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Comparative plastid genomics of Synurophyceae: inverted repeat dynamics and gene content variation

Published on Jan 11, 2019in BMC Evolutionary Biology 3.04
· DOI :10.1186/s12862-018-1316-9
Jong Im Kim10
Estimated H-index: 10
(CNU: Chungnam National University),
Hyunmoon Shin1
Estimated H-index: 1
(CNU: Chungnam National University)
+ 4 AuthorsWoongghi Shin15
Estimated H-index: 15
(CNU: Chungnam National University)
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Abstract
The Synurophyceae is one of most important photosynthetic stramenopile algal lineages in freshwater ecosystems. They are characterized by siliceous scales covering the cell or colony surface and possess plastids of red-algal secondary or tertiary endosymbiotic origin. Despite their ecological and evolutionary significance, the relationships amongst extant Synurophyceae are unclear, as is their relationship to most other stramenopiles. Here we report a comparative analysis of plastid genomes sequenced from five representative synurophycean algae. Most of these plastid genomes are highly conserved with respect to genome structure and coding capacity, with the exception of gene re-arrangements and partial duplications at the boundary of the inverted repeat and single-copy regions. Several lineage-specific gene loss/gain events and intron insertions were detected (e.g., cemA, dnaB, syfB, and trnL). Unexpectedly, the cemA gene of Synurophyceae shows a strong relationship with sequences from members of the green-algal lineage, suggesting the occurrence of a lateral gene transfer event. Using a molecular clock approach based on silica fossil record data, we infer the timing of genome re-arrangement and gene gain/loss events in the plastid genomes of Synurophyceae.
  • References (50)
  • Citations (2)
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References50
Newest
Published on Aug 1, 2018in Bioinformatics 4.53
Jaehee Jung3
Estimated H-index: 3
(Hongik University),
Jong Im Kim10
Estimated H-index: 10
(CNU: Chungnam National University)
+ 1 AuthorsGangman Yi6
Estimated H-index: 6
(Dongguk University)
Published on Apr 1, 2018in Genome Biology and Evolution 3.73
Ma. Chiela M. Cremen5
Estimated H-index: 5
(University of Melbourne),
Frederik Leliaert30
Estimated H-index: 30
(UGent: Ghent University)
+ 1 AuthorsHeroen Verbruggen28
Estimated H-index: 28
(University of Melbourne)
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...
Published on Nov 1, 2017in Phycologia 1.98
Robert A. Andersen29
Estimated H-index: 29
(UW: University of Washington),
Louis Graf4
Estimated H-index: 4
(SKKU: Sungkyunkwan University)
+ 1 AuthorsHwan Su Yoon19
Estimated H-index: 19
(SKKU: Sungkyunkwan University)
Abstract: Ochromonas triangulata, the type species for a genus with over 125 taxa, was collected for only the second time, again from the type locality. Cell morphology, cell division, palmelloid stage and cyst structure generally agreed with the original description. Molecular phylogenetic analysis based on the 18S rRNA gene revealed 13 clades of Ochromonas-like flagellates as well as the clade represented by our O. triangulata strain and the nearly identical strain RCC-21/AC025. We also conduc...
Published on Sep 13, 2017in Symmetry 2.14
Jaehee Jung3
Estimated H-index: 3
,
Jong Im Kim10
Estimated H-index: 10
+ 1 AuthorsGangman Yi6
Estimated H-index: 6
Big data research on genomic sequence analysis has accelerated considerably with the development of next-generation sequencing. Currently, research on genomic sequencing has been conducted using various methods, ranging from the assembly of reads consisting of fragments to the annotation of genetic information using a database that contains known genome information. According to the development, most tools to analyze the new organelles’ genetic information requires different input formats such a...
Published on Jul 1, 2017in Genome Biology and Evolution 3.73
Jong Im Kim10
Estimated H-index: 10
(CNU: Chungnam National University),
Christa E. Moore4
Estimated H-index: 4
(Dal: Dalhousie University)
+ 4 AuthorsWoongghi Shin15
Estimated H-index: 15
(CNU: Chungnam National University)
Published on Mar 1, 2017in Scientific Reports 4.01
C. L. Gandini1
Estimated H-index: 1
,
M. V. Sanchez-Puerta1
Estimated H-index: 1
Angiosperm mitochondrial genomes (mtDNA) exhibit variable quantities of alien sequences. Many of these sequences are acquired by intracellular gene transfer (IGT) from the plastid. In addition, frequent events of horizontal gene transfer (HGT) between mitochondria of different species also contribute to their expanded genomes. In contrast, alien sequences are rarely found in plastid genomes. Most of the plant-to-plant HGT events involve mitochondrion-to-mitochondrion transfers. Occasionally, for...
