Cryptophyte and chlorarachniophyte algae are transitional forms in the widespread secondary endosymbiotic acquisition of photosynthesis by engulfment of eukaryotic algae. Unlike most secondary plastid-bearing algae, miniaturized versions of the endosymbiont nuclei (nucleomorphs) persist in cryptophytes and chlorarachniophytes. To determine why, and to address other fundamental questions about eukaryote–eukaryote endosymbiosis, we sequenced the nuclear genomes of the cryptophyte Guillardia theta and the chlorarachniophyte Bigelowiella natans. Both genomes have >21,000 protein genes and are intron rich, and B. natans exhibits unprecedented alternative splicing for a single-celled organism. Phylogenomic analyses and subcellular targeting predictions reveal extensive genetic and biochemical mosaicism, with both host- and endosymbiont-derived genes servicing the mitochondrion, the host cell cytosol, the plastid and the remnant endosymbiont cytosol of both algae. Mitochondrion-to-nucleus gene transfer still occurs in both organisms but plastid-to-nucleus and nucleomorph-to-nucleus transfers do not, which explains why a small residue of essential genes remains locked in each nucleomorph.
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- Supplementary Information (10.2M)
This file contains Supplementary Methods, Data and Analyses for the Guillardia theta and Bigelowiella natans nuclear genome sequences. Supplementary References, 35 Supplementary Figures and 24 Supplementary Tables are also included (see Table of Contents for more details).
- Supplementary Table S184.108.40.206.1 (79K)
This file contains datasets used for support vector machine prediction of PPC proteins in Bigelowiella natans and Guillardia theta.
- Supplementary Table S220.127.116.11.2 (22K)
This file contains dataset sizes used for support vector machine prediction of PPC proteins in Bigelowiella natans and Guillardia theta.
- Supplementary Table S1.12.1 (107K)
This file contains a list of taxa used in phylogenomic analyses of the nuclear genomes of Bigelowiella natans and Guillardia theta.
- Supplementary Table S2.3.3 (56K)
This file contains proteins identified in the search for putative carbohydrate-active enzymes in Guillardia theta.
- Supplementary Table S2.3.4 (50K)
This file contains proteins identified in the search for putative carbohydrate-active enzymes in Bigelowiella natans.
- Supplementary Table S18.104.22.168 (27K)
This file contains a list of proteins possibly involved in the ER-localized synthesis of N-glycanes in Guillardia theta and Bigelowiella natans.