Nucleomorph Genomes

Abstract

Nucleomorphs are the remnant nuclei of algal endosymbionts in cryptophytes and chlorarachniophytes, two evolutionarily distinct unicellular eukaryotic lineages that acquired photosynthesis secondarily by the engulfment of red and green algae, respectively. At less than one million base pairs in size, nucleomorph genomes are the most highly reduced nuclear genomes known, with three small linear chromosomes and a gene density similar to that seen in prokaryotes. The independent origin of nucleomorphs in cryptophytes and chlorarachniophytes presents an interesting opportunity to study the reductive evolutionary forces that have led to their remarkable convergence upon similar genome architectures and coding capacities. In this article, we review the current state of knowledge with respect to the structure, function, origin, and evolution of nucleomorph genomes across the known diversity of cryptophyte and chlorarachniophyte algae.

Gene similarity networks provide tools for understanding eukaryote origins and evolution

“…This observation might be the result of eukaryotic genes of eubacterial ancestry being preferentially lost during genome reductions and/or gained during genome expansions, consistent with the higher evolvability of this set of genes (13,(15)(16)(17). In agreement with this hypothesis, microsporidia (including E. intestinalis), and in particular nucleomorphs, are the result of extensive genome reductions, and E. histolytica has experienced genome reduction involving most mitochondrial pathways (56)(57)(58). Nucleomorphs are highly reduced eukaryotic nuclei present in the plastids of certain secondarily photosynthetic eukaryotes (for a review, see ref.…”

Genomic perspectives on the birth and spread of plastids

“…Two algal groups, the euglenids and chlorarachniophytes, harbor chlorophyll a+b-pigmented plastids, which are surrounded by three and four membranes, respectively (41)(42)(43). The chlorarachniophytes are of particular interest in that the nucleus of the green algal endosymbiont persists in a miniaturized form called a "nucleomorph" (44,45). Nucleomorphs are considered the "smoking guns" of secondary endosymbiosis-most complex algae do not have them-although as we shall see their genomes are minuscule compared with the algal nuclear genomes from which they evolved; most of their genes have been lost or transferred to the host nucleus by EGT (45) (Fig.…”

On the concept of biological function, junk DNA and the gospels of ENCODE and Grauret al.

“…Perhaps one of the most revealing examples of genome size evolution is found in cryptophytes and chlorarachniophytes, which contain 4 evolutionary distinct genomes [26]. The algal endosymbionts of these species have a small nucleus (called nucleomorph) with a genome ranging from ~330 to 1,030 kilobase pairs, which is within the range of viral genomes.…”

“…The evolution of these remarkable endosymbiotic algae support the notion that deletion mutagenesis and the selection forces for eliminating jDNA, including introns, can be highly efficient in eukaryal genomes. In the context of the model discussed here, it is important to emphasize that, unlike the genome of their free living ancestors or that of most other eukaryotic cells, the genome of these endosymbionts is separated from host cytoplasm by several membranes (the nuclear envelope and the cellular and phagosomal membranes [26]), which constitute an effective 'physical' barrier and defensive system against exogenous inserting viral elements [18]. In the absence of newly introduced viral elements, the selective pressure associated with insertional mutagenesis had diminished, which led to the elimination of introns and of most jDNA, which are no longer needed as protective mechanisms; interestingly, the presence of membranes and the lack of mobile elements in these endosymbionts might also be responsible for the lack of transfer of their genes to the host genome and, therefore, for their evolutionary survival as nucleomorphs [28].…”