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Plastid Genomes of Algae
Abstract
Algae are characterized by the presence of plastids (chloroplasts), which are organelles of cyanobacterial origin. Plastids have their own genome, machineries for replication, transcription and translation, and are the site of photosynthesis (except in secondarily non-photosynthetic species) and a variety of other biological functions. Algae are subdivided into those whose plastids can be traced back to a common cyanobacterial endosymbiont (algae with primary plastids), and others in which plastids are second-hand acquisitions that were introduced by eukaryote-eukaryote endosymbioses.
  • References (156)
  • Cited By (19)
Friederike Hörmann6
Estimated H-index: 6
(Ludwig Maximilian University of Munich),
Jürgen Soll63
Estimated H-index: 63
(Ludwig Maximilian University of Munich),
Bettina Bölter24
Estimated H-index: 24
(Ludwig Maximilian University of Munich)
50 Citations Source Cite
Donald H. Williamson32
Estimated H-index: 32
(National Institute for Medical Research),
Malcolm J. Gardner12
Estimated H-index: 12
+ 3 AuthorsR. J. M. Wilson32
Estimated H-index: 32
(National Institute for Medical Research)
In common with other Apicomplexan parasites, Plasmodium falciparum carries two extrachromosomal DNAs, one of which, the 6 kb element, is undoubtedly mitochondrial. The second, generally referred to as the 35 kb circle, is of unknown provenance, but the nature and organization of its genetic content makes a mitochondrial association unlikely and the molecule has features reminiscent of plastid genomes. We now report the occurrence on the circle of an open reading frame specifying a predicted 470 ...
93 Citations Source Cite
Wolfgang Löffelhardt24
Estimated H-index: 24
(University of Vienna),
Hans J. Bohnert75
Estimated H-index: 75
(University of Arizona)
Publisher Summary This chapter describes the importance of Cyanophora cyanelles for the comprehension of plastid evolution. It summarizes cyanelle biochemistry, wall structure, and genome organization. Cyanelles, like cyanobacteria, are surrounded by a peptidoglycan wall. In addition, cyanelles resemble cyanobacteria in their pigment composition and in possessing a carboxysome-like structure. Cyanophora cyanelles, especially in the stationary phase of growth, develop a characteristic protein inc...
11 Citations Source Cite
2004 in Current GeneticsIF: 3.57
Danja Schünemann15
Estimated H-index: 15
(Ruhr University Bochum)
The targeting of proteins, including the insertion and translocation of proteins in or across membranes, is a fundamental process within a cell, and a variety of specialized mechanisms for protein transport have been developed during evolution. The signal recognition particle (SRP) is found in the cytoplasm of most, if not all, eukaryotes and prokaryotes where it plays a central role in the co-translational insertion of membrane proteins into the endoplasmic reticulum and plasma membrane, respec...
78 Citations Source Cite
2005 in Methods in EnzymologyIF: 1.98
Robert K. Jansen49
Estimated H-index: 49
,
Linda A. Raubeson14
Estimated H-index: 14
+ 12 AuthorsSallie J. Herman1
Estimated H-index: 1
Abstract During the past decade, there has been a rapid increase in our understanding of plastid genome organization and evolution due to the availability of many new completely sequenced genomes. There are 45 complete genomes published and ongoing projects are likely to increase this sampling to nearly 200 genomes during the next 5 years. Several groups of researchers including ours have been developing new techniques for gathering and analyzing entire plastid genome sequences and details of th...
200 Citations Download PDF Cite
Bernardo J. Foth19
Estimated H-index: 19
(University of Melbourne),
Geoffrey I. McFadden59
Estimated H-index: 59
(University of Melbourne)
Apicomplexan parasites cause severe diseases such as malaria, toxoplasmosis, and coccidiosis (caused by Plasmodium spp., Toxoplasma , and Eimeria , respectively). These parasites contain a relict plastid—termed “apicoplast”—that originated from the engulfment of an organism of the red algal lineage. The apicoplast is indispensable but its exact role in parasites is unknown. The apicoplast has its own genome and expresses a small number of genes, but the vast majority of the apicoplast proteome i...
151 Citations Source Cite
2004 in BMC BioinformaticsIF: 2.21
Robert C. Edgar13
Estimated H-index: 13
(University of California, Berkeley)
Background In a previous paper, we introduced MUSCLE, a new program for creating multiple alignments of protein sequences, giving a brief summary of the algorithm and showing MUSCLE to achieve the highest scores reported to date on four alignment accuracy benchmarks. Here we present a more complete discussion of the algorithm, describing several previously unpublished techniques that improve biological accuracy and / or computational complexity. We introduce a new option, MUSCLE-fast, designed f...
