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Robust Dinoflagellata phylogeny inferred from public transcriptome databases

Published on Jun 1, 2017in Journal of Phycology 2.83
· DOI :10.1111/jpy.12529
Dana C. Price19
Estimated H-index: 19
(RU: Rutgers University),
Debashish Bhattacharya64
Estimated H-index: 64
(RU: Rutgers University)
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Abstract
Dinoflagellates are dominant members of the plankton and play key roles in ocean ecosystems as primary producers, predators, parasites, coral photobionts, and causative agents of algal blooms that produce toxins harmful to humans and commercial fisheries. These unicellular protists exhibit remarkable trophic and morphological diversity and include species with some of the largest reported nuclear genomes. Despite their high ecological and economic importance, comprehensive genome (or transcriptome) based dinoflagellate trees of life are few in number. To address this issue, we used recently generated public sequencing data, including from the Moore Microbial Eukaryote Transcriptome Sequencing Project (MMETSP), to identify dinoflagellate-specific ortholog groups. These orthologs were combined to create a broadly sampled and highly resolved phylogeny of dinoflagellates. Our results emphasize the scope and utility of public sequencing databases in creating broad and robust phylogenies for large and complex taxonomic lineages, while also providing unique insights into the evolution of thecate dinoflagellates. This article is protected by copyright. All rights reserved.
  • References (44)
  • Citations (10)
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References44
Newest
Jan Janouškovec20
Estimated H-index: 20
,
Gregory S. Gavelis5
Estimated H-index: 5
(UBC: University of British Columbia)
+ 12 AuthorsCharles F. Delwiche44
Estimated H-index: 44
(UMD: University of Maryland, College Park)
Abstract Dinoflagellates are key species in marine environments, but they remain poorly understood in part because of their large, complex genomes, unique molecular biology, and unresolved in-group relationships. We created a taxonomically representative dataset of dinoflagellate transcriptomes and used this to infer a strongly supported phylogeny to map major morphological and molecular transitions in dinoflagellate evolution. Our results show an early-branching position of Noctiluca, monophyly...
64 Citations Source Cite
Published on Dec 1, 2016in Environmental Microbiology 5.15
Dana C. Price19
Estimated H-index: 19
(RU: Rutgers University),
Natalie Farinholt1
Estimated H-index: 1
(UH: University of Hawaii)
+ 4 AuthorsDebashish Bhattacharya64
Estimated H-index: 64
(RU: Rutgers University)
5 Citations Source Cite
Published on Nov 4, 2016in Molecular Biology and Evolution 14.80
Richard G. Dorrell11
Estimated H-index: 11
('ENS Paris': École Normale Supérieure),
Christen M. Klinger8
Estimated H-index: 8
(U of A: University of Alberta)
+ 6 AuthorsChris Bowler71
Estimated H-index: 71
('ENS Paris': École Normale Supérieure)
10 Citations Source Cite
Published on Oct 1, 2016in Molecular Ecology 5.86
Mickael Le Gac13
Estimated H-index: 13
('IFREMER': IFREMER),
Gabriel Metegnier1
Estimated H-index: 1
(UPMC: Pierre-and-Marie-Curie University)
+ 7 AuthorsAnnie Chapelle14
Estimated H-index: 14
('IFREMER': IFREMER)
Understanding divergence in the highly dispersive and seemingly homogeneous pelagic environment for organisms living as free drifters in the water column remains a challenge. Here, we analysed the transcriptome-wide mRNA sequences, as well as the morphology of 18 strains of Alexandrium minutum, a dinoflagellate responsible for harmful algal blooms worldwide, to investigate the functional bases of a divergence event. Analysis of the joint site frequency spectrum (JSFS) pointed towards an ancestra...
6 Citations Source Cite
Published on Feb 1, 2016in Environmental Microbiology 5.15
Noan Le Bescot1
Estimated H-index: 1
(University of Paris),
Frédéric Mahé18
Estimated H-index: 18
(TUK: Kaiserslautern University of Technology)
+ 6 AuthorsRaffaele Siano17
Estimated H-index: 17
('IFREMER': IFREMER)
Dinoflagellates (Alveolata) are one of the ecologically most important groups of modern phytoplankton. Their biological complexity makes assessment of their global diversity and community structure difficult. We used massive V9 18S rDNA sequencing from 106 size-fractionated plankton communities collected across the world's surface oceans during the Tara Oceans expedition (2009-2012) to assess patterns of pelagic dinoflagellate diversity and community structuring over global taxonomic and ecologi...
29 Citations Source Cite
Published on Dec 1, 2015in Genome Biology 14.03
David Emms9
Estimated H-index: 9
(University of Oxford),
Steven L. Kelly55
Estimated H-index: 55
(University of Oxford)
Identifying homology relationships between sequences is fundamental to biological research. Here we provide a novel orthogroup inference algorithm called OrthoFinder that solves a previously undetected gene length bias in orthogroup inference, resulting in significant improvements in accuracy. Using real benchmark datasets we demonstrate that OrthoFinder is more accurate than other orthogroup inference methods by between 8 % and 33 %. Furthermore, we demonstrate the utility of OrthoFinder by pro...
449 Citations Source Cite
Published on Dec 1, 2015in Protist 3.00
Juliane Kretschmann4
Estimated H-index: 4
(LMU: Ludwig Maximilian University of Munich),
Natalia Filipowicz8
Estimated H-index: 8
(Gdańsk Medical University)
+ 2 AuthorsMarc Gottschling25
Estimated H-index: 25
(LMU: Ludwig Maximilian University of Munich)
The Gymnodiniaceae –even in a strict sense– comprise a vast diversity of dinophytes regarding morphology and ecology. Taxonomy and nomenclature of their constituent species remain problematic, although crucial to fully explore the biology of the group. Here, we present the rarely documented dinophyte Gymnodinium limneticum from its type locality at Lake Morskie Oko in Poland, for which we established strains and made extensive morphological studies. The species was unusual in exhibiting capsoid ...
9 Citations Source Cite
Published on Sep 1, 2015in Journal of Eukaryotic Microbiology 2.36
Gregory S. Mendez2
Estimated H-index: 2
(UMD: University of Maryland, College Park),
Charles F. Delwiche44
Estimated H-index: 44
(UMD: University of Maryland, College Park)
+ 1 AuthorsJ. Casey Lippmeier8
Estimated H-index: 8
(DSM)
Dinoflagellates are one of the last major lineages of eukaryotes for which little is known about genome structure and organization. We report here the sequence and gene structure of a clone isolated from a cosmid library which, to our knowledge, represents the largest contiguously sequenced, dinoflagellate genomic, tandem gene array. These data, combined with information from a large transcriptomic library, allowed a high level of confidence of every base pair call. This degree of confidence is ...
5 Citations Source Cite
Published on May 22, 2015in Science 41.04
Colomban de Vargas37
Estimated H-index: 37
(UPMC: Pierre-and-Marie-Curie University),
Stéphane Audic43
Estimated H-index: 43
(UPMC: Pierre-and-Marie-Curie University)
+ 52 AuthorsIan Probert35
Estimated H-index: 35
(UPMC: Pierre-and-Marie-Curie University)
Marine plankton support global biological and geochemical processes. Surveys of their biodiversity have hitherto been geographically restricted and have not accounted for the full range of plankton size. We assessed eukaryotic diversity from 334 size-fractionated photic-zone plankton communities collected across tropical and temperate oceans during the circumglobal Tara Oceans expedition. We analyzed 18S ribosomal DNA sequences across the intermediate plankton-size spectrum from the smallest uni...
495 Citations Source Cite
Sebastian G. Gornik12
Estimated H-index: 12
(University of Melbourne),
Febrimarsa1
Estimated H-index: 1
(University of Melbourne)
+ 8 AuthorsArnab Pain46
Estimated H-index: 46
(KAUST: King Abdullah University of Science and Technology)
We thank Nick Katris for assistance with Toxoplasma transformation and Ellen Nisbet for critically reading this report. This work was supported by Australian Research Council (ARC) Grants DP130100572 and DP1093395; a King Abdullah University of Science and Technology Faculty Baseline Research Fund; and Victorian Life Sciences Computation Initiative Grant VR0254. S.G.G. was supported by Science Foundation Ireland Grant 13/SIRG/2125; F. was supported by an Australia Award; A.M.C. and A.B. were sup...
35 Citations Source Cite
Cited By10
Newest
Published on May 16, 2019in DNA Research 4.00
Dana C. Price19
Estimated H-index: 19
(RU: Rutgers University),
Ursula Goodenough49
Estimated H-index: 49
(WashU: Washington University in St. Louis)
+ 12 AuthorsUgo Cenci7
Estimated H-index: 7
(CNRS: Centre national de la recherche scientifique)
Glaucophyta are members of the Archaeplastida, the founding group of photosynthetic eukaryotes that also includes red algae (Rhodophyta), green algae, and plants (Viridiplantae). Here we present a high-quality assembly, built using long-read sequences, of the ca. 100 Mb nuclear genome of the model glaucophyte Cyanophora paradoxa. We also conducted a quick-freeze deep-etch electron microscopy (QFDEEM) analysis of C. paradoxa cells to investigate glaucophyte morphology in comparison to other organ...
