Nucleomorph comparative genomics

Nucleomorphs are vestigial nuclei of endosymbiotic origin found in cryptomonad and chlorarachniophyte algae. A wealth of molecular and comparative genomic data has been generated in recent years providing insight on the origins and evolution of these peculiar organelles. The cryptomonad nucleomorph (and its associated plastid) has been shown to be the product of a secondary (i.e., eukaryote-eukaryote) endosymbiotic event involving a red alga and a heterotrophic host, while chlorarachniophytes have a green algal-derived nucleomorph. Despite their independent origins, the nucleomorphs of both lineages show similar features, most notably the presence of three linear chromosomes and sub-telomeric ribosomal DNA operons. Recent study has revealed similarities between the cryptomonad and chlorarachniophyte nucleomorphs not only in their genome structures but also in their coding content. Significant differences nevertheless exist. For example, spliceosomal introns are rare (or completely absent) in cryptomonad nucleomorph genomes but highly abundant in chlorarachniophytes. In this chapter, we review the current state of knowledge of nucleomorph genome biology, focusing on the evolution, diversity, and function of nucleomorphs in the two lineages that bear them.