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Abstract
Summary Red algal plastid genomes are often considered ancestral and evolutionarily stable, and thus more closely resembling the last common ancestral plastid genome of all photosynthetic eukaryotes [1, 2]. However, sampling of red algal diversity is still quite limited (e.g., [2–5]). We aimed to remedy this problem. To this end, we sequenced six new plastid genomes from four undersampled and phylogenetically disparate red algal classes (Porphyridiophyceae, Stylonematophyceae, Compsopogonophyceae, and Rhodellophyceae) and discovered an unprecedented degree of genomic diversity among them. These genomes are rich in introns, enlarged intergenic regions, and transposable elements (in the rhodellophycean Bulboplastis apyrenoidosa ), and include the largest and most intron-rich plastid genomes ever sequenced (that of the rhodellophycean Corynoplastis japonica ; 1.13 Mbp). Sophisticated phylogenetic analyses accounting for compositional heterogeneity show that these four "basal" red algal classes form a larger monophyletic group, Proteorhodophytina subphylum nov., and confidently resolve the large-scale relationships in the Rhodophyta. Our analyses also suggest that secondary red plastids originated before the diversification of all mesophilic red algae. Our genomic survey has challenged the current paradigmatic view of red algal plastid genomes as "living fossils" [1, 2, 6] by revealing an astonishing degree of divergence in size, organization, and non-coding DNA content. A closer look at red algae shows that they comprise the most ancestral (e.g., [2, 7, 8]) as well as some of the most divergent plastid genomes known.
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Debashish Bhattacharya61
Estimated H-index: 61
(Rutgers University),
Hwan Su Yoon18
Estimated H-index: 18
(Bigelow Laboratory For Ocean Sciences),
Giuseppe C. Zuccarello23
Estimated H-index: 23
(Victoria University of Wellington)
Dr. Hwan Su Yoon is currently a Senior Research Scientist at the Bigelow Laboratory for Ocean Sciences. He obtained his Ph.D. from Chungnam National University, Korea, in 1999 under the supervision of Prof. Sung Min Boo, and thereafter joined the lab of Debashish Bhattacharya at the University of Iowa. His research interests are in the areas of plastid evolution of chromalveolates, genome evolutio...
Cited 19 Download Pdf Cite this paper
2015 in PeerJ [IF: 2.18]
Georg Mohr21
Estimated H-index: 21
(University of Texas at Austin),
Dana C. Price17
Estimated H-index: 17
(Rutgers University),
Debashish Bhattacharya61
Estimated H-index: 61
(Rutgers University)
... (1 others)
Group II introns are closely linked to eukaryote evolution because nuclear spliceosomal introns and the small RNAs associated with the spliceosome are thought to trace their ancient origins to these mobile elements. Therefore, elucidating how group II introns move, and how they lose mobility can potentially shed light on fundamental aspects of eukaryote biology. To this end, we studied five strain...
Ref 42Cited 8 Download Pdf Cite this paper
2012 in Phycological Research [IF: 1.34]
Mitsunori Iwataki2
Estimated H-index: 2
(Yamagata University),
John A. West20
Estimated H-index: 20
(University of Melbourne),
Yoshiaki Hara16
Estimated H-index: 16
(Yamagata University)
... (3 others)
SUMMARY A novel unicellular red alga collected from a mangrove area on Iriomote Island in southwest Japan is described as Bulboplastis apyrenoidosa gen. et sp. nov. The cells are spherical, mean 11.2 µm in diameter, and surrounded by a thick mucilaginous sheath. The grayish-green chloroplast has many lobes extending throughout the cell and lacks a pyrenoid. This chloroplast type is similar to Glau...
Ref 28Cited 6 Source Cite this paper
Jeremiah D. Hackett25
Estimated H-index: 25
(University of Iowa),
Gabriele Pinto22
Estimated H-index: 22
(University of Naples Federico II),
Debashish Bhattacharya61
Estimated H-index: 61
(University of Iowa)
... (1 others)
Abstract Algae include a diverse array of photosynthetic eukaryotes excluding land plants. Explaining the origin of algal plastids continues to be a major challenge in evolutionary biology. Current knowledge suggests that plastid primary endosymbiosis, in which a single-celled protist engulfs and “enslaves” a cyanobacterium, likely occurred once and resulted in the primordial alga. This eukaryote ...
Ref 2Cited 281 Download Pdf Cite this paper
Susan E. Douglas32
Estimated H-index: 32
(National Research Council)
Ref 187Cited 70 Source Cite this paper
2001 in Genome Biology [IF: 11.91]
Steven L. Salzberg115
Estimated H-index: 115
(J. Craig Venter Institute),
Brian J. Haas74
Estimated H-index: 74
(J. Craig Venter Institute),
Natalia Volfovsky14
Estimated H-index: 14
(National Institutes of Health)
Background A computational system for analysis of the repetitive structure of genomic sequences is described. The method uses suffix trees to organize and search the input sequences; this data structure has been used previously for efficient computation of exact and degenerate repeats.
Ref 23Cited 118 Download Pdf Cite this paper
Eunsoo Kim12
Estimated H-index: 12
(Dalhousie University),
John M. Archibald39
Estimated H-index: 39
(Dalhousie University)
Plastids, the light-harvesting organelles of plants and algae, are the descendants of cyanobacterial endosymbionts that became permanent fixtures inside nonphotosynthetic eukaryotic host cells. This chapter provides an overview of the structural, functional and molecular diversity of plastids in the context of current views on the evolutionary relationships among the eukaryotic hosts in which they...
