Publications by authors named "Romain Gastineau"

28 Publications

  • Page 1 of 1

SARS-CoV-2 Whole-Genome Sequencing by Ion S5 Technology-Challenges, Protocol Optimization and Success Rates for Different Strains.

Viruses 2022 06 6;14(6). Epub 2022 Jun 6.

Department of Forensic Medicine, Pomeranian Medical University in Szczecin, 70-111 Szczecin, Poland.

The COVID-19 pandemic demonstrated how rapidly various molecular methods can be adapted for a Public Health Emergency. Whether a need arises for whole-genome studies (next-generation sequencing), fast and high-throughput diagnostics (reverse-transcription real-time PCR) or global immunization (construction of mRNA or viral vector vaccines), the scientific community has been able to answer all these calls. In this study, we aimed at the assessment of effectiveness of the commercially available solution for full-genome SARS-CoV-2 sequencing (AmpliSeq™ SARS-CoV-2 Research Panel and Ion AmpliSeq™ Library Kit Plus, Thermo Fisher Scientific). The study is based on 634 samples obtained from patients from Poland, with varying viral load, assigned to a number of lineages. Here, we also present the results of protocol modifications implemented to obtain high-quality genomic data. We found that a modified library preparation protocol required less viral RNA input in order to obtain the optimal library quantity. Concurrently, neither concentration of cDNA nor reamplification of libraries from low-template samples improved the results of sequencing. On the basis of the amplicon success rates, we propose one amplicon to be redesigned, namely, the r1_1.15.1421280, for which less than 50 reads were produced by 44% of samples. Additionally, we found several mutations within different SARS-CoV-2 lineages that cause the neighboring amplicons to underperform. Therefore, due to constant SARS-CoV-2 evolution, we support the idea of conducting ongoing sequence-based surveillance studies to continuously validate commercially available RT-PCR and whole-genome sequencing solutions.
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http://dx.doi.org/10.3390/v14061230DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9227152PMC
June 2022

Redescription, complete mitochondrial genome and phylogenetic relationships of Hexostoma thynni (Delaroche, 1811) Rafinesque, 1815 (Monogenea, Hexostomatidae).

Parasite 2022 23;29:29. Epub 2022 May 23.

ISYEB, Institut de Systématique, Évolution, Biodiversité (UMR7205 CNRS, EPHE, MNHN, UPMC, Université des Antilles), Muséum National d'Histoire Naturelle, CP 51, 55 rue Buffon, 75231 Paris Cedex 05, France.

Specimens of Hexostoma thynni (Delaroche, 1811) Rafinesque, 1815 were collected from their type-host, the bluefin tuna Thunnus thynnus, caught off Algeria, i.e. close to the type-locality, off Mallorca, which is also in the Mediterranean. The species is briefly redescribed and compared to previous descriptions, under the same name or as its synonym Plagiopeltis duplicata Diesing, 1858, to ascertain identity of specimens. The three genera within the Hexostomatidae (Hexostoma Rafinesque, 1815, Neohexostoma Price, 1961 and Homostoma Unnithan, 1965) are briefly discussed, with comments on the fragility of characters used to distinguish them. Using next-generation sequencing, the complete mitogenome and the cluster of ribosomal genes (SSU, LSU, ITS1, ITS2, 5.8S) were obtained. The mitogenome is 14,649 bp long and codes for 12 protein-coding genes, 2 ribosomal RNA genes and 22 transfer RNA genes; its size is similar to other mitogenomes obtained from polyopisthocotylean monogeneans. A phylogeny based on concatenated mitogenome protein-coding genes from nine species of polyopisthocotylean monogeneans produced a tree in which the Hexostomatidae H. thynni was associated with other Mazocraeidea, such as Chauhaneidae and Diclidophoridae. This invalidates the hypothesis of Boeger & Kritsky (1993) of Hexostomatidae as sister-group to the Mazocraeidea and suggests the demise of the suborder Hexostomatinea Boeger & Kritsky, 1993. We insist on the usefulness of depositing parts of specimens used for molecular analyses, prepared on permanent slides, in a curated collection.
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http://dx.doi.org/10.1051/parasite/2022030DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9126124PMC
May 2022

What Was Old Is New Again: The Pennate Diatom (Gaillon) Simonsen in the Multi-Omic Age.

Mar Drugs 2022 Mar 29;20(4). Epub 2022 Mar 29.

Laboratoire Biologie des Organismes, Stress, Santé, Environnement (BiOSSE), Le Mans Université, Avenue Olivier Messiaen, 72085 Le Mans, France.

The marine pennate diatom has long been known for its characteristic blue pigment marennine, which is responsible for the greening of invertebrate gills, a natural phenomenon of great importance for the oyster industry. For two centuries, this taxon was considered unique; however, the recent description of a new blue species revealed unsuspected biodiversity. Marennine-like pigments are natural blue dyes that display various biological activities-e.g., antibacterial, antioxidant and antiproliferative-with a great potential for applications in the food, feed, cosmetic and health industries. Regarding fundamental prospects, researchers use model organisms as standards to study cellular and physiological processes in other organisms, and there is a growing and crucial need for more, new and unconventional model organisms to better correspond to the diversity of the tree of life. The present work, thus, advocates for establishing as a new model organism by presenting its pros and cons-i.e., the interesting aspects of this peculiar diatom (representative of benthic-epiphytic phytoplankton, with original behavior and chemodiversity, controlled sexual reproduction, fundamental and applied-oriented importance, reference genome, and transcriptome will soon be available); it will also present the difficulties encountered before this becomes a reality as it is for other diatom models (the genetics of the species in its infancy, the transformation feasibility to be explored, the routine methods needed to cryopreserve strains of interest).
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http://dx.doi.org/10.3390/md20040234DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9033121PMC
March 2022

Hammerhead flatworms (Platyhelminthes, Geoplanidae, Bipaliinae): mitochondrial genomes and description of two new species from France, Italy, and Mayotte.

PeerJ 2022 1;10:e12725. Epub 2022 Feb 1.

James Cook University, Townsville, Queensland, Australia.

Background: New records of alien land planarians are regularly reported worldwide, and some correspond to undescribed species of unknown geographic origin. The description of new species of land planarians (Geoplanidae) should classically be based on both external morphology and histology of anatomical structures, especially the copulatory organs, ideally with the addