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June 1988 - June 1998
Publications
Publications (190)
Six monophyletic groups of charophycean green algae are recognized within the Streptophyta. Although incongruent with earlier studies based on genes from three cellular compartments, chloroplast and nuclear phylogenomic analyses have resolved identical relationships among these groups, placing the Zygnematales or the Zygnematales + Coleochaetales a...
The green algae belonging to the Chlorophyta-the lineage sister to that comprising the land plants and their charophycean green algal relatives (Streptophyta)-have been subdivided into four classes (Prasinophyceae, Ulvophyceae, Trebouxiophyceae, and Chlorophyceae). Yet the Pedinomonadales, an assemblage consisting of tiny, naked uniflagellates with...
Because they represent the earliest divergences of the Chlorophyta and include the smallest known eukaryotes (e.g., the coccoid Ostreococcus), the morphologically diverse unicellular green algae making up the Prasinophyceae are central to our understanding of the evolutionary patterns that accompanied the radiation of chlorophytes and the reduction...
Sequence comparisons suggest that all living green plants belong to one of two major phyla: Streptophyta (land plants and their closest green algal relatives, the charophytes); and Chlorophyta (the rest of green algae). Because no green algae are known that pre-date the Streptophyta/Chlorophyta split, and also because the earliest diverging green a...
The Viridiplantae comprise two major phyla: the Streptophyta, containing the charophycean green algae and all land plants, and the Chlorophyta, containing the remaining green algae. Despite recent progress in unravelling phylogenetic relationships among major green plant lineages, problematic nodes still remain in the green tree of life. One of the...
Citation: Gastineau R, Otis C, Boyle B, Lemieux C, Turmel M, St-Cyr J, Koken M (2023) The mitochondrial genome of the bioluminescent fish Malacosteus niger Ayres, 1848 (Stomiidae, Actinopterygii) is large and complex, and contains an inverted-repeat structure. ZooKeys Abstract We determined the complete mitogenome sequence of the bioluminescent fis...
Haslea ostrearia represents the model species of blue diatoms, a cluster of benthic marine species all belonging to the genus Haslea, noticeable for producing a blue pigment called marennine famous for its greening activity on the gills of bivalves but also for its potential in biotechnology. The exact distribution of H. ostrearia is unknown. It ha...
The current article focuses on the morphological and molecular characterization of the often inconspicuous genus Amicula. This recently erected genus from brackish and marine sediments was monotypic but here we describe two new tropical species: Amicula micronesica sp. nov. and Amicula vermiculata sp. nov. Once considered an incertae sedis genus re...
In this article we describe Nitzschia anatoliensis Górecka, Gastineau & Solak sp. nov., an example of a diatom species inhabiting extreme habitats. The new species has been isolated and successfully grown from the highly alkaline Van Lake in East Turkey. The description is based on morphology (light and scanning electron microscopy), the sequencing...
We provide for the first time the complete plastid and mitochondrial genomes of a monoraphid diatom: Schizostauron trachyderma. The mitogenome is 41,957 bp in size and displays two group II introns in the cox1 gene. The 187,029 bp plastid genome features the typical quadripartite architecture of diatom genomes. It contains a group II intron in the...
We sequenced the chloroplast genome of Poterioochromonas malhamensis (Pringsheim) R.A.Andersen strain SZCZR2049, which originates from Van Lake in Turkey. This genome is 133,923 bp long, and like those currently available for six phototrophic chrysophytes, it displays a long, gene-rich inverted repeat and a very short single-copy region. Compared t...
We sequenced the plastid genomes of three diatoms from the genus Climaconeis, including
two strains formerly designated as Climaconeis scalaris. At 208,097 and 216,580 bp, the plastid genomes
of the latter strains are the largest ever sequenced among diatoms and their increased size is explained
by the massive expansion of the inverted repeat regio...
Specimens of a new species of blue diatoms from the genus Haslea Simonsen were discovered in geographically distant sampling sites, first in the Canary Archipelago, then North Carolina, Gulf of Naples, the Croatian South Adriatic Sea, and Turkish coast of the Eastern Mediterranean Sea. An exhaustive characterization of these specimens, using a comb...
We report the complete chloroplast genome of the MED1 strain of Nephroselmis pyriformis from the Eastern Mediterranean Sea. At 111,026 bp, this genome is smaller and more compact than those of Nephroselmis olivacea and Nephroselmis astigmatica, and in contrast to the latter taxa, its inverted repeat contains no complete protein-coding genes. It enc...