4,077 Citations Download PDF Cite
Gernot Glöckner33
Estimated H-index: 33
,
André Rosenthal51
Estimated H-index: 51
,
Klaus Valentin9
Estimated H-index: 9
(University of Giessen)
Photosynthetic eukaryotes can, according to features of their chloroplasts, be divided into two major groups: the red and the green lineage of plastid evolution. To extend the knowledge about the evolution of the red lineage we have sequenced and analyzed the chloroplast genome (cp-genome) of Cyanidium caldarium RK1, a unicellular red alga (AF022186). The analysis revealed that this genome shows several unusual structural features, such as a hypothetical hairpin structure in a gene-free region a...
118 Citations Source Cite
2006 in BMC Evolutionary BiologyIF: 3.03
Jean-Charles de Cambiaire5
Estimated H-index: 5
(Laval University),
Christian Otis34
Estimated H-index: 34
(Laval University)
+ 1 AuthorsMonique Turmel41
Estimated H-index: 41
(Laval University)
Background The phylum Chlorophyta contains the majority of the green algae and is divided into four classes. While the basal position of the Prasinophyceae is well established, the divergence order of the Ulvophyceae, Trebouxiophyceae and Chlorophyceae (UTC) remains uncertain. The five complete chloroplast DNA (cpDNA) sequences currently available for representatives of these classes display considerable variability in overall structure, gene content, gene density, intron content and gene order....
59 Citations Source Cite
1999 in NatureIF: 41.58
Zhaoduo Zhang5
Estimated H-index: 5
,
Beverley R. Green39
Estimated H-index: 39
,
Thomas Cavalier-Smith68
Estimated H-index: 68
Photosynthetic dinoflagellates are important aquatic primary producers and notorious causes of toxic 'red tides', Typical dinoflagellate chloroplasts differ from all other plastids in having a combination of three envelope membranes' and peridinin-chlorophyll a/c light-harvesting pigments 2 . Despite evidence of a dinoflagellete satellite DNA containing chloroplast genes 3 , previous attempts to obtain chloroplast gene sequences have been uniformly unsuccessful. Here we show that the dinoflagell...
270 Citations Source Cite
  • References (156)
  • Cited By (19)
Christopher J. Jackson9
Estimated H-index: 9
(University of New Brunswick),
Susan L. Clayden6
Estimated H-index: 6
(University of New Brunswick),
Adrian Reyes-Prieto11
Estimated H-index: 11
(Canadian Institute for Advanced Research)
The Glaucophyta is one of the three major lineages of photosynthetic eukaryotes, together with viridiplants and red algae, united in the presumed monophyletic supergroup Archaeplastida. Glaucophytes constitute a key algal lineage to investigate both the origin of primary plastids and the evolution of algae and plants. Glaucophyte plastids possess exceptional characteristics retained from their cyanobacterial ancestor: phycobilisome antennas, a vestigial peptidoglycan wall, and carboxysome-like b...
7 Citations Download PDF Cite
Lira A. Gaysina5
Estimated H-index: 5
(Pedagogical University),
Yvonne Němcová11
Estimated H-index: 11
(Charles University in Prague)
+ 2 AuthorsMarek Eliáš26
Estimated H-index: 26
(Charles University in Prague)
Soil hosts diverse communities of photosynthetic eukaryotes (algae) that have not yet been fully explored. Here we describe an interesting coccoid green alga isolated from a soil sample from a forest-steppe in South Urals (Bashkortostan, Russia) that, based on a phylogenetic analysis of 18S rRNA gene sequence, appears to represent a new phylogenetic lineage related to the genus Leptosira within the class Trebouxiophyceae. This new alga is characterized by uninucleate cells with a shape ranging f...
8 Citations Source Cite
Monique Turmel41
Estimated H-index: 41
(Laval University),
Christian Otis34
Estimated H-index: 34
(Laval University),
Claude Lemieux44
Estimated H-index: 44
(Laval University)
Previous studies of trebouxiophycean chloroplast genomes revealed little information regarding the evolutionary dynamics of this genome because taxon sampling was too sparse and the relationships between the sampled taxa were unknown. We recently sequenced the chloroplast genomes of 27 trebouxiophycean and 2 pedinophycean green algae to resolve the relationships among the main lineages recognized for the Trebouxiophyceae. These taxa and the previously sampled members of the Pedinophyceae and Tre...
38 Citations Source Cite
2014 in BMC GenomicsIF: 3.73
Haeyoung Jeong18
Estimated H-index: 18
(Korea Research Institute of Bioscience and Biotechnology),
Jong-Min Lim6
Estimated H-index: 6
(Korea Research Institute of Bioscience and Biotechnology)
+ 4 AuthorsWon-Joong Jeong14
Estimated H-index: 14
(Korea Research Institute of Bioscience and Biotechnology)
Background Chorella is the representative taxon of Chlorellales in Trebouxiophyceae, and its chloroplast (cp) genomic information has been thought to depend only on studies concerning Chlorella vulgaris and GenBank information of C. variablis. Mitochondrial (mt) genomic information regarding Chlorella is currently unavailable. To elucidate the evolution of organelle genomes and genetic information of Chlorella, we have sequenced and characterized the cp and mt genomes of Arctic Chlorella sp. ArM...
