ancient origin of cryptophyte plastids within Rhodophyta

The evolutionary origin of red algae-derived complex plastids remains obscure. Cryptophyta, one of four eukaryotic lineages harboring these plastids, still contain nucleomorphs, highly reduced remnants of red algal nuclei. The genes present on nucleomorph genomes can be used for phylogenomic reconstruction in order to unravel the evolutionary origin of all red complex plastids and provide data independent from previously analyzed plastid-encoded datasets. Here, we leverage these genes in a first attempt at pinpointing the position of cryptophyte nucleomorphs within a comprehensive diversity of Rhodophyta, including new sequence representatives from seven deep-branching red algae. Our analyses place cryptophyte nucleomorphs as sister to the extremophilic subphylum Cyanidiophytina. This conflicts with published analyses based on plastidial genes that placed red complex plastids closer to the mesophilic Rhodophytina. Our results reject a nucleomorph origin within any known subgroup of Rhodophyta, instead suggesting a deep and possibly freshwater origin of complex red plastids.