Nucleomorph

cell cell Before 2020, only two monophyletic groups of organisms were known to contain plastids with a vestigial nucleus or nucleomorph: the cryptomonads of the supergroup Cryptista and the chlorarachniophytes of the supergroup Rhizaria, both of which have examples of sequenced nucleomorph genomes. The transcriptomes of the nucleomorphs have been sequenced. One slight issue in understanding the sequence of evolution is that although the phylogenetic tree built from Lepidodinium-MGD-TGD's plastid is monophyletic, the tree built from their host-nucleus DNA is not, implying that they might have acquired very similar algae independently. == Structure ==

'' (Cryptomonada). Nm: nucleomorph A cryptomonad nucleomorph is typically much smaller than the host nucleus. A relatively large portion of its size is devoted to the nucleolus, which contains its own ribosomes and rRNA. There seems to be nuclear pores observable by imaging, but genetic work has failed to find any protein appropriate for forming the nuclear pore complex. There is one nucleomorph per plastid. The nucleomorph divides before the accompanying plastid. The dividing nucleomorph lacks a mitotic spindle, and the nucleomorph envelope persists throughout division. Some sort of a pore may then move the peptide into the periplastid space, but there seems to be no SELMA-like pore in this group. It's only known that the TIC/TOC complex exists for crossing the last two layers. ==Nucleomorph genome==

Nucleomorphs represent some of the smallest genomes ever sequenced. After the red or green alga was engulfed by a cryptomonad or chlorarachniophyte, respectively, its genome was reduced. The nucleomorph genomes of both cryptomonads and chlorarachniophytes converged upon a similar size from larger genomes. They retained only three chromosomes and many genes were transferred to the nucleus of the host cell, while others were lost entirely. The unique combination of host cell and complex plastid results in cells with four genomes: two prokaryotic genomes (mitochondrion and plastid of the red or green algae) and two eukaryotic genomes (nucleus of host cell and nucleomorph). The model cryptomonad Guillardia theta became an important focus for scientists studying nucleomorphs. Its complete nucleomorph sequence was published in 2001, coming in at 551 Kbp. The G. theta sequence gave insight as to what genes were retained in nucleomorphs. Most of the genes that moved to the host cell involved protein synthesis, leaving behind a compact genome with mostly single-copy “housekeeping” genes (affecting transcription, translation, protein folding and degradation and splicing) and no mobile elements. The genome contains 513 genes, 465 of which code for protein. Thirty genes are considered “plastid” genes, coding for plastid proteins. It has three chromosomes with eukaryotic telomeres subtended by rRNA. Genes encoded in cryptophyte nucleomorph genomes have been used in phylogenomic attempts at reconstructing the evolutionary history of cryptophyte secondary plastids, resulting in topologies different from those reconstructed based on plastid genome-encoded genes. The nucleomorph-based phylogenetic trees point toward the mostly extremophilic red algae of the subdivision Cyanidiophytina as the closest relatives of the cryptophyte plastid donor lineage, while the plastid-based trees point toward the mostly mesophilic Rhodophytina. ==Persistence of nucleomorphs==

There are no recorded instances of vestigial nuclei in any other secondary plastid-containing organisms, yet they have been retained independently in the cryptomonads and chlorarachniophytes. Plastid gene transfer happens frequently in many organisms, and it is unusual that these nucleomorphs have not disappeared entirely. One theory as to why these nucleomorphs have not disappeared as they have in other groups is that introns present in nucleomorphs are not recognized by host spliceosomes because they are too small and therefore cannot be cut and later incorporated into host DNA. Nucleomorphs also often code for many of their own critical functions, like transcription and translation. Some say that as long as there exists a gene in the nucleomorph that codes for proteins necessary for the plastid’s functioning that are not produced by the host cell, the nucleomorph will persist. == Tertiary endosymbiosis ==

The standard nucleomorph is the result of secondary endosymbiosis: a cyanobacterium first became the chloroplast of ancestral plants, which diverged into green and red algae among other groups; the algal cell is then captured by another eukaryote. The chloroplast is surrounded by 4 membranes: 2 layers resulting from the primary, and 2 resulting from the secondary. When the nucleus of the algal endosymbiont remains, it's called a "nucleomorph". ==See also==