A water sample was obtained from an arheic oasis in the deep Sahara Desert, the Gueltates Afilal in Tamanrasset (Algeria). Five diatom strains were isolated, cultivated and identified as Tryblionella apiculata, Nitzschia supralitorea, Fistulifera saprophila, Navicula veneta and Thalassiosira pseudonana using a combination of scanning electron micro...
Haslea ostrearia
(Gaillon) Simonsen is famous among diatoms for producing a blue pigment. Genome sequencing of different strains of H. ostrearia led to the discovery of the complete genomes of two new bacilladnaviruses, HOV-148 and HOV-235. The DNA sequences of these viruses were identified in H. ostrearia strains that had been maintained for sever...
Method used to eliminate bacterial contamination of a marine micro-algal culture. Note, this method is not guaranteed to be 100% successful either due to the fact that the antibiotic combination is not lethal to the bacteria present or it is possible that the strain may not be capable of prolonged growth without the presence of bacteria. This metho...
We sequenced the complete mitogenome of the invasive flatworm Platydemus manokwari (Tricladida order, Geoplanidae family). This 19,959-bp genome contains 36 genes and is almost colinear with the mitogenomes of the two other species previously sampled from the Geoplanidae, Bipalium kewense and Obama nungara, both of which feature an extra tRNA gene....
We sampled the first mitogenomes from a novel lineage of the Chlorophyceae that is sister to Sphaeropleales. Although the Jenufa perforata (27,180 bp) and Jenufa minuta (41,488 bp) mitogenomes differ markedly in size, gene order and intron content, their repertoires of conserved genes are essentially identical. Their rRNA genes display the same fra...
We sequenced the complete mitogenome of a specimen of Cymbiola nobilis (Neogastropoda, Volutidae) from Phú Quốc Island in Vietnam. The mitogenome of this predatory sea snail is 16,314-bp long and comprises the typical set of genes encoding 13 proteins, 2 rRNAs, and 22 tRNAs. It features a complex control region that contains two copies of an invert...
We describe the plastome of Jenufa minuta, a unicellular green alga whose precise relationship with the Sphaeropleales (Chlorophyceae) remains uncertain. This 206,680-bp genome contains 100 conserved genes, 11 of which exhibit 16 group I and seven group II introns. We discovered a trans-spliced group II intron in the rpl32 gene of J. minuta and its...
Marine picoalgae from the Prasinococcales order occupy the deepest branch of the Chlorophyta (Palmophyllophyceae). Here, we describe the mitogenomes of Prasinoderma sp. MBIC 10622 and Prasinococcus capsulatus CCMP 1194. At 37,590 and 41,006 bp, respectively, they are smaller than their Prasinoderma coloniale homolog and unlike the latter, lack an i...
Mitogenome evolution in the Chlorophyceae is characterized by the acquisition of a reduced-derived pattern by the Chlamydomonadales + Sphaeropleales clade. Because no mitogenomes are available for the sister clade Oedogoniales + Chaetophorales + Chaetopeltidales, it remains unclear whether the common ancestor of chlorophycean green algae harbored a...
The 25,137-bp mitogenome of the green alga Pedinomonas minor (Pedinomonadales, Pedinophyceae), which belongs to a basal class of the core Chlorophyta, is unusual in displaying a reduced gene content as well as other derived traits. Here, we present the mitogenome of Marsupiomonas sp. NIES 1824 (Marsupiomonadales, Pedinophyceae). Despite its smaller...
We report here the first mitogenome sequences for the chlorophyte class Chlorodendrophyceae. The mitogenomes of Tetraselmis sp. CCMP 881 and Scherffelia dubia (SAG 17.86) are 46,904 bp and 78,958 bp long, respectively, but their gene repertoires are almost identical. Each genome harbors an inverted repeat (IR). The 14,105-bp IR of S. dubia encodes...
We report the chloroplast genome sequence ofNanofrustulum shiloi, a tiny araphid pennate diatomcollected from the Adriatic Sea. The 160,994-bpN.shiloigenome displays a quadripartite structure andits gene repertoire resembles those of other diatom chloroplast genomes. Besides the genes located inthe inverted repeat,psbYis duplicated. A gene-poor reg...
