Robust Dinoflagellata phylogeny inferred from public transcriptome databases

Published on Jun 1, 2017in Journal of Phycology 3.00
· DOI :10.1111/jpy.12529
Dana C. Price19
Estimated H-index: 19
(Rutgers University),
Debashish Bhattacharya64
Estimated H-index: 64
(Rutgers University)
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 (8)
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References44
Published on Jan 1, 2009in Methods of Molecular Biology
Patrick J. Keeling69
Estimated H-index: 69
(University of British Columbia)
Plastids are the organelles derived from a cyanobacterium through endosymbiosis. Unlike mitochondria, plastids are not found in all eukaryotes, but their evolution has an added layer of complexity since plastids have moved between eukaryotic lineages by secondary and tertiary endosymbiotic events. This complex history, together with the genetic integration between plastids and their host, has led to many opportunities for gene flow between phylogenetically distinct lineages. Some intracellular t...
19 Citations Source Cite
Published on Sep 1, 2015in Journal of Eukaryotic Microbiology 2.54
Gregory S. Mendez2
Estimated H-index: 2
(University of Maryland, College Park),
Charles F. Delwiche41
Estimated H-index: 41
(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 Feb 1, 2016in Environmental Microbiology 4.97
Noan Le Bescot1
Estimated H-index: 1
(University of Paris),
Frédéric Mahé19
Estimated H-index: 19
(Kaiserslautern University of Technology)
+ 6 AuthorsRaffaele Siano16
Estimated H-index: 16
(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...
27 Citations Source Cite
Published on Dec 1, 2015in Protist 2.70
Juliane Kretschmann4
Estimated H-index: 4
(Ludwig Maximilian University of Munich),
Natalia Filipowicz7
Estimated H-index: 7
(Gdańsk Medical University)
+ 2 AuthorsMarc Gottschling24
Estimated H-index: 24
(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 May 22, 2015in Science 41.06
Colomban de Vargas36
Estimated H-index: 36
(Pierre-and-Marie-Curie University),
Stéphane Audic45
Estimated H-index: 45
(Pierre-and-Marie-Curie University)
+ 52 AuthorsIan Probert34
Estimated H-index: 34
(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...
471 Citations Source Cite
Published on Dec 1, 2015in Genome Biology 13.21
David Emms8
Estimated H-index: 8
(University of Oxford),
Steven L. Kelly54
Estimated H-index: 54
(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...
377 Citations Source Cite
Published on Oct 1, 2012in Journal of Phycology 3.00
Cheong Xin Chan19
Estimated H-index: 19
(Rutgers University),
Marcelo Bento Soares44
Estimated H-index: 44
(Northwestern University)
+ 5 AuthorsDebashish Bhattacharya64
Estimated H-index: 64
(Rutgers University)
Microbial eukaryotes may extinguish much of their nuclear phylogenetic history due to endosymbiotic/horizontal gene transfer (E/HGT). We studied E/HGT in 32,110 contigs of expressed sequence tags (ESTs) from the dinoflagellate Alexandrium tamarense (Dinophyceae) using a conservative phylogenomic approach. The vast majority of predicted proteins (86.4%) in this alga are novel or dinoflagellate-specific. We searched for putative homologs of these predicted proteins against a taxonomically broadly ...
19 Citations Source Cite
Published on May 1, 2005in Molecular Biology and Evolution 10.22
Hwan Su Yoon24
Estimated H-index: 24
(University of Iowa),
Jeremiah D. Hackett24
Estimated H-index: 24
(University of Iowa)
+ 3 AuthorsDebashish Bhattacharya64
Estimated H-index: 64
(University of Iowa)
Dinoflagellates are important aquatic primary producers and cause "red tides." The most widespread plastid (photosynthetic organelle) in these algae contains the unique accessory pigment peridinin. This plastid putativelyoriginated via a red algal secondary endosymbiosis and has some remarkable features, the most notable being a genome that is reduced to 1-3 gene minicircles with about 14 genes (out of an original 130-200) remaining in the organelle and a nuclear-encoded proteobacterial Form II ...
