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

Published on Jan 1, 2014in Phycologia 1.80
· DOI :10.2216/13-198.1
Matthew S. Bennett11
Estimated H-index: 11
(Michigan State University),
Krystle E. Wiegert5
Estimated H-index: 5
(Michigan State University),
Richard E. Triemer25
Estimated H-index: 25
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...
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  • Citations (20)
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References26
Published on Jan 1, 2000in Methods of Molecular Biology
Steve Rozen43
Estimated H-index: 43
(Massachusetts Institute of Technology),
Helen Skaletsky29
Estimated H-index: 29
(Massachusetts Institute of Technology)
12.7k Citations Source Cite
Published on Aug 1, 2012in Nature Methods 26.92
Diego Darriba7
Estimated H-index: 7
,
Guillermo L. Taboada14
Estimated H-index: 14
+ 1 AuthorsDavid Posada50
Estimated H-index: 50
5,840 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
Published on Jan 1, 2010in International Journal on Algae
Th. E. Smith2
Estimated H-index: 2
(Ave Maria University)
7 Citations Source Cite
Published on Jun 14, 2004in Genome Research 10.10
Aaron E. Darling34
Estimated H-index: 34
,
Bob Mau16
Estimated H-index: 16
+ 1 AuthorsNicole T. Perna40
Estimated H-index: 40
As genomes evolve, they undergo large-scale evolutionary processes that present a challenge to sequence comparison not posed by short sequences. Recombination causes frequent genome rearrangements, horizontal transfer introduces new sequences into bacterial chromosomes, and deletions remove segments of the genome. Consequently, each genome is a mosaic of unique lineage-specific segments, regions shared with a subset of other genomes and segments conserved among all the genomes under consideratio...
1,784 Citations Source Cite
Published on Mar 1, 2013in Journal of Eukaryotic Microbiology 2.54
Krystle E. Wiegert5
Estimated H-index: 5
(Michigan State University),
Matthew S. Bennett11
Estimated H-index: 11
(Michigan State University),
Richard E. Triemer25
Estimated H-index: 25
(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 Nov 1, 2012in Protist 2.70
Krystle E. Wiegert5
Estimated H-index: 5
(Michigan State University),
Matthew S. Bennett11
Estimated H-index: 11
(Michigan State University),
Richard E. Triemer25
Estimated H-index: 25
(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 Oct 1, 2010in Protist 2.70
Eric W. Linton10
Estimated H-index: 10
(Central Michigan University),
Anna Karnkowska-Ishikawa8
Estimated H-index: 8
(University of Warsaw)
+ 5 AuthorsRichard E. Triemer25
Estimated H-index: 25
(Michigan State University)
Using Maximum Likelihood and Bayesian analyses of three genes, nuclear SSU (nSSU) and LSU (nLSU) rDNA, and chloroplast SSU (cpSSU) rDNA, the relationships among 82 plastid-containing strains of euglenophytes were clarified. The resulting tree split into two major clades: clade one contained Euglena , Trachelomonas , Strombomonas , Colacium , Monomorphina , Cryptoglena and Euglenaria ; clade two contained Lepocinclis , Phacus and Discoplastis . The majority of the members of Euglena were containe...
44 Citations Source Cite
Published on Jan 1, 1994in Nucleic Acids Research 11.56
Umesh S. Muchhal5
Estimated H-index: 5
(University of Nebraska–Lincoln),
Steven D. Schwartzbach25
Estimated H-index: 25
(University of Nebraska–Lincoln)
Abstract The precursor to the Euglena light harvesting chlorophyll a/b binding protein of photosystem II (LHCPII) is a polyprotein containing multiple copies of LHCPII covalently joined by a decapeptide linker. cDNA and genomic clones encoding the 5' and 3' end of a 6.6 kb LHCPII mRNA were sequenced. A 3.1 kb genomic region encoding 1.05 kb of the 5' end of LHCPII mRNA contains 4 introns. A 7.6 kb genomic region encoding 3.3 kb of the 3' end of LHCPII mRNA contains 10 introns. The 5' and 3' ends...