We sequenced the complete mitogenome of a Baltic Sea specimen of the invasive bivalve Rangia cuneata. The mitogenome is 18,993 bp long and encodes 13 proteins, 2 rRNAs, and 22 tRNAs. A large intergenic region between ND6 and ND2 contains an open reading frame that may originate from duplication of ND2. The R. cuneata mitogenome is rearranged in gen...
Tiny marine green algae issued from two deep branches of the Chlorophyta, the Mamiellophyceae and Chloropicophyceae, dominate different regions of the oceans and play key roles in planktonic communities. Considering that the Mamiellophyceae is the sole lineage of prasinophyte algae that has been intensively investigated, the extent to which these t...
Background and aims-The present study aims to describe a new species of pennate blue diatom from the genus Haslea, H. nusantara sp. nov., collected from Semak Daun Island, the Seribu Archipelago, in Indonesian marine waters. Methods-Assessment for species identification was conducted using light microscopy, Scanning Electron Microscopy and molecula...
We have sequenced the mitogenome of Coleochaete scutata strain SAG 110.80M. This mitogenome is the largest among the streptophyte green algae examined to date. At 242,024 bp, it is 4.3-fold larger than the mitogenome of Chaetosphaeridium globosum, the only other mitogenome available for the Coleochaetophyceae. This size difference is mainly explain...
The tiny green algae belonging to the Chloropicophyceae play a key role in marine phytoplankton communities; this newly erected class of prasinophytes comprises two genera (Chloropicon and Chloroparvula) containing each several species. We sequenced the plastomes and mitogenomes of eight Chloropicon and five Chloroparvula species to better delineat...
We determined the sequence of the complete mitogenome of Bipalium kewense, an invasive land flat-worm with worldwide distribution. All 37 genes encoded on this 15,666-bp genome reside on the same DNA strand. Phylogenomic analyses of mitochondrial proteins from taxa of the order Tricladida associated B. kewense with another invasive species of land...
We sequenced the chloroplast genome of Skeletonema pseudocostatum clone SZCZ 1832 from Algeria. The genome is 127,013 bp long. The inverted repeat region is 18,240 bp long and the order of the genes it encodes appeared as highly conserved when compared with other Thalassiosirales. The maximum likelihood phylogeny also evidenced the belonging of S....
The tiny green algae belonging to the Chloropicophyceae play a key role in marine phytoplankton communities; this newly erected class of prasinophytes comprises two genera ( Chloropicon and Chloroparvula ) containing each several species. We sequenced the plastomes and mitogenomes of eight Chloropicon and five Chloroparvula species to better deline...
We sequenced the complete mitogenome of Marenzelleria neglecta, a non-indigenous polychaete of
the Baltic Sea originating from North America. This is the first complete mitogenome made available
for the family Spionidae. The genome is 15,339 bp with a gene order identical to the generic order of
the Pleistoannelida. The multigene maximum likelihood...
Anthropogenic activities have a major impact on the global environment. Canada's natural resources are threatened by the spread of fungal pathogens, which is facilitated by agricultural practices and international trade. Fungi are introduced to new environments and sometimes become established, in which case they can cause disease outbreaks resulti...
We obtained the complete mitogenome of Proschkinia sp. strain SZCZR1824, a strain belonging to a poorly known diatom genus with no previous molecular data. This genome is 48,863 bp long, with two group I introns in rnl and three group II introns in cox1. Using mitogenomic data, Proschkinia sp. was recovered with Fistulifera solaris, far distant fro...
Because hornworts occupy a pivotal position in early land colonization as sister to other bryophytes, sister to tracheophytes, or sister to all other land plants, a renewed interest has arisen in their phylogenetic diversity, morphology, and genomes. To date, only five organellar genome sequences are available for hornworts. We sequenced the plasto...
Percentage of reads in each edited site with respect to total reads in the plastome.
Coverage goes from 165 times up to 65770 times (in position 85532, PsaM).
(PDF)
Percentage of reads in each edited site from total reads in the mitogenome.
Coverage goes from 102 times up to 44015 times (in position 63551, nad5 gene).
(PDF)
RNA edited sites in the plastome of L. dussii.
(DOCX)
RNA edited sites in the mitogenome of L. dussii.
(DOCX)
A. Transcriptome read coverage of the L. dussii plastome. The x-axis shows the gene map of this genome, starting with the LSC region, while the y-axis indicates read depth. B. Transcriptome read coverage of the L. dussii mitogenome. The x-axis shows the gene map of this genome, while the y-axis indicates read depth. A color-coded scale classifies t...
