Algal genomes reveal evolutionary mosaicism and the fate of nucleomorphs

  title={Algal genomes reveal evolutionary mosaicism and the fate of nucleomorphs},
  author={Bruce A. Curtis and Goro Tanifuji and Fabien Burki and Ansgar Gruber and Manuel Irimia and Shinichiro Maruyama and Maria Cecilia Arias and Steven G Ball and Gillian H. Gile and Yoshihisa Hirakawa and Julia F. Hopkins and Alan Kuo and Stefan Andreas Rensing and Jeremy Schmutz and Aikaterini Symeonidi and Marek Eli{\'a}{\vs} and Robert Jm Eveleigh and Emily K. Herman and Mary J. Klute and Takuro Nakayama and Miroslav Oborn{\'i}k and Adri{\'a}n Reyes-Prieto and E. Virginia Armbrust and Stephen J Aves and Robert G. Beiko and Pedro M. Coutinho and Joel B. Dacks and Dion G Durnford and Naomi M. Fast and Beverley R. Green and Cameron J. Grisdale and Franziska Hempel and Bernard Henrissat and Marc P. H{\"o}ppner and Ken-Ichiro Ishida and Eunsoo Kim and Ludek Koreny and Peter G. Kroth and Yuan Liu and Shehre-Banoo Malik and Uwe G. Maier and Darcy L. McRose and Thomas Mock and Jonathan A. D. Neilson and Naoko T. Onodera and Anthony M. Poole and Ellen J. Pritham and Thomas A. Richards and Gabrielle Rocap and Scott William Roy and Chihiro Sarai and Sarah Schaack and Shu Shirato and Claudio H. Slamovits and D. F. Spencer and Shigekatsu Suzuki and Alexandra Z. Worden and Stefan Zauner and Kerrie W. Barry and Callum J. Bell and Arvind Kumar Bharti and John Allen Crow and Jane Grimwood and Robin Kramer and Erika A. Lindquist and Susan M. Lucas and Asaf A. Salamov and Geoffrey Ian McFadden and Christopher E. Lane and Patrick J. Keeling and Michael W. Gray and Igor V. Grigoriev and John M. Archibald},
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… 

Polyploidy of Endosymbiotically Derived Genomes in Complex Algae

Chlorarachniophyte and cryptophyte algae have complex plastids that were acquired by the uptake of a green or red algal endosymbiont via secondary endosymbiosis. The plastid is surrounded by four

Nucleomorph Comparative Genomics

The current state of knowledge of nucleomorphic genome biology is reviewed, focusing on the evolution, diversity, and function of nucleomorphs in the two lineages that bear them.

Endosymbiotic Gene Transfer in the Nucleomorph containing organisms Bigelowiella natans and Guillardia theta

To understand the process of EGT and endosymbiosis in general, the nuclear genomes of the cryptophyte Guillardia theta and the chlorarachniophyte Bigelowiella natans were sequenced and nuclear genes whose encoded proteins appear to function in the mitochondrion were investigated.

Diurnal Transcriptional Regulation of Endosymbiotically Derived Genes in the Chlorarachniophyte Bigelowiella natans

The results of this study suggest that nucleomorph genes have lost transcriptional regulation along the diurnal cycles, and nuclear genes exert control over the complex plastid including the nucleomorph.

Comparative genomics of mitochondria in chlorarachniophyte algae: endosymbiotic gene transfer and organellar genome dynamics

The results suggest that chlorarachniophyte mtDNAs are more evolutionarily dynamic than their plastid counterpart, despite being of similar size and coding capacity.

Algal endosymbionts as vectors of horizontal gene transfer in photosynthetic eukaryotes

The idea that Plantae (in particular red algae) are one of the major players in eukaryote genome evolution by virtue of their ability to act as "sinks" and "sources" of foreign genes through HGT and endosymbiosis, respectively is discussed.

