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Characterization of Euglenaformis gen. nov. and the chloroplast genome of Euglenaformis (Euglena) proxima (Euglenophyta)

Published on Jan 1, 2014in Phycologia 1.98
· DOI :10.2216/13-198.1
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)
Cite
Abstract
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. To clarify the taxonomy, the chloroplast genome of E. proxima was sequenced and compared with those of other photosynthetic euglenoids. Phylogenomic analyses were performed comparing 79 chloroplast-encoded genes from E. proxima with those found in seven photosynthetic euglenoids and three prasinophytes, the group from which the euglenoid chloroplast was probably derived. These analyses resulted in highly supported phylogenomic trees with topologies that were consistent with all previous phylogenetic analyses, i.e...
  • References (26)
  • Citations (20)
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References26
Newest
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 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 Aug 1, 2012in Nature Methods 28.47
Diego Darriba8
Estimated H-index: 8
,
Guillermo L. Taboada14
Estimated H-index: 14
+ 1 AuthorsDavid Posada51
Estimated H-index: 51
6,098 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
Published on Feb 1, 2012in Journal of Phycology 2.83
Matthew S. Bennett11
Estimated H-index: 11
(MSU: Michigan State University),
Richard E. Triemer25
Estimated H-index: 25
(MSU: Michigan State University)
One of the foremost issues in the field of algal taxonomy is the inability to acquire, grow, and sequence new taxa. This problem is particularly true in the study of photosynthetic euglenoids where most of the distinct taxa in culture collections have been sequenced, and many other taxa of interest have been resistant to culturing, and thus, sequencing. In an effort to address this problem, we have utilized a new technique, novel to the field of taxonomy, which allows for the sequencing of nucle...
15 Citations Source Cite
Published on Oct 1, 2011in Molecular Biology and Evolution 14.80
Koichiro Tamura28
Estimated H-index: 28
(ASU: Arizona State University),
Daniel S. Peterson14
Estimated H-index: 14
(ASU: Arizona State University)
+ 3 AuthorsSudhir Kumar63
Estimated H-index: 63
(ASU: Arizona State University)
Comparative analysis of molecular sequence data is essential for reconstructing the evolutionary histories of species and inferring the nature and extent of selective forces shaping the evolution of genes and species. Here, we announce the release of Molecular Evolutionary Genetics Analysis version 5 (MEGA5), which is a user-friendly software for mining online databases, building sequence alignments and phylogenetic trees, and using methods of evolutionary bioinformatics in basic biology, biomed...
30.8k Citations Source Cite
Published on Dec 1, 2010in Journal of Phycology 2.83
Jong Im Kim10
Estimated H-index: 10
(CNU: Chungnam National University),
Woongghi Shin15
Estimated H-index: 15
(CNU: Chungnam National University),
Richard E. Triemer25
Estimated H-index: 25
(MSU: Michigan State University)
Bayesian and maximum-likelihood (ML) analyses of the combined multigene data (nuclear SSU rDNA, and plastid SSU and LSU rDNA) were conducted to evaluate the phylogeny of photosynthetic euglenoids. The combined data set consisted of 108 strains of photosynthetic euglenoids including a colorless sister taxon. Bayesian and ML analyses recovered trees of almost identical topology. The results indicated that photosynthetic euglenoids were divided into two major clades, the Euglenaceae clade (Euglena,...
28 Citations Source Cite
Cited By20
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
Christopher J. Jackson10
Estimated H-index: 10
(University of Melbourne),
Andrew H. Knoll103
Estimated H-index: 103
(Harvard University)
+ 1 AuthorsHeroen Verbruggen28
Estimated H-index: 28
(University of Melbourne)
Secondary plastids derived from green algae occur in chlorarachniophytes, photosynthetic euglenophytes, and the dinoflagellate genus Lepidodinium. Recent advances in understanding the origin of these plastids have been made, but analyses suffer from relatively sparse taxon sampling within the green algal groups to which they are related. In this study we aim to derive new insights into the identity of the plastid donors, and when in geological time the independent endosymbiosis events occurred. ...
9 Citations Source Cite
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 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 Feb 1, 2017in Journal of Phycology 2.83
Bryan Lakey1
Estimated H-index: 1
(MSU: Michigan State University),
Richard E. Triemer25
Estimated H-index: 25
(MSU: Michigan State University)
The history of euglenoids may have begun as early as ~2 bya. These early phagotrophs ate cyanobacteria, archaea, and eubacteria, and the subsequent appearance of red algae and chromalveolates provided euglenoids with additional food sources. Following the appearance of green algae, euglenoids acquired a chloroplast via a secondary endosymbiotic event with a green algal ancestor. This endosymbiosis also involved a massive transfer of nuclear-encoded genes from the symbiont nucleus to the host. Ex...
4 Citations Source Cite
Published on Jan 1, 2017
Bożena Zakryś11
Estimated H-index: 11
(University of Warsaw),
Rafał Milanowski11
Estimated H-index: 11
(University of Warsaw),
Anna Karnkowska6
Estimated H-index: 6
(University of Warsaw)
Euglenids (Excavata, Discoba, Euglenozoa, Euglenida) is a group of free-living, single-celled flagellates living in the aquatic environments. The uniting and unique morphological feature of euglenids is the presence of a cell covering called the pellicle. The morphology and organization of the pellicle correlate well with the mode of nutrition and cell movement. Euglenids exhibit diverse modes of nutrition, including phagotrophy and photosynthesis. Photosynthetic species (Euglenophyceae) constit...
6 Citations Source Cite
Published on Jan 1, 2017in Journal of Eukaryotic Microbiology 2.36
Nadja Dabbagh2
Estimated H-index: 2
,
Angelika Preisfeld2
Estimated H-index: 2
A comparative analysis of the chloroplast genome of Euglena mutabilis underlined a high diversity in the evolution of plastids in euglenids. Gene clusters in more derived Euglenales increased in complexity with only a few, but remarkable changes in the genus Euglena. Euglena mutabilis differed from other Euglena species in a mirror-inverted arrangement of 12 from 15 identified clusters, making it very likely that the emergence at the base of the genus Euglena, which has been considered a long br...
7 Citations Source Cite