Number of RNA edited sites per gene in the Leiosporoceros and Anthoceros plastomes.
The numbers on the right of the histograms indicate the edited sites that are shared between the two hornworts.
(TIFF)
We sequenced the complete mitogenome of the red chut-chut snail Cerithidea obtusa, from the Cần Giờ mangrove in Vietnam. The mitogenome is 15,708 bp long. It is colinear with the mitogenomes of other members of the superfamily Cerithioidea, and the maximum-likelihood phylogeny obtained with the cox1, cox2 and cox3 genes of several Caenogastropoda a...
The complete mitochondrial genome of the oyster Crassostrea belcheri from the Cần Giò’ mangrove in Vietnam has been sequenced. It consists of a circular DNA molecule of 21020 base pairs (bp), coding for 12 proteins, 20 transfer RNAs, and two ribosomal RNAs. Like the mitogenomes of Crassostrea iredalei and Crassostrea sp. DB1, it contains a non-codi...
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...
A recent scientific discipline, bioinformatics, defined as using informatics for the study of biological problems, is now a requirement for the study of biological sciences. Bioinformatics has become such a powerful and popular discipline that several academic institutions have created programs in this field, allowing students to become specialized...
Comparative analyses of green algal plastid genomes (plastomes) have flourished in the past decade. In addition to improving our understanding of the phylogenetic relationships among green algal lineages, the expanded collection of plastome sequences has provided new insights into the ancestral architecture of this genome in the common ancestor of...
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:...
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...
The Streptophyta comprises all land plants and six main lineages of freshwater green algae: Mesostigmatophyceae, Chlorokybophyceae, Klebsormidiophyceae, Charophyceae, Coleochaetophyceae and Zygnematophyceae. Previous comparisons of the chloroplast genome from nine streptophyte algae (including four zygnematophyceans) revealed that, although land pl...
The green plants (Viridiplantae) are an ancient group of eukaryotes comprising two main clades: the Chlorophyta, which includes a wide diversity of green algae, and the Streptophyta, which consists of freshwater green algae and the land plants. The early-diverging lineages of the Viridiplantae comprise unicellular algae, and multicellularity has ev...
The Chlorodendrophyceae is a small class of green algae belonging to the core Chlorophyta, an assemblage that also comprises the Pedinophyceae, Trebouxiophyceae, Ulvophyceae and Chlorophyceae. Here we describe for the first time the chloroplast genomes of chlorodendrophycean algae (Scherffelia dubia, 137,161 bp; Tetraselmis sp. CCMP 881, 100,264 bp...
Secondary structure model of the RNA species encoded by the Scherffelia chloroplast rnpB gene.
The model is based on the secondary structure of the E. coli RNase P RNA, and helical regions are numbered accordingly [33]. The residues participating in the long-range P4 pairing are denoted by the brackets. The bases in boldface and italics are conserv...
Compared secondary structure models of the Scherffelia group II introns.
(A) Consensus secondary structure of the Scherffelia atpA and cemA introns. (B) Consensus secondary structure of the Scherffelia petA and petB introns. Intron modeling was according to the nomenclature proposed for group II introns [32]. Exon sequences are shown in lowercase l...
Sources and GenBank accession numbers of the chloroplast genomes used in the phylogenomic analyses.
(PDF)
List of all oligonucleotide primers employed in this study.
(PDF)
Background
The class Chlorophyceae (Chlorophyta) includes morphologically and ecologically diverse green algae. Most of the documented species belong to the clade formed by the Chlamydomonadales (also called Volvocales) and Sphaeropleales. Although studies based on the nuclear 18S rRNA gene or a few combined genes have shed light on the diversity a...
Previous studies of trebouxiophycean chloroplast genomes revealed little information regarding the evolutionary dynamics of this genome because taxon sampling was too sparse and the relationships between the sampled taxa were unknown. We recently sequenced the chloroplast genomes of 27 trebouxiophycean and two pedinophycean green algae to resolve t...
Background
Because they represent the earliest divergences of the Chlorophyta, the morphologically diverse unicellular green algae making up the prasinophytes hold the key to understanding the nature of the first viridiplants and the evolutionary patterns that accompanied the radiation of chlorophytes. Nuclear-encoded 18S rDNA phylogenies unveiled...