PolyploidyofEndosymbioticallyDerivedGenomes inComplex Algae

Chlorarachniophyte and cryptophyte algae have complex plastids that were acquired by the uptake of a green or red algal endosymbiont via secondary endosymbiosis. The plastid is surrounded by four

Nucleomorph Genome Sequences of Two Chlorarachniophytes, Amorphochlora amoebiformis and Lotharella vacuolata

Comparative analyses among four chlorarachniophyte nucleomorph genomes revealed that these sequences share 171 function-predicted genes, including the same set of genes encoding 17 plastid-associated proteins, and no evidence of a recent nucleomorph-to-nucleus gene transfer was found, suggesting that chlorarchniophytes nucleomorph genome underwent most of their reductive evolution prior to the radiation of extent members of the group.

Evolutionary Dynamics of Cryptophyte Plastid Genomes

A comparative analysis of plastid genomes from six representative cryptophyte genera reveals examples of gene loss and intron insertion in cryptophytes, and the chlB/chlL/ chlN genes, which encode light-independent (dark active) protochlorophyllide oxidoreductase (LIPOR) proteins have undergone recent gene loss, pseudogenization, and pseudogenized in Cryptomonas paramecium.

Regulation of chloroplast and nucleomorph replication by the cell cycle in the cryptophyte Guillardia theta

The results of this study and previous studies on chlorarachniophytes suggest that there was a common evolutionary pattern in which an endosymbiont lost its replication cycle- dependent transcription while cell-cycle-dependent transcriptional regulation of host nuclear genes came to restrict the timing of nucleomorph replication and chloroplast division.



Complete nucleotide sequence of the chlorarachniophyte nucleomorph: nature's smallest nucleus.

Although originating by two independent endosymbioses, chlorarachniophyte and cryptomonad nucleomorph genomes have converged upon remarkably similar architectures but differ in many molecular details that reflect two distinct trajectories to hypercompaction and reduction.

Complete Nucleomorph Genome Sequence of the Nonphotosynthetic Alga Cryptomonas paramecium Reveals a Core Nucleomorph Gene Set

An unexpected degree of overlap in the genes present in the independently evolved chlorarachniophyte and cryptomonad nucleomorph genomes is revealed, suggesting that similar reductive processes have taken place in unrelated lineages of nucleomorph-containing algae.

The highly reduced genome of an enslaved algal nucleus

Complete sequences for all three nucleomorph chromosomes from the cryptomonad Guillardia theta are reported, offering a means for studying eukaryotic chromosome replication, segregation and evolution.

The complete chloroplast genome of the chlorarachniophyte Bigelowiella natans: evidence for independent origins of chlorarachniophyte and euglenid secondary endosymbionts.

Chlorarachniophytes are amoeboflagellate cercozoans that acquired a plastid by secondary endosymbiosis. Chlorarachniophytes are the last major group of algae for which there is no completely

Nucleus‐ and nucleomorph‐targeted histone proteins in a chlorarachniophyte alga

These findings provide the first evidence of how the nucleomorph may be regulated by host‐encoded gene products, as well as developing a method to temporarily synchronize B. natans cells, and confirming that both host and symbiont histone expression is controlled during the cell cycle.

Nucleomorph genome of Hemiselmis andersenii reveals complete intron loss and compaction as a driver of protein structure and function

The results indicate that genome compaction can eliminate both coding and noncoding DNA and, consequently, drive the evolution of protein structure and function.

Are algal genes in nonphotosynthetic protists evidence of historical plastid endosymbioses?

Signal from "algal" genes in oomycete genomes is inconsistent with the chromalveolate hypothesis, and better explained by alternative models of sequence and genome evolution.

Lateral gene transfer and the evolution of plastid-targeted proteins in the secondary plastid-containing alga Bigelowiella natans

The results underscore the importance of lateral gene transfer in contributing foreign proteins to eukaryotic cells and their organelles, and also suggest that its impact can vary from lineage to lineage.

Nucleus-to-nucleus gene transfer and protein retargeting into a remnant cytoplasm of cryptophytes and diatoms.

Further nucleus-encoded PPC proteins from G. theta are presented, such as the eukaryotic translation elongation factor-1alpha, evidence for their nucleus-to-nucleus gene transfer, and retargeting of the proteins, to allow the elucidation of the processes by which proteins are involved in different levels of host control over its eUKaryotic organelle.

Nucleus-encoded periplastid-targeted EFL in chlorarachniophytes.

The data suggest that the system that directs proteins to the PPC in chlorarachniophytes uses a bipartite targeting sequence, as does the P PC-targeting system that evolved independently in cryptomonads.