2 Citations Source Cite
Published on Dec 1, 2018
Huanle Liu1
Estimated H-index: 1
(UQ: University of Queensland),
Timothy G. Stephens3
Estimated H-index: 3
(UQ: University of Queensland)
+ 12 AuthorsSylvain Forêt25
Estimated H-index: 25
(JCU: James Cook University)
Symbiosis between dinoflagellates of the genus Symbiodinium and reef-building corals forms the trophic foundation of the world’s coral reef ecosystems. Here we present the first draft genome of Symbiodinium goreaui (Clade C, type C1: 1.03 Gbp), one of the most ubiquitous endosymbionts associated with corals, and an improved draft genome of Symbiodinium kawagutii (Clade F, strain CS-156: 1.05 Gbp) to further elucidate genomic signatures of this symbiosis. Comparative analysis of four available Sy...
4 Citations Source Cite
Published on Dec 1, 2018in Scientific Reports 4.01
Timothy G. Stephens3
Estimated H-index: 3
(UQ: University of Queensland),
Mark A. Ragan47
Estimated H-index: 47
(UQ: University of Queensland)
+ 1 AuthorsCheong Xin Chan19
Estimated H-index: 19
(UQ: University of Queensland)
Dinoflagellates are a diverse group of unicellular primary producers and grazers that exhibit some of the most remarkable features known among eukaryotes. These include gigabase-sized nuclear genomes, permanently condensed chromosomes and highly reduced organelle DNA. However, the genetic inventory that allows dinoflagellates to thrive in diverse ecological niches is poorly characterised. Here we systematically assess the functional capacity of 3,368,684 predicted proteins from 47 transcriptome ...
1 Citations Source Cite
Published on Dec 1, 2018in Revue de Micropaléontologie
Aurélie Penaud11
Estimated H-index: 11
(CNRS: Centre national de la recherche scientifique),
William Hardy2
Estimated H-index: 2
(CNRS: Centre national de la recherche scientifique)
+ 6 AuthorsKenneth Neil Mertens18
Estimated H-index: 18
('IFREMER': IFREMER)
Abstract Dinoflagellates are part of the marine plankton and about 200 species produce a cyst (dinocyst) during their life cycle, these organic-walled sexually-produced cysts being fossilizable in sediments for hundreds of millions of years. Over the past 40–50 years, dinocysts have led to major advances on Mesozoic-Cenozoic research, in terms of biostratigraphy and paleogeogeography. Dinocyst taxonomy has then been continuously revised, with the tabulation being the main morphological link betw...
1 Citations Source Cite
Published on Nov 1, 2018in Molecular Phylogenetics and Evolution 3.99
Benjamin Linard12
Estimated H-index: 12
(CNRS: Centre national de la recherche scientifique),
Alex Crampton-Platt1
Estimated H-index: 1
(Imperial College London)
+ 14 AuthorsAmie Hunter1
Estimated H-index: 1
(Natural History Museum)
Abstract A phylogenetic tree at the species level is still far off for highly diverse insect orders, including the Coleoptera, but the taxonomic breadth of public sequence databases is growing. In addition, new types of data may contribute to increasing taxon coverage, such as metagenomic shotgun sequencing for assembly of mitogenomes from bulk specimen samples. The current study explores the application of these techniques for large-scale efforts to build the tree of Coleoptera. We used shotgun...
4 Citations Source Cite
Published on Mar 1, 2018in Organisms Diversity & Evolution 2.14
Anže Žerdoner Čalasan3
Estimated H-index: 3
(LMU: Ludwig Maximilian University of Munich),
Juliane Kretschmann4
Estimated H-index: 4
(LMU: Ludwig Maximilian University of Munich),
Marc Gottschling25
Estimated H-index: 25
(LMU: Ludwig Maximilian University of Munich)
Tertiary endosymbiosis is proven through dinophytes, some of which (i.e. Kryptoperidiniaceae) have engulfed diatom algae containing a secondary plastid. Chloroplasts are usually inherited together permanently with the host cell, leading to co-phylogeny. We compiled a diatom sequence data matrix of two nuclear and two chloroplast loci. Almost all endosymbionts of Kryptoperidiniaceae found their closest relatives in free-living diatoms and not in other harboured algae, rejecting co-phylogeny and i...
2 Citations Source Cite
Published on Jan 2, 2018in European Journal of Phycology 2.53
Nicolás Raho7
Estimated H-index: 7
(UAM: Autonomous University of Madrid),
Santiago Fraga27
Estimated H-index: 27
+ 1 AuthorsIrma Marín15
Estimated H-index: 15
(UAM: Autonomous University of Madrid)
ABSTRACTA new euryhaline and eurythermal dinoflagellate species, Biecheleria tirezensis sp. nov., is described based on samples taken from an extreme environment, the athalassohaline and particularly sulphate-rich Tirez natural pond (Spain). This species is able to survive in salinities from almost fresh water up to 56 and over a 5–25°C temperature range. Thus, the ecological characteristics of this isolate differentiate it from other species of the same genus. Its morphology, as examined by lig...
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