Ref 219Cited 33 Download Pdf Cite this paper
B. Franz Lang1
Estimated H-index: 1
(Université de Montréal),
Aurora M. Nedelcu21
Estimated H-index: 21
(University of New Brunswick)
Ref 156Cited 19 Download Pdf Cite this paper
Richard E. Triemer24
Estimated H-index: 24
(Michigan State University),
Matthew S. Bennett12
Estimated H-index: 12
(Michigan State University)
Over the last few years multiple studies have been published outlining chloroplast genomes that represent many of the photosynthetic euglenid genera. However, these genomes were scattered throughout the euglenophyceaean phylogenetic tree, and focused on comparisons with Euglena gracilis. Here, we present a study exclusively on taxa within the Euglenaceae. Six new chloroplast genomes were character...
Ref 28Cited 21 Source Cite this paper
A Mousseau1
Estimated H-index: 1
(Centre national de la recherche scientifique),
J P Dubacq1
Estimated H-index: 1
(Centre national de la recherche scientifique),
N Tandeau de Marsac21
Estimated H-index: 21
(Centre national de la recherche scientifique)
... (4 others)
Abstract The phycobilisome of the eukaryotic unicellular red alga Rhodella violacea presents in some respects an organization that is intermediate between those of the homologous counterparts found in cyanobacteria (the putative chloroplast progenitor) and more advanced, pluricellular red algae. This suggests evolutionary relationships that we investigated at the genome level. The present work des...
Cited 25 Source Cite this paper
Cited by18
Huan Qiu16
Estimated H-index: 16
(Rutgers University),
Hwan Su Yoon18
Estimated H-index: 18
(Sungkyunkwan University),
JunMo Lee4
Estimated H-index: 4
(Sungkyunkwan University)
... (3 others)
Source Cite this paper
2017 in Genome Biology and Evolution [IF: 3.98]
Debashish Bhattacharya61
Estimated H-index: 61
(Rutgers University),
Christa E. Moore3
Estimated H-index: 3
(Dalhousie University),
Woongghi Shin14
Estimated H-index: 14
(Chungnam National University)
... (4 others)
Cited 2 Source Cite this paper
Pilar Díaz-Tapia5
Estimated H-index: 5
(University of Melbourne),
Christopher J. Jackson6
Estimated H-index: 6
(University of Melbourne),
Valéria Cassano9
Estimated H-index: 9
(University of São Paulo)
... (6 others)
ABSTRACTIn recent years, the use of molecular data in algal systematics has increased as high-throughput sequencing (HTS) has become more accessible, generating very large datasets at a reasonable cost. In this perspectives paper, our goal is to describe how HTS technologies can advance algal systematics. Following an introduction to some common HTS technologies, we discuss how metabarcoding can a...
Source Cite this paper
2017 in Frontiers in Plant Science [IF: 4.29]
David Roy Smith23
Estimated H-index: 23
(University of Western Ontario)
There is a strong positive relationship between nuclear genome size and cell size across the eukaryotic domain, but the cause and effect of this relationship is unclear. A positive coupling of cell size and DNA content has also been recorded for various bacteria, suggesting that, with some exceptions, this association might be universal throughout the tree of life. However, the link between cell s...
Cited 1 Source Cite this paper
2018 in Genome Biology and Evolution [IF: 3.98]
Heroen Verbruggen14
Estimated H-index: 14
(University of Melbourne),
Frederik Leliaert30
Estimated H-index: 30
(Botanic Garden Meise),
Ma. Chiela M. Cremen1
Estimated H-index: 1
(University of Melbourne)
... (1 others)
Source Cite this paper
2017 in eLife [IF: 7.72]
Christen M. Klinger7
Estimated H-index: 7
(University of Alberta),
Richard G. Dorrell9
Estimated H-index: 9
(École Normale Supérieure),
Katalina D. Freeman (Arizona State University) ... (6 others)
The cells of most plants and algae contain compartments called chloroplasts that enable them to capture energy from sunlight in a process known as photosynthesis. Chloroplasts are the remnants of photosynthetic bacteria that used to live freely in the environment until they were consumed by a larger cell. “Complex” chloroplasts can form if a cell that already has a chloroplast is swallowed by anot...
Cited 10 Source Cite this paper
Mark Arick5
Estimated H-index: 5
(Mississippi State University),
Daniel G. Peterson28
Estimated H-index: 28
(Mississippi State University)
Download Pdf Cite this paper
Chris Bowler71
Estimated H-index: 71
(École Normale Supérieure),
Richard G. Dorrell9
Estimated H-index: 9
(École Normale Supérieure)
Abstract The stramenopiles encompass an incredible diversity of organisms, including ecologically fundamental single-celled algae such as diatoms, giant macroalgae such as kelps, as well as photo-mixotrophic and heterotrophic species. The photosynthetic species possess plastids of secondary or higher red algal origin. The diversity of stramenopile species provides an ideal system for exploring the...
Source Cite this paper
2017 in Current Biology [IF: 8.85]
Kenny A. Bogaert3
Estimated H-index: 3
(Ghent University),
Andrea Del Cortona (Ghent University), Klaas Vandepoele53
Estimated H-index: 53
(Ghent University)
... (6 others)
Summary Virtually all plastid (chloroplast) genomes are circular double-stranded DNA molecules, typically between 100 and 200 kb in size and encoding circa 80–250 genes. Exceptions to this universal plastid genome architecture are very few and include the dinoflagellates, where genes are located on DNA minicircles. Here we report on the highly deviant chloroplast genome of Cladophorales green alga...
Cited 4 Source Cite this paper