Chloroplast Genome Evolution in the Euglenaceae

Published on Nov 1, 2015in Journal of Eukaryotic Microbiology 2.54
· DOI :10.1111/jeu.12235
Matthew S. Bennett11
Estimated H-index: 11
(Michigan State University),
Richard E. Triemer25
Estimated H-index: 25
(Michigan State University)
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
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 Jun 1, 2006in Journal of Phycology 3.00
Richard E. Triemer25
Estimated H-index: 25
(Michigan State University),
Eric W. Linton2
Estimated H-index: 2
(Michigan State University)
+ 4 AuthorsStacy Brosnan5
Estimated H-index: 5
(Rutgers University)
A Bayesian analysis, utilizing a combined data set developed from the small subunit (SSU) and large subunit (LSU) rDNA gene sequences, was used to resolve relationships and clarify generic boundaries among 84 strains of plastid-containing euglenophytes representing 11 genera. The analysis produced a tree with three major clades: a Phacus and Lepocinlis clade, a Discoplastis clade, and a Euglena, Colacium, Trachelomonas, Strombomonas, Monomorphina, and Cryptoglena clade. The majority of the speci...
45 Citations Source Cite
Published on Dec 1, 2000in Protist 2.70
Gaby Gockel2
Estimated H-index: 2
(University of Bonn),
Wolfgang Hachtel14
Estimated H-index: 14
(University of Bonn)
Summary Astasia longa is a colourless heterotrophic flagellate closely related to the photoautotrophic Euglena gracilis . A circular 73 kb plastid DNA (ptDNA) has been isolated from A. longa that is about half the size of the chloroplast DNA of E. gracilis (143 kb). We have determined the complete sequence of the ptDNA of A. longa and established a complete gene map. All chloroplast genes for photosynthesis-related proteins are completely absent from the A. longa plastid DNA except for rbc L, th...
92 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 Dec 1, 1993in Trends in Biochemical Sciences 15.68
Donald W. Copertino6
Estimated H-index: 6
(University of Arizona),
Richard B. Hallick23
Estimated H-index: 23
(University of Arizona)
Abstract Two new and important features of introns have emerged from analysis of the Euglena gracilis chloroplast genome. One is a new class of introns, designated group III, that may be the closest contemporaries to nuclear pre-mRNA introns. The second is introns that are interrupted by other introns termed twintrons.
76 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
Published on Nov 1, 2012in Phycologia 1.80
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
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
Cited By22
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 8, 2016in PLOS ONE 2.77
Kristína Záhonová4
Estimated H-index: 4
,
Zoltán Füssy6
Estimated H-index: 6
+ 2 AuthorsVyacheslav Yurchenko28
Estimated H-index: 28
Euglena longa, a close relative of the photosynthetic model alga Euglena gracilis, possesses an enigmatic non-photosynthetic plastid. Its genome has retained a gene for the large subunit of the enzyme RuBisCO (rbcL). Here we provide new data illuminating the putative role of RuBisCO in E. longa. We demonstrated that the E. longa RBCL protein sequence is extremely divergent compared to its homologs from the photosynthetic relatives, suggesting a possible functional shift upon the loss of photosyn...
10 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
Published on Sep 1, 2016in 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)
To probe organelle genome evolution in the Ulvales/Ulotrichales clade, the newly sequenced chloroplast and mitochondrial genomes of Gloeotilopsis planctonica and Gloeotilopsis sarcinoidea (Ulotrichales) were compared with those of Pseudendoclonium akinetum (Ulotrichales) and of the few other green algae previously sampled in the Ulvophyceae. At 105,236 bp, the G. planctonica mitochondrial DNA (mtDNA) is the largest mitochondrial genome reported so far among chlorophytes, whereas the 221,431-bp G...
7 Citations Source Cite
Published on Nov 1, 2016in Journal of Microbiological Methods 1.70
Masashi Ohmachi1
Estimated H-index: 1
(Kyoto University),
Yoshie Fujiwara2
Estimated H-index: 2
(Kyoto University)
+ 4 AuthorsDan Ohtan Wang10
Estimated H-index: 10
(Kyoto University)
Abstract Single-cell transfection is a powerful technique for delivering chemicals, drugs, or probes into arbitrary, specific single cells. This technique is especially important when the analysis of molecular function and cellular behavior in individual microscopic organisms such as protists requires the precise identification of the target cell, as fluorescence labeling of bulk populations makes tracking of individual motile protists virtually impossible. Herein, we have modified current singl...
4 Citations Source Cite
Published on May 1, 2017in Current Genetics 3.57
Lucia Hadariová2
Estimated H-index: 2
(Comenius University in Bratislava),
Matej Vesteg8
Estimated H-index: 8
(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...
3 Citations Source Cite
Published on Oct 25, 2016in PeerJ 2.12
Jean-Simon Brouard6
Estimated H-index: 6
(Laval University),
Monique Turmel41
Estimated H-index: 41
(Laval University)
+ 1 AuthorsClaude Lemieux45
Estimated H-index: 45
(Laval University)
Background. The chloroplast genome sustained extensive changes in architecture during the evolution of the Chlorophyceae, a morphologically and ecologically diverse class of green algae belonging to the Chlorophyta; however, the forces driving these changes are poorly understood. The five orders recognized in the Chlorophyceae form two major clades: the CS clade consisting of the Chlamydomonadales and Sphaeropleales, and the OCC clade consisting of the Oedogoniales, Chaetophorales, and Chaetopel...
6 Citations Source Cite