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 contains nucleomorphs, which are 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 red complex plastids and provide data independent from previously analyzed plastid-encoded proteins. Here, we leverage these genes in a first phylogenomic 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 analysis, supported by a series of rigorous topology tests, places cryptophyte nucleomorphs as sister to the extremophilic, freshwater subphylum Cyanidiophytina. This conflicts with previously published analyses based on plastidial genes that placed red complex plastids closer to the mesophilic Rhodophytina. While the precise sister group remains debated, our results robustly reject a nucleomorph origin from within any currently recognized class of Rhodophyta, instead suggesting an ancient origin of complex red plastids among the deepest branches of the red algal tree of life.