Plastid Origin and Evolution: New Models Provide Insights into Old Problems

Chan, Cheong Xin; Gross, Jeferson; Yoon, Hwan Su; Bhattacharya, Debashish

doi:10.1104/pp.111.173500

Cited by 52 publications

(34 citation statements)

References 88 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…We investigated the placement of the Archaeplastida lineage within the cyanobacterial phylum by building a "plastidome tree" using a concatenation of 25 conserved plastid proteins. Although most studies support the monophyly of primary plastids (16,17), others have reported a polyphyletic origin (18,19). We find strong support for the monophyletic placement of plastids near the base of the cyanobacterial tree ( Fig.…”

Section: Prochlorococcus Marinus Mit 9215supporting

confidence: 53%

Improving the coverage of the cyanobacterial phylum using diversity-driven genome sequencing

Shih

Latifi

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

734

883

View full text Add to dashboard Cite

The cyanobacterial phylum encompasses oxygenic photosynthetic prokaryotes of a great breadth of morphologies and ecologies; they play key roles in global carbon and nitrogen cycles. The chloroplasts of all photosynthetic eukaryotes can trace their ancestry to cyanobacteria. Cyanobacteria also attract considerable interest as platforms for "green" biotechnology and biofuels. To explore the molecular basis of their different phenotypes and biochemical capabilities, we sequenced the genomes of 54 phylogenetically and phenotypically diverse cyanobacterial strains. Comparison of cyanobacterial genomes reveals the molecular basis for many aspects of cyanobacterial ecophysiological diversity, as well as the convergence of complex morphologies without the acquisition of novel proteins. This phylum-wide study highlights the benefits of diversity-driven genome sequencing, identifying more than 21,000 cyanobacterial proteins with no detectable similarity to known proteins, and foregrounds the diversity of lightharvesting proteins and gene clusters for secondary metabolite biosynthesis. Additionally, our results provide insight into the distribution of genes of cyanobacterial origin in eukaryotic nuclear genomes. Moreover, this study doubles both the amount and the phylogenetic diversity of cyanobacterial genome sequence data. Given the exponentially growing number of sequenced genomes, this diversity-driven study demonstrates the perspective gained by comparing disparate yet related genomes in a phylum-wide context and the insights that are gained from it.

show abstract

Section: Prochlorococcus Marinus Mit 9215supporting

confidence: 53%

Improving the coverage of the cyanobacterial phylum using diversity-driven genome sequencing

Shih

Latifi

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

734

883

View full text Add to dashboard Cite

show abstract

“…However, the analysis of an ongoing domestication process-the conversion of a Synechococcus cyanobacterium into a "cyanelle" ( protochloroplast) in the testate amoeba Paulinella chromatophora (Rhizaria)-is providing fascinating insights into what is entailed (Chan et al 2011;Bodyl et al 2012;Nowack and Grossman 2012). During the 60 million years since the estimated onset of this conversion, the genome of the endosymbiont has undergone an estimated 75% reduction in size, and roughly 1% of the amoeba's nuclear genes are of endosymbiont origin.…”

Section: Mating-type-regulated Transmission Of Organelle Genomes Theomentioning

confidence: 99%

Origins of Eukaryotic Sexual Reproduction

Goodenough

Heitman

2014

Cold Spring Harbor Perspectives in Biology

172

134

View full text Add to dashboard Cite

Sexual reproduction is a nearly universal feature of eukaryotic organisms. Given its ubiquity and shared core features, sex is thought to have arisen once in the last common ancestor to all eukaryotes. Using the perspectives of molecular genetics and cell biology, we consider documented and hypothetical scenarios for the instantiation and evolution of meiosis, fertilization, sex determination, uniparental inheritance of organelle genomes, and speciation.

show abstract

“…Moreover, primary plastids from all Archaeplastida representatives as well as their descendants (higher-order plastids) share the same unique atpA gene cluster in the genome [11] and translocase supercomplex (Toc/Tic apparatus) responsible for protein import of nuclear-encoded proteins. The complex is composed of a conserved set of cyanobacterium-derived homologs and subunits that are presumed to have arisen de novo in the common host [19][20][21][22]. The Archaeplastida also evolved a common mosaic feature of nuclear plastidtargeted genes of Calvin cycle enzymes [23].…”

Section: Introductionmentioning

confidence: 99%

Monophyly of Archaeplastida supergroup and relationships among its lineages in the light of phylogenetic and phylogenomic studies. Are we close to a consensus?

Mackiewicz

Gagat

2014

Acta Soc Bot Pol

View full text Add to dashboard Cite

One of the key evolutionary events on the scale of the biosphere was an endosymbiosis between a heterotrophic eukaryote and a cyanobacterium, resulting in a primary plastid. Such an organelle is characteristic of three eukaryotic lineages, glaucophytes, red algae and green plants. The three groups are usually united under the common name Archaeplastida or Plantae in modern taxonomic classifications, which indicates they are considered monophyletic. The methods generally used to verify this monophyly are phylogenetic analyses. In this article we review up-to-date results of such analyses and discussed their inconsistencies. Although phylogenies of plastid genes suggest a single primary endosymbiosis, which is assumed to mean a common origin of the Archaeplastida, different phylogenetic trees based on nuclear markers show monophyly, paraphyly, polyphyly or unresolved topologies of Archaeplastida hosts. The difficulties in reconstructing host cell relationships could result from stochastic and systematic biases in data sets, including different substitution rates and patterns, gene paralogy and horizontal/endosymbiotic gene transfer into eukaryotic lineages, which attract Archaeplastida in phylogenetic trees. Based on results to date, it is neither possible to confirm nor refute alternative evolutionary scenarios to a single primary endosymbiosis. Nevertheless, if trees supporting monophyly are considered, relationships inferred among Archaeplastida lineages can be discussed. Phylogenetic analyses based on nuclear genes clearly show the earlier divergence of glaucophytes from red algae and green plants. Plastid genes suggest a more complicated history, but at least some studies are congruent with this concept. Additional research involving more representatives of glaucophytes and many understudied lineages of Eukaryota can improve inferring phylogenetic relationships related to the Archaeplastida. In addition, alternative approaches not directly dependent on phylogenetic methods should be developed.

show abstract

Plastid Origin and Evolution: New Models Provide Insights into Old Problems

Cited by 52 publications

References 88 publications

Improving the coverage of the cyanobacterial phylum using diversity-driven genome sequencing

Improving the coverage of the cyanobacterial phylum using diversity-driven genome sequencing

Origins of Eukaryotic Sexual Reproduction

Monophyly of Archaeplastida supergroup and relationships among its lineages in the light of phylogenetic and phylogenomic studies. Are we close to a consensus?

Contact Info

Product

Resources

About