25 Citations Source Cite
Cited By20
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 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 May 1, 2015in Journal of Eukaryotic Microbiology 2.54
Anna Karnkowska5
Estimated H-index: 5
(University of Warsaw),
Matthew S. Bennett11
Estimated H-index: 11
(Michigan State University)
+ 3 AuthorsRichard E. Triemer25
Estimated H-index: 25
(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 ...
16 Citations Source Cite
Published on Oct 14, 2015in Frontiers in Microbiology 4.02
Paul B. Hamilton1
Estimated H-index: 1
,
Keely E. Lefebvre3
Estimated H-index: 3
(University of Ottawa),
Roger D. Bull1
Estimated H-index: 1
Single cell Chelex® DNA extraction and nested PCR amplification were used to examine partial gene sequences from natural diatom populations for taxonomic and phylogenetic studies at and above the level of species. DNA was extracted from cells that were either fresh collected or stored in RNAlater. Extractions from Lugol’s fixation were also attempted with limited success. Three partial gene sequences (rbcL, 18S and psbA) were recovered using existing and new primers with a nested or double neste...
14 Citations Source Cite
Published on May 1, 2016in Journal of Eukaryotic Microbiology 2.54
Chelsea M. Markunas1
Estimated H-index: 1
(Michigan State University),
Richard E. Triemer25
Estimated H-index: 25
(Michigan State University)
Euglenids are an ancient lineage that may have existed as early as 2 billion years ago. A mere 65 years ago, Melvin Calvin and Andrew A. Benson performed experiments on Euglena gracilis and elucidated the series of reactions by which carbon was fixed and reduced during photosynthesis. However, the evolutionary history of this pathway (Calvin-Benson cycle) in euglenids was more complex than Calvin and Benson could have imagined. The chloroplast present today in euglenophytes arose from a secondar...
7 Citations Source Cite
Published on Dec 1, 2016in BMC Evolutionary Biology 3.03
Rafał Milanowski10
Estimated H-index: 10
(University of Warsaw),
Natalia Gumińska1
Estimated H-index: 1
(University of Warsaw)
+ 2 AuthorsBożena Zakryś11
Estimated H-index: 11
(University of Warsaw)
Background Nuclear genes of euglenids contain two major types of introns: conventional spliceosomal and nonconventional introns. The latter are characterized by variable non-canonical borders, RNA secondary structure that brings intron ends together, and an unknown mechanism of removal. Some researchers also distinguish intermediate introns, which combine features of both types. They form a stable RNA secondary structure and are classified into two subtypes depending on whether they contain one ...
5 Citations Source Cite
Published on Jun 1, 2016in Journal of Phycology 3.00
Beth A. Kasiborski1
Estimated H-index: 1
(Central Michigan University),
Matthew S. Bennett11
Estimated H-index: 11
(Michigan State University),
Eric W. Linton10
Estimated H-index: 10
(Central Michigan University)
8 Citations Source Cite
Published on Mar 16, 2016in Frontiers in Ecology and Evolution
Carlos Eduardo de Mattos Bicudo2
Estimated H-index: 2
,
Mariângela Menezes7
Estimated H-index: 7
(Federal University of Rio de Janeiro)
Euglenophyceae (phototrophic euglenids) are an important lineage within the Euglenida, Euglenozoa. Most of the approximately 3,000 described species are free-living, phototrophic, unicellular flagellates with one to several plastids of secondary origin, three bounding membranes and chlorophylls a and b; but, the lineage also includes colorless species that lost their photosynthesizing capability. They show a typical cell membrane consisting of parallel proteinaceous strips and microtubules locat...
5 Citations Source Cite
Published on Jul 7, 2016in International Journal of Molecular Sciences 3.69
Weiwei Zheng2
Estimated H-index: 2
,
Jinhui Chen11
Estimated H-index: 11
+ 1 AuthorsJisen Shi12
Estimated H-index: 12
Chinese fir (Cunninghamia lanceolata (Lamb.) Hook) is an important coniferous tree species for timber production, which accounts for ~40% of log supply from plantations in southern China. Chloroplast genetic engineering is an exciting field to engineer several valuable tree traits. In this study, we revisited the published complete Chinese fir (NC_021437) and four other coniferous species chloroplast genome sequence in Taxodiaceae. Comparison of their chloroplast genomes revealed three unique in...
4 Citations Source Cite
Published on Jan 1, 2017in Journal of Eukaryotic Microbiology 2.54
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