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Chloroplast Genome Evolution in the Euglenaceae

Published on Nov 1, 2015in Journal of Eukaryotic Microbiology 2.36
· DOI :10.1111/jeu.12235
Matthew S. Bennett11
Estimated H-index: 11
(MSU: Michigan State University),
Richard E. Triemer25
Estimated H-index: 25
(MSU: Michigan State University)
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Abstract
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, Monomorphina parapyrum, and Trachelomonas volvocina, and added to six previously published chloroplast genomes to determine if trends existed within the family. With this study: at least one genome has now been characterized for each genus, the genomes of different strains from two taxa were characterized to explore intraspecific variability, and a second taxon has been characterized for the genus Monomorphina to examine intrageneric variability. Overall results showed a large amount of variability among the genomes, though a few trends could be identified both within Euglenaceae and within Euglenophyta. In addition, the intraspecific analysis indicated that the similarity of a genome sequence between strains was taxon dependent, and the intrageneric analysis indicated that the majority of the evolutionary changes within the Euglenaceae occurred intergenerically.
  • References (28)
  • Citations (22)
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References28
Newest
Published on May 1, 2015in Journal of Eukaryotic Microbiology 2.36
Anna Karnkowska6
Estimated H-index: 6
(University of Warsaw),
Matthew S. Bennett11
Estimated H-index: 11
(MSU: Michigan State University)
+ 3 AuthorsRichard E. Triemer25
Estimated H-index: 25
(MSU: Michigan State University)
Photosynthetic euglenids acquired chloroplasts by secondary endosymbiosis, which resulted in changes to their mode of nutrition and affected the evolution of their morphological characters. Mapping morphological characters onto a reliable molecular tree could elucidate major trends of those changes. We analyzed nucleotide sequence data from regions of three nuclear-encoded genes (nSSU, nLSU, hsp90), one chloroplast-encoded gene (cpSSU) and one nuclear-encoded chloroplast gene (psbO) to estimate ...
17 Citations Source Cite
Published on Jan 1, 2014in Phycologia 1.98
Matthew S. Bennett11
Estimated H-index: 11
(MSU: Michigan State University),
Krystle E. Wiegert5
Estimated H-index: 5
(MSU: Michigan State University),
Richard E. Triemer25
Estimated H-index: 25
(MSU: Michigan State University)
Euglena proxima is a common, globally dispersed, and easily identified photosynthetic euglenoid. Previous phylogenetic analyses using nuclear-encoded small subunit (SSU) and large subunit (LSU) rRNA genes revealed that this taxon was paraphyletic with other Euglena species and was positioned as sister to all Euglenaceae. Despite this, authors were reluctant to remove this taxon from Euglena until additional data, or taxa pairing with E. proxima, were obtained because it created a monotypic genus...
20 Citations Source Cite
Published on Jan 1, 2014in Nucleic Acids Research 11.15
Robert D. Finn43
Estimated H-index: 43
(Wellcome Trust Sanger Institute),
Alex Bateman67
Estimated H-index: 67
+ 10 AuthorsJaina Mistry14
Estimated H-index: 14
Pfam, available via servers in the UK (http://pfam.sanger.ac.uk/) and the USA (http://pfam.janelia.org/), is a widely used database of protein families, containing 14 831 manually curated entries in the current release, version 27.0. Since the last update article 2 years ago, we have generated 1182 new families and maintained sequence coverage of the UniProt Knowledgebase (UniProtKB) at nearly 80%, despite a 50% increase in the size of the underlying sequence database. Since our 2012 article des...
2,773 Citations Source Cite
Published on Dec 1, 2013in Molecular Biology and Evolution 14.80
Obed W. Odom20
Estimated H-index: 20
(University of Texas at Austin),
David L. Herrin24
Estimated H-index: 24
(University of Texas at Austin)
Reverse transcription of mRNA is thought to be an important first step in a model that explains certain evolutionary changes within genes, such as the loss of introns or RNA editing sites. In this model, reverse transcription of mRNA produces cDNA molecules that replace part of the parental gene by homologous recombination. In vivo evidence of reverse transcription of physiologically relevant mRNAs is generally lacking, however, except in genetically engineered cells. Here, we provide in vivo ev...
