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Dynamic evolution of inverted repeats in Euglenophyta plastid genomes

Published on Dec 1, 2018in Scientific Reports 4.01
· DOI :10.1038/s41598-018-34457-w
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)
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Abstract
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 synteny and gene content, except for genes mat2 and mat5 encoding maturases. The observed diversity of intron number and presence/absence of maturases corroborated previously suggested correlation between the number of maturases in the pt genome and intron proliferation. Surprisingly, pt genomes of taxa belonging to Discoplastis and Lepocinclis encode two inverted repeat (IR) regions containing the rDNA operon, which are absent from the Euglenaceae. By mapping the presence/absence of IR region on the obtained phylogenomic tree, we reconstructed the most probable events in the evolution of IRs in the Euglenophyta. Our study highlights the dynamic nature of the Euglenophyta plastid genome, in particular with regards to the IR regions that underwent losses repeatedly.
  • References (64)
  • Citations (1)
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References64
Newest
Published on Dec 1, 2017in Scientific Reports 4.01
Monique Turmel41
Estimated H-index: 41
(Laval University),
Christian Otis34
Estimated H-index: 34
(Laval University),
Claude Lemieux45
Estimated H-index: 45
(Laval University)
The chloroplast genomes of many algae and almost all land plants carry two identical copies of a large inverted repeat (IR) sequence that can pair for flip-flop recombination and undergo expansion/contraction. Although the IR has been lost multiple times during the evolution of the green algae, the underlying mechanisms are still largely unknown. A recent comparison of IR-lacking and IR-containing chloroplast genomes of chlorophytes from the Ulvophyceae (Ulotrichales) suggested that differential...
12 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 Jun 1, 2017in Nature Methods 28.47
Subha Kalyaanamoorthy8
Estimated H-index: 8
,
Bui Quang Minh15
Estimated H-index: 15
+ 2 AuthorsLars S. Jermiin35
Estimated H-index: 35
ModelFinder is a fast model-selection method that greatly improves the accuracy of phylogenetic estimates.
440 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
Published on Nov 1, 2016in Systematic Biology 10.27
Olga Chernomor4
Estimated H-index: 4
(Medical University of Vienna),
Arndt von Haeseler48
Estimated H-index: 48
(Medical University of Vienna),
Bui Quang Minh15
Estimated H-index: 15
(Medical University of Vienna)
In phylogenomics the analysis of concatenated gene alignments, the so-called supermatrix, is commonly accompanied by the assumption of partition models. Under such models each gene, or more generally partition, is allowed to evolve under its own evolutionary model. Although partition models provide a more comprehensive analysis of supermatrices, missing data may hamper the tree search algorithms due to the existence of phylogenetic (partial) terraces. Here, we introduce the phylogenetic terrace ...
128 Citations Source Cite
Published on Jun 1, 2016in Journal of Phycology 2.83
Beth A. Kasiborski1
Estimated H-index: 1
(CMU: Central Michigan University),
Matthew S. Bennett11
Estimated H-index: 11
(MSU: Michigan State University),
Eric W. Linton10
Estimated H-index: 10
(CMU: Central Michigan University)
8 Citations Source Cite
Cited By1
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Published on Apr 26, 2019in Brazilian Journal of Botany
Anna Victoria Silvério Righetto Mauad1
Estimated H-index: 1
(UFPR: Federal University of Paraná),
Leila do Nascimento Vieira (UFPR: Federal University of Paraná)+ 5 AuthorsEric de Camargo Smidt10
Estimated H-index: 10
(UFPR: Federal University of Paraná)
Anathallis (Pleurothallidinae) is a Neotropical orchid genus with over 150 species. Although previous phylogenetic studies suggest the polyphyletism of the genus, there is little information about the group in the literature due to the lack of Anathallis-focused molecular studies and the absence of genomic research in Pleurothallidinae. Here, we sequenced and characterized the complete chloroplast genome (plastome) of Anathallis obovata (Lindl.) Pridgeon & M.W. Chase, the type species of the gen...
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