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A rare case of plastid protein‐coding gene duplication in the chloroplast genome of Euglena archaeoplastidiata (Euglenophyta)

Published on Jun 1, 2017in Journal of Phycology 2.83
· DOI :10.1111/jpy.12531
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)
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  • References (34)
  • Citations (4)
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References34
Newest
Published on Nov 1, 2015in Journal of Eukaryotic Microbiology 2.36
Matthew S. Bennett11
Estimated H-index: 11
(MSU: Michigan State University),
Richard E. Triemer25
Estimated H-index: 25
(MSU: 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 Aug 20, 2015in Frontiers in Ecology and Evolution
Jong Im Kim10
Estimated H-index: 10
(CNU: Chungnam National University),
Eric W. Linton10
Estimated H-index: 10
(CMU: Central Michigan University),
Woongghi Shin15
Estimated H-index: 15
(CNU: 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 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, 2015in BMC Plant Biology 3.67
Seongjun Park5
Estimated H-index: 5
(University of Texas at Austin),
Robert K. Jansen47
Estimated H-index: 47
(University of Texas at Austin),
SeonJoo Park7
Estimated H-index: 7
(Yeungnam University)
Background Plastids originated from cyanobacteria and the majority of the ancestral genes were lost or functionally transferred to the nucleus after endosymbiosis. Comparative genomic investigations have shown that gene transfer from plastids to the nucleus is an ongoing evolutionary process but molecular evidence for recent functional gene transfers among seed plants have only been documented for the four genes accD, infA, rpl22, and rpl32.
23 Citations Source Cite
Published on Jan 1, 2015in Nature Methods 28.47
Jianyi Yang18
Estimated H-index: 18
(UM: University of Michigan),
Renxiang Yan2
Estimated H-index: 2
(UM: University of Michigan)
+ 3 AuthorsYang Zhang50
Estimated H-index: 50
1,480 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 Dec 1, 2013in Molecular Biology and Evolution 14.80
Koichiro Tamura28
Estimated H-index: 28
(Tokyo Metropolitan University),
Glen Stecher6
Estimated H-index: 6
(ASU: Arizona State University)
+ 2 AuthorsSudhir Kumar63
Estimated H-index: 63
(ASU: Arizona State University)
We announce the release of an advanced version of the Molecular Evolutionary Genetics Analysis (MEGA) software, which currently contains facilities for building sequence alignments, inferring phylogenetic histories, and conducting molecular evolutionary analysis. In version 6.0, MEGA now enables the inference of timetrees, as it implements the RelTime method for estimating divergence times for all branching points in a phylogeny. A new Timetree Wizard in MEGA6 facilitates this timetree inference...
22.6k Citations Source Cite
Published on Aug 15, 2013in PLOS Genetics 5.22
Jianbo Zhang12
Estimated H-index: 12
,
Tao Zuo3
Estimated H-index: 3
,
Thomas Peterson31
Estimated H-index: 31
Tandem direct duplications are a common feature of the genomes of eukaryotes ranging from yeast to human, where they comprise a significant fraction of copy number variations. The prevailing model for the formation of tandem direct duplications is non-allelic homologous recombination (NAHR). Here we report the isolation of a series of duplications and reciprocal deletions isolated de novo from a maize allele containing two Class II Ac/Ds transposons. The duplication/deletion structures suggest t...
20 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
Cited By4
Newest
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