Published on Jan 1, 2017
Zoltán Füssy6
Estimated H-index: 6
,
Miroslav Oborník27
Estimated H-index: 27
(Sewanee: The University of the South)
Abstract Chrompodellids, a monophyletic group consisting of predatory colpodellids and the chromerid algae Chromera velia and Vitrella brassicaformis , are the closest known relatives to apicomplexan parasites. The photosynthetic plastids of Chromera and Vitrella are evolutionarily linked to apicoplasts, nonphotosynthetic plastids of apicomplexans, allowing the reconstruction of processes that shaped these organelles into their current form and function. Chromerid and apicomplexan plastids are d...
Published on Dec 1, 2016in BMC Biology 6.72
JunMo Lee6
Estimated H-index: 6
(SKKU: Sungkyunkwan University),
Chung Hyun Cho2
Estimated H-index: 2
(SKKU: Sungkyunkwan University)
+ 5 AuthorsHwan Su Yoon19
Estimated H-index: 19
(SKKU: Sungkyunkwan University)
Background The red algae (Rhodophyta) diverged from the green algae and plants (Viridiplantae) over one billion years ago within the kingdom Archaeplastida. These photosynthetic lineages provide an ideal model to study plastid genome reduction in deep time. To this end, we assembled a large dataset of the plastid genomes that were available, including 48 from the red algae (17 complete and three partial genomes produced for this analysis) to elucidate the evolutionary history of these organelles...
Published on Nov 1, 2016in Molecular Biology and Evolution 14.80
Romain Derelle12
Estimated H-index: 12
(CNRS: Centre national de la recherche scientifique),
Purificación López-García46
Estimated H-index: 46
(CNRS: Centre national de la recherche scientifique)
+ 1 AuthorsDavid Moreira54
Estimated H-index: 54
(CNRS: Centre national de la recherche scientifique)
Stramenopiles or heterokonts constitute one of the most speciose and diverse clades of protists. It includes ecologically important algae (such as diatoms or large multicellular brown seaweeds), as well as heterotrophic (e.g., bicosoecids, MAST groups) and parasitic (e.g., Blastocystis, oomycetes) species. Despite their evolutionary and ecological relevance, deep phylogenetic relationships among stramenopile groups, inferred mostly from small-subunit rDNA phylogenies, remain unresolved, especial...
Cited By2
Newest
Published on Apr 8, 2019in F1000Research
Jon Bråte12
Estimated H-index: 12
(University of Oslo),
Janina Fuss2
Estimated H-index: 2
(CAU: University of Kiel)
+ 1 AuthorsDag Klaveness27
Estimated H-index: 27
(University of Oslo)
Hydrurus foetidus is a freshwater alga belonging to the phylum Heterokonta. It thrives in cold rivers in polar and high alpine regions. It has several morphological traits reminiscent of single-celled eukaryotes, but can also form macroscopic thalli. Despite its ability to produce polyunsaturated fatty acids, its life under cold conditions and its variable morphology, very little is known about its genome and transcriptome. Here, we present an extensive set of next-generation sequencing data, in...
Richard G. Dorrell11
Estimated H-index: 11
,
Tomonori Azuma1
Estimated H-index: 1
(Kyoto University)
+ 8 AuthorsGillian H. Gile15
Estimated H-index: 15
(ASU: Arizona State University)
The division of life into producers and consumers is blurred by evolution. For example, eukaryotic phototrophs can lose the capacity to photosynthesize, although they may retain vestigial plastids that perform other essential cellular functions. Chrysophyte algae have undergone a particularly large number of photosynthesis losses. Here, we present a plastid genome sequence from a nonphotosynthetic chrysophyte, “ Spumella ” sp. NIES-1846, and show that it has retained a nearly identical set of pl...