Molecular Phylogeny of Oxygenic Cells and Organelles Based on Small-Subunit Ribosomal RNA Sequences

Giovannoni, Stephen J.; Wood, N. D.; Huss, Volker A. R.

doi:10.1007/978-1-4615-2818-0_10

Cited by 8 publications

(7 citation statements)

References 22 publications

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“…In support of a common origin of primary plastids, the first phylogenetic analyses involving plastid SSU (16S) rRNA genes grouped all representatives of Archaeplastida together [34][35][36]. In agreement with earlier assumptions based on structural similarities of plastids and cyanobacteria, the three eukaryotic lineages branched from the cyanobacterial clade in phylogenetic trees.…”

Section: Testing the Monophyly Of Archaeplastida Based On Plastid Genessupporting

confidence: 74%

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

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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.

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Section: Testing the Monophyly Of Archaeplastida Based On Plastid Genessupporting

confidence: 74%

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

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“…The origin of GAPCp in cryptomonads is proposed to be proteobacterial, while that of their chloroplasts is evidently cyanobacterial, as indicated by sequences of several plastid-encoded genes, including 16S rRNAs and tufA (Delwiche et al 1995;Douglas 1993;Giovannoni et al 1993). In dinoflagellates RuBisCO is also reported to be proteobacterial in origin (Morse et al 1995;Rowan et al 1996;Watson and Tabita 1997), while the intrinsic peridinin-chlorophyll binding protein (iPCP) is of cyanobacterial origin [part of a larger gene family encompassing the fucoxanthin-chlorophyll proteins of the chromophytes and the chlorophyll a/b-binding proteins of the land plants (Durnford et al 1996)].…”

Section: Resultsmentioning

confidence: 99%

The Phylogeny of Glyceraldehyde-3-Phosphate Dehydrogenase Indicates Lateral Gene Transfer from Cryptomonads to Dinoflagellates

1998

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Sequence analysis of two nuclear-encoded glyceraldehyde-3-phosphate dehydrogenase (GAPDH) genes isolated from the dinoflagellate Gonyaulax polyedra distinguishes them as cytosolic and chloroplastic forms of the enzyme. Distance analysis of the cytosolic sequence shows the Gonyaulax gene branching early within the cytosolic clade, consistent with other analyses. However, the plastid sequence forms a monophyletic group with the plastid isoforms of cryptomonads, within an otherwise cytosolic clade, distinct from all other plastid GAPDHs. This is attributed to lateral gene transfer from an ancestral cryptomonad to a dinoflagellate, providing the first example of genetic exchange accompanying symbiotic associations between the two, which are common in present day cells.

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“…1B, Douglas and Turner 1991;Giovannoni et al 1993) whereas protein phylogenies position the chlorophyll-a+b-containing euglenophytes with green plastids (Morden et al 1992). Lockhart et al (1992Lockhart et al ( , 1994 and Turner (pers.…”

Section: The Evolution Of Plastidsmentioning

confidence: 99%

“…Usage of partial sequences, different outgroups and species sets, and different phylogenetic methods renders impossible, however, a direct comparison of these data to our phylogenies. A partial (1,118 nt) 16S rRNA sequence analysis using a least-squares method with the JukesCantor (1969) correction positioned C. paradoxa, with moderate bootstrap support (75.5%), as a sister group to nongreen plastids with eubacteria as the outgroup (Douglas and Turner 1991) Giovannoni et al (1993),. using a similar data set (1,184 nt) and the maximum-parsimony method with Anabaena sp.…”

mentioning

confidence: 99%

Analyses of ribosomal RNA sequences from glaucocystophyte cyanelles provide new insights into the evolutionary relationships of plastids

1995

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Glaucocystophyte algae (sensu Kies, Berl. Deutsch. Bot. Ges. 92, 1979) contain plastids (cyanelles) that retain the peptidoglycan wall of the putative cyano-bacterial endosymbiont; this and other ultrastructural characters (e.g., unstacked thylakoids, phycobilisomes) have suggested that cyanelles are "primitive" plastids that may represent undeveloped associations between heterotrophic "host" cells (i.e., glaucocystophytes) and cyanobacteria. To test the monophyly of glaucocystophyte cyanelles and to determine their evolutionary relationship to other plastids, complete 16S ribosomal RNA sequences were determined for Cyanophora paradoxa, Glaucocystis nostochinearum, Glaucosphaera vacuolata, and Gloeochaete wittrockiana. Plastid rRNAs were analyzed with the maximum-likelihood, maximum-parsimony, and neighbor-joining methods. The phylogenetic analyses show that the cyanelles of C. paradoxa, G. nostochinearum, and G. wittrockiana form a distinct evolutionary lineage; these cyanelles presumably share a monophyletic origin. The rDNA sequence of G. vacuolata was positioned within the nongreen plastid lineage. This result is consistent with analyses of nuclear-encoded rRNAs that identify G. vacuolata as a rhodophyte and support is removal from the Glaucocystophyta. Results of a global search with the maximum-likelihood method suggest that cyanelles are the first divergence among all plastids; this result is consistent with a single loss of the peptidoglycan wall in plastids after the divergence of the cyanelles. User-defined tree analyses with the maximum-likelihood method indicate, however, that the position of the cyanelles is not stable within the rRNA phylogenies. Both maximum-parsimony and neighbor-joining analyses showed a close evolutionary relationship between cyanelles and non-green plastids; these phylogenetic methods were sensitive to inclusion/exclusion of the G. wittrockiana cyanelle sequence.(ABSTRACT TRUNCATED AT 250 WORDS)

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Molecular Phylogeny of Oxygenic Cells and Organelles Based on Small-Subunit Ribosomal RNA Sequences

Cited by 8 publications

References 22 publications

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

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

The Phylogeny of Glyceraldehyde-3-Phosphate Dehydrogenase Indicates Lateral Gene Transfer from Cryptomonads to Dinoflagellates

Analyses of ribosomal RNA sequences from glaucocystophyte cyanelles provide new insights into the evolutionary relationships of plastids

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