124 Citations Source Cite
Published on Jul 1, 1999in Journal of Eukaryotic Microbiology 2.54
Diane K. Stoecker39
Estimated H-index: 39
(University of Maryland Center for Environmental Science)
Mixotrophy, used herein for the combination of phototrophy and phagotrophy, is widespread among dinoflagellates. It occurs among most, perhaps all, of the extant orders, including the Prorocentrales, Dinophysiales, Gymnodiniales, Noctilucales, Gonyaulacales, Peridiniales, Blastodiniales, Phytodiniales, and Dinamoebales. Many cases of mixotrophy among dinoflagellates are probably undocumented. Primarily photosynthetic dinoflagellates with their "own" plastids can often supplement their nutrition ...
289 Citations Source Cite
Published on Jan 1, 2014in Molecular Phylogenetics and Evolution 4.41
Tsvetan R. Bachvaroff19
Estimated H-index: 19
(Smithsonian Environmental Research Center),
Sebastian G. Gornik12
Estimated H-index: 12
(University of Melbourne)
+ 4 AuthorsCharles F. Delwiche41
Estimated H-index: 41
(University of Maryland, College Park)
The alveolates are composed of three major lineages, the ciliates, dinoflagellates, and apicomplexans. Together these ‘protist’ taxa play key roles in primary production and ecology, as well as in illness of humans and other animals. The interface between the dinoflagellate and apicomplexan clades has been an area of recent discovery, blurring the distinction between these two clades. Moreover, phylogenetic analysis has yet to determine the position of basal dinoflagellate clades hence the deepe...
42 Citations Source Cite
Cited By8
Published on Dec 1, 2017in Journal of Phycology 3.00
Urban Tillmann31
Estimated H-index: 31
,
Mona Hoppenrath23
Estimated H-index: 23
+ 2 AuthorsMalte Elbrächter19
Estimated H-index: 19
One of the most common marine dinophytes is a species known as Heterocapsa triquetra. When Stein introduced the taxon Heterocapsa, he formally based the type species H. triquetra on the basionym Glenodinium triquetrum. The latter was described by Ehrenberg and is most likely a species of Kryptoperidinium. In addition to that currently unresolved nomenclatural situation, the thecal plate composition of H. triquetra sensu Stein (1883) was controversial in the past. To clarify the debate, we collec...
3 Citations Source Cite
Published on Mar 1, 2018in Organisms Diversity & Evolution 2.37
Anže Žerdoner Čalasan3
Estimated H-index: 3
(Ludwig Maximilian University of Munich),
Juliane Kretschmann4
Estimated H-index: 4
(Ludwig Maximilian University of Munich),
Marc Gottschling24
Estimated H-index: 24
(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 2.48
Nicolás Raho7
Estimated H-index: 7
(Autonomous University of Madrid),
Santiago Fraga23
Estimated H-index: 23
+ 1 AuthorsIrma Marín14
Estimated H-index: 14
(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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Published on Nov 1, 2018in Molecular Phylogenetics and Evolution 4.41
Benjamin Linard10
Estimated H-index: 10
(Centre national de la recherche scientifique),
Alex Crampton-Platt8
Estimated H-index: 8
(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...
3 Citations Source Cite
Published on Dec 1, 2018in Revue de Micropaléontologie
Aurélie Penaud11
Estimated H-index: 11
(Centre national de la recherche scientifique),
William Hardy2
Estimated H-index: 2
(Centre national de la recherche scientifique)
+ 6 AuthorsKenneth Neil Mertens18
Estimated H-index: 18
(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...
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Published on Dec 1, 2018in Scientific Reports 4.12
Timothy G. Stephens2
Estimated H-index: 2
(University of Queensland),
Mark A. Ragan46
Estimated H-index: 46
(University of Queensland)
+ 1 AuthorsCheong Xin Chan19
Estimated H-index: 19
(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 ...
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