20 Citations Source Cite
2015 in Journal of PhycologyIF: 3.00
Heroen Verbruggen27
Estimated H-index: 27
(University of Melbourne),
Joana F. Costa6
Estimated H-index: 6
(University of Melbourne)
We present the 174,935 nt long plastid genome of the red alga Laurencia sp. JFC0032. It is the third plastid genome characterized for the largest order of red algae (Ceramiales). The circular-mapping plastid genome is small compared to most florideophyte red algae, and our comparisons show a trend toward smaller plastid genome sizes in the family Rhodomelaceae, independent from a similar trend in Cyanidiophyceae. The Laurencia genome is densely packed with 200 annotated protein-coding genes (188...
12 Citations Source Cite
2015 in BMC GenomicsIF: 3.73
Frederik Leliaert29
Estimated H-index: 29
(University of Alabama),
Juan M. López-Bautista16
Estimated H-index: 16
(University of Alabama)
Background Species of Bryopsidales form ecologically important components of seaweed communities worldwide. These siphonous macroalgae are composed of a single giant tubular cell containing millions of nuclei and chloroplasts, and harbor diverse bacterial communities. Little is known about the diversity of chloroplast genomes (cpDNAs) in this group, and about the possible consequences of intracellular bacteria on genome composition of the host. We present the complete cpDNAs of Bryopsis plumosa ...
34 Citations Download PDF Cite
2013 in PLOS ONEIF: 2.77
Michael S. DePriest3
Estimated H-index: 3
(University of Alabama),
Debashish Bhattacharya63
Estimated H-index: 63
(Rutgers University),
Juan M. López-Bautista16
Estimated H-index: 16
(University of Alabama)
The complete plastid genome sequence of the red macroalga Grateloupia taiwanensis S.-M.Lin & H.-Y.Liang (Halymeniaceae, Rhodophyta) is presented here. Comprising 191,270 bp, the circular DNA contains 233 protein-coding genes and 29 tRNA sequences. In addition, several genes previously unknown to red algal plastids are present in the genome of G. taiwanensis. The plastid genomes from G. taiwanensis and another florideophyte, Gracilaria tenuistipitata var. liui, are very similar in sequence and sh...
21 Citations Source Cite
2015 in PLOS ONEIF: 2.77
James T. Melton3
Estimated H-index: 3
(University of Alabama),
Frederik Leliaert29
Estimated H-index: 29
(University of Alabama)
+ 1 AuthorsJuan M. López-Bautista16
Estimated H-index: 16
(University of Alabama)
Sequencing mitochondrial and chloroplast genomes has become an integral part in understanding the genomic machinery and the phylogenetic histories of green algae. Previously, only three chloroplast genomes (Oltmannsiellopsis viridis, Pseudendoclonium akinetum, and Bryopsis hypnoides) and two mitochondrial genomes (O. viridis and P. akinetum) from the class Ulvophyceae have been published. Here, we present the first chloroplast and mitochondrial genomes from the ecologically and economically impo...
29 Citations Download PDF Cite
2014 in BMC Evolutionary BiologyIF: 3.03
Brad R. Ruhfel11
Estimated H-index: 11
(Eastern Kentucky University),
Matthew A. Gitzendanner20
Estimated H-index: 20
(University of Florida)
+ 2 AuthorsJ. Gordon Burleigh25
Estimated H-index: 25
(University of Florida)
Background Next-generation sequencing has provided a wealth of plastid genome sequence data from an increasingly diverse set of green plants (Viridiplantae). Although these data have helped resolve the phylogeny of numerous clades (e.g., green algae, angiosperms, and gymnosperms), their utility for inferring relationships across all green plants is uncertain. Viridiplantae originated 700-1500 million years ago and may comprise as many as 500,000 species. This clade represents a major source of p...
209 Citations Download PDF Cite
2015 in Scientific ReportsIF: 4.12
Tereza Ševčíková7
Estimated H-index: 7
,
Aleš Horák17
Estimated H-index: 17
+ 12 AuthorsJan Fousek6
Estimated H-index: 6
Algae with secondary plastids of a red algal origin, such as ochrophytes (photosynthetic stramenopiles), are diverse and ecologically important, yet their evolutionary history remains controversial. We sequenced plastid genomes of two ochrophytes, Ochromonas sp. CCMP1393 (Chrysophyceae) and Trachydiscus minutus (Eustigmatophyceae). A shared split of the clpC gene as well as phylogenomic analyses of concatenated protein sequences demonstrated that chrysophytes and eustigmatophytes form a clade, t...
42 Citations Source Cite
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