6 Citations Source Cite
Published on Mar 1, 2013in Journal of Eukaryotic Microbiology 2.36
Krystle E. Wiegert5
Estimated H-index: 5
(MSU: Michigan State University),
Matthew S. Bennett11
Estimated H-index: 11
(MSU: Michigan State University),
Richard E. Triemer25
Estimated H-index: 25
(MSU: Michigan State University)
The chloroplast genomes of two photosynthetic euglenoids, Colacium vesiculosum Ehrenberg (128,889 bp), and Strombomonas acuminata (Schmarda) Deflandre (144,167 bp) have been sequenced. These chloroplast genomes in combination with those of Euglena gracilis, Eutreptia viridis, and Eutreptiella gymnastica provide a snapshot of euglenoid chloroplast evolution allowing comparisons of gene content, arrangement, and expansion. The gene content of the five chloroplast genomes is very similar varying on...
18 Citations Source Cite
Published on Jan 1, 2013in Nucleic Acids Research 11.15
Sarah W. Burge4
Estimated H-index: 4
(HHMI: Howard Hughes Medical Institute),
Jennifer Daub21
Estimated H-index: 21
(HHMI: Howard Hughes Medical Institute)
+ 6 AuthorsAlex Bateman67
Estimated H-index: 67
(HHMI: Howard Hughes Medical Institute)
The Rfam database (available via the website at http://rfam.sanger.ac.uk and through our mirror at http://rfam.janelia.org) is a collection of non-coding RNA families, primarily RNAs with a conserved RNA secondary structure, including both RNA genes and mRNA cis-regulatory elements. Each family is represented by a multiple sequence alignment, predicted secondary structure and covariance model. Here we discuss updates to the database in the latest release, Rfam 11.0, including the introduction of...
505 Citations Source Cite
Published on Dec 31, 2012in PLOS ONE 2.78
Jean-François Pombert17
Estimated H-index: 17
(UBC: University of British Columbia),
Erick R. James21
Estimated H-index: 21
(UBC: University of British Columbia)
+ 1 AuthorsPatrick J. Keeling72
Estimated H-index: 72
(UBC: University of British Columbia)
Background: Photosynthetic euglenids acquired their plastid by secondary endosymbiosis of a prasinophyte-like green alga. But unlike its prasinophyte counterparts, the plastid genome of the euglenid Euglena gracilis is riddled with introns that interrupt almost every protein-encoding gene. The atypical group II introns and twintrons (introns-within-introns) found in the E. gracilis plastid have been hypothesized to have been acquired late in the evolution of euglenids, implying that massive numb...
22 Citations Source Cite
Published on Nov 1, 2012in Phycologia 1.98
Matthew S. Bennett11
Estimated H-index: 11
(MSU: Michigan State University),
Krystle E. Wiegert5
Estimated H-index: 5
(MSU: Michigan State University),
Richard E. Triemer25
Estimated H-index: 25
(MSU: Michigan State University)
Bennett M.S., Wiegert K.E. and Triemer R.E. 2012. Comparative chloroplast genomics between Euglena viridis and Euglena gracilis (Euglenophyta). Phycologia 51: 711–718. DOI: 10.2216/12-017.1 The chloroplast genomes of Euglena gracilis, Eutreptia viridis, Eutreptiella gymnastica, Colacium vesiculosum, Strombomonas acuminata and the colourless Euglena (Astasia) longa, which had secondarily lost the ability to photosynthesize, were previously reported. These studies had shown that there was a great ...
16 Citations Source Cite
Published on Nov 1, 2012in Protist 3.00
Krystle E. Wiegert5
Estimated H-index: 5
(MSU: Michigan State University),
Matthew S. Bennett11
Estimated H-index: 11
(MSU: Michigan State University),
Richard E. Triemer25
Estimated H-index: 25
(MSU: Michigan State University)
The chloroplast genome of Eutreptia viridis Perty, a basal taxon in the photosynthetic euglenoid lineage, was sequenced and compared with that of Euglena gracilis Ehrenberg, a crown species. Several common gene clusters were identified and gene order, conservation, and sequence similarity was assessed through comparisons with Euglena gracilis . Significant gene rearrangements were present between Eutreptia viridis and Euglena gracilis chloroplast genomes. In addition, major expansion has occurre...
26 Citations Source Cite
Published on Mar 20, 2012in PLOS ONE 2.78
Štěpánka Hrdá4
Estimated H-index: 4
(Charles University in Prague),
Jan Fousek6
Estimated H-index: 6
(CAS: Academy of Sciences of the Czech Republic)
+ 2 AuthorsCestmir Vlcek30
Estimated H-index: 30
(CAS: 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
Cited By22
Newest
Published on Dec 1, 2018in Journal of Applied Phycology 2.63
Madhavi Ellala Hewadikaramge (CMU: Central Michigan University), Eric W. Linton10
Estimated H-index: 10
(CMU: Central Michigan University)
The genus Euglena is composed of six subclades with a diversity of chloroplast morphologies, unlike that found in the other genera of Euglenaceae. This genus contains five published chloroplast genomes (cpGenome) and the colorless plastid genome (ptGenome) of the non-photosynthetic euglenoid Euglena longa within the same subclade as Euglena gracilis. Previous studies of cpGenomes revealed that Euglena viridis and E. gracilis, although in separate subclades, had few cpGenome differences, while Eu...
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Published on Dec 1, 2018in Scientific Reports 4.01
Anna Karnkowska6
Estimated H-index: 6
(University of Warsaw),
Matthew S. Bennett11
Estimated H-index: 11
(MSU: Michigan State University),
Richard E. Triemer25
Estimated H-index: 25
(MSU: Michigan State University)
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 sy...
1 Citations Source Cite
Published on Dec 22, 2017in PeerJ 2.35
Yanqiang Ding1
Estimated H-index: 1
,
Yang Fang10
Estimated H-index: 10
(CAS: Chinese Academy of Sciences)
+ 4 AuthorsHai Zhao16
Estimated H-index: 16
(CAS: Chinese Academy of Sciences)
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Published on Dec 1, 2017in Nordic Journal of Botany 0.89
Yan Li (XJU: Xinjiang University), Guanghui Lv4
Estimated H-index: 4
(XJU: Xinjiang University)
+ 2 AuthorsXiao-Dong Yang5
Estimated H-index: 5
(XJU: Xinjiang University)
Source Cite
Published on Aug 25, 2017in PeerJ 2.35
Nadja Dabbagh2
Estimated H-index: 2
,
Matthew S. Bennett11
Estimated H-index: 11
(MSU: Michigan State University)
+ 1 AuthorsAngelika Preisfeld2
Estimated H-index: 2
BACKGROUND:Over the last few years multiple studies have been published showing a great diversity in size of chloroplast genomes (cpGenomes), and in the arrangement of gene clusters, in the Euglenales. However, while these genomes provided important insights into the evolution of cpGenomes across the Euglenales and within their genera, only two genomes were analyzed in regard to genomic variability between and within Euglenales and Eutreptiales. To better understand the dynamics of chloroplast g...
3 Citations Source Cite
Published on Aug 14, 2017in Advances in Botanical Research 2.29
Anna M. G. Novák Vanclová2
Estimated H-index: 2
(Charles University in Prague),
Lucia Hadariová2
Estimated H-index: 2
(Charles University in Prague)
+ 1 AuthorsVladimír Hampl21
Estimated H-index: 21
(Charles University in Prague)
Abstract Euglenophytes obtained their plastids from a primary green alga related to extant genus Pyramimonas . The relatively recent establishment of this new organelle is an intriguing evolutionary phenomenon worth studying and comparing with other secondary plastids with a regard to their similarities and differences. A remarkably fast evolution driven by rapid intron gain and diversification is observed in euglenid plastid genomes which often tend to swell in size and rearrange while keeping ...
2 Citations Source Cite
Published on Jun 1, 2017in Journal of Phycology 2.83
Matthew S. Bennett11
Estimated H-index: 11
(MSU: Michigan State University),
Shin Han Shiu43
Estimated H-index: 43
(MSU: Michigan State University),
Richard E. Triemer25
Estimated H-index: 25
(MSU: Michigan State University)
4 Citations Source Cite
Published on Jun 1, 2017in Current Biology 9.19
Sergio A. Muñoz-Gómez7
Estimated H-index: 7
(Dal: Dalhousie University),
Fabian G. Mejía-Franco1
Estimated H-index: 1
+ 4 AuthorsClaudio H. Slamovits26
Estimated H-index: 26
(CIFAR: Canadian Institute for Advanced Research)
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, Compsopogonophycea...
30 Citations Source Cite
Published on May 1, 2017in Current Genetics 3.46
Lucia Hadariová2
Estimated H-index: 2
(Comenius University in Bratislava),
Matej Vesteg9
Estimated H-index: 9
(Matej Bel University)
+ 2 AuthorsJuraj Krajčovič17
Estimated H-index: 17
(Comenius University in Bratislava)
Euglena gracilis growth with antibacterial agents leads to bleaching, permanent plastid gene loss. Colorless Euglena (Astasia) longa resembles a bleached E. gracilis. To evaluate the role of bleaching in E. longa evolution, the effect of streptomycin, a plastid protein synthesis inhibitor, and ofloxacin, a plastid DNA gyrase inhibitor, on E. gracilis and E. longa growth and plastid DNA content were compared. E. gracilis growth was unaffected by streptomycin and ofloxacin. Quantitative PCR analys...
4 Citations Source Cite