Dynamic evolution of inverted repeats in Euglenophyta plastid genomes

Published on Dec 1, 2018in Scientific Reports 4.12
· DOI :10.1038/s41598-018-34457-w
Anna Karnkowska5
Estimated H-index: 5
(University of Warsaw),
Matthew S. Bennett11
Estimated H-index: 11
(Michigan State University),
Richard E. Triemer25
Estimated H-index: 25
(Michigan State University)
Abstract
Photosynthetic euglenids (Euglenophyta) are a monophyletic group of unicellular eukaryotes characterized by the presence of plastids, which arose as the result of the secondary endosymbiosis. Many Euglenophyta plastid (pt) genomes have been characterized recently, but they represented mainly one family – Euglenaceae. Here, we report a comparative analysis of plastid genomes from eight representatives of the family Phacaceae. Newly sequenced plastid genomes share a number of features including synteny and gene content, except for genes mat2 and mat5 encoding maturases. The observed diversity of intron number and presence/absence of maturases corroborated previously suggested correlation between the number of maturases in the pt genome and intron proliferation. Surprisingly, pt genomes of taxa belonging to Discoplastis and Lepocinclis encode two inverted repeat (IR) regions containing the rDNA operon, which are absent from the Euglenaceae. By mapping the presence/absence of IR region on the obtained phylogenomic tree, we reconstructed the most probable events in the evolution of IRs in the Euglenophyta. Our study highlights the dynamic nature of the Euglenophyta plastid genome, in particular with regards to the IR regions that underwent losses repeatedly.
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References64
Published on Nov 16, 2005in Journal of Phycology 3.00
Sylwia Kosmala5
Estimated H-index: 5
(University of Warsaw),
Anna Karnkowska5
Estimated H-index: 5
(University of Warsaw)
+ 2 AuthorsBożena Zakryś11
Estimated H-index: 11
(University of Warsaw)
We studied the morphological diversity and analyzed the small subunit rDNA sequences of two taxa formerly known as Euglena spirogyra Ehr. and Euglena fusca (Klebs) Lemmermann. Our studies confirmed that the two should have the rank of a species, namely Lepocinclis spirogyroides (Ehr.) Marin et Melkonian and Lepocinclis fusca (Klebs) Kosmala et Zakrys comb. nov. (Euglenophyceae). We are defining new diagnostic features for these species, namely the size and the shape of the cells and the shape of...
24 Citations Source Cite
Published on Aug 20, 2015in Frontiers in Ecology and Evolution
Jong Im Kim10
Estimated H-index: 10
(Chungnam National University),
Eric W. Linton10
Estimated H-index: 10
(Central Michigan University),
Woongghi Shin14
Estimated H-index: 14
(Chungnam National University)
To establish taxonomy and understand phylogenetic relationships among strains and species of the photosynthetic euglenoids, we performed phylogenetic analyses based on a four gene sequence dataset (nr SSU and LSU rDNA, and pt SSU and LSU rDNA) from 343 taxa (including three outgroup). The phylogenetic tree based on the combined dataset was split into two major clades: Euglenaceae and Phacaceae. The family Euglenaceae was a well-supported monophyletic group containing eight genera (Colacium, Cryp...
11 Citations Source Cite
Published on Jan 20, 2010in Journal of Phycology 3.00
Anna Karnkowska-Ishikawa8
Estimated H-index: 8
(University of Warsaw),
Rafał Milanowski10
Estimated H-index: 10
(University of Warsaw)
+ 1 AuthorsBożena Zakryś11
Estimated H-index: 11
(University of Warsaw)
The establishment of epitypes (together with emended diagnoses) for seven species of Phacus Dujard. [Phacus oscillans G. A. Klebs, Phacus parvulus G. A. Klebs, Phacus pusillus Lemmerm., Phacus skujae Skvortzov, Phacus inflexus (Kisselew) Pochm., Phacus polytrophos Pochm., and Phacus smulkowskianus (Zakrys ´) Kusber] was achieved by literature studies, verification of morphological diagnostic features (cell size, cell shape), as well as molecular characters (SSU rDNA). The investigated Phacus spe...
17 Citations Source Cite
Published on Jan 4, 2016in Nucleic Acids Research 11.56
Maciej Szymanski19
Estimated H-index: 19
(Adam Mickiewicz University in Poznań),
Andrzej Zielezinski7
Estimated H-index: 7
(Adam Mickiewicz University in Poznań)
+ 2 AuthorsWojciech M. Karlowski19
Estimated H-index: 19
(Adam Mickiewicz University in Poznań)
Ribosomal 5S RNA (5S rRNA) is the ubiquitous RNA component found in the large subunit of ribosomes in all known organisms. Due to its small size, abundance and evolutionary conservation 5S rRNA for many years now is used as a model molecule in studies on RNA structure, RNA-protein interactions and molecular phylogeny. 5SRNAdb (http://combio.pl/5srnadb/) is the first database that provides a high quality reference set of ribosomal 5S RNAs (5S rRNA) across three domains of life. Here, we give an o...
7 Citations Source Cite
Published on Jul 1, 2015in Genome Biology and Evolution 3.94
Monique Turmel41
Estimated H-index: 41
(Laval University),
Christian Otis34
Estimated H-index: 34
(Laval University),
Claude Lemieux45
Estimated H-index: 45
(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...
39 Citations Source Cite
Published on Nov 1, 2015in Journal of Eukaryotic Microbiology 2.54
Matthew S. Bennett11
Estimated H-index: 11
(Michigan State University),
Richard E. Triemer25
Estimated H-index: 25
(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 characterized, those of Cryptoglena skujai, E. gracilis var. bacillaris, Euglena viridis, Euglenaria anabaena...
22 Citations Source Cite
Published on Jan 1, 1993in Journal of Cell Science 4.40
Sabine Heinhorst27
Estimated H-index: 27
,
Gordon C. Cannon27
Estimated H-index: 27
Chloroplasts contain multiple copies of a DNA molecule (the plastome) that encodes many of the gene products required to perform photosynthesis. The plastome is replicated by nuclear-encoded proteins and its copy number seems to be highly regulated by the cell in a tissue-specific and developmental manner. Our understanding of the biochemical mechanism by which the plastome is replicated and the molecular basis for its regulation is limited. In this commentary we review our present understanding...
54 Citations
Published on Mar 1, 2007in Nature Protocols 12.42
Gertraud Burger42
Estimated H-index: 42
(Canadian Institute for Advanced Research),
Dennis V. Lavrov29
Estimated H-index: 29
(Canadian Institute for Advanced Research)
+ 1 AuthorsB. Franz Lang47
Estimated H-index: 47
(Canadian Institute for Advanced Research)
1Departement de Biochimie, Robert Cedergren Centre, Program in Evolutionary Biology, Canadian Institute for Advanced Research, Universite de Montreal, 2900 Boulevard Edouard-Montpetit, CP 6128, Montreal, Quebec, H3T 1J4 Canada. 2Present address: Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, Iowa 50011, USA. Correspondence should be addressed to G.B. (Gertraud.Burger@UMontreal.CA) or B.F.L. (Franz.lang@Umontreal.ca).
81 Citations Source Cite
Published on Mar 1, 2009in Molecular Biology and Evolution 10.22
Monique Turmel41
Estimated H-index: 41
(Laval University),
Marie-Christine Gagnon1
Estimated H-index: 1
(Laval University)
+ 2 AuthorsClaude Lemieux45
Estimated H-index: 45
(Laval University)
Because they represent the earliest divergences of the Chlorophyta and include the smallest known eukaryotes (e.g., the coccoid Ostreococcus), the morphologically diverse unicellular green algae making up the Prasinophyceae are central to our understanding of the evolutionary patterns that accompanied the radiation of chlorophytes and the reduction of cell size in some lineages. Seven prasinophyte lineages, four of which exhibit a coccoid cell organization (no flagella nor scales), were uncovere...
142 Citations Source Cite
Published on Mar 20, 2012in PLOS ONE 2.77
Štěpánka Hrdá4
Estimated H-index: 4
(Charles University in Prague),
Jan Fousek6
Estimated H-index: 6
(Academy of Sciences of the Czech Republic)
+ 2 AuthorsCestmir Vlcek30
Estimated H-index: 30
(Academy of Sciences of the Czech Republic)
Euglenids are a group of protists that comprises species with diverse feeding modes. One distinct and diversified clade of euglenids is photoautotrophic, and its members bear green secondary plastids. In this paper we present the plastid genome of the euglenid Eutreptiella, which we assembled from 454 sequencing of Eutreptiella gDNA. Comparison of this genome and the only other available plastid genomes of photosynthetic euglenid, Euglena gracilis, revealed that they contain a virtually identica...
36 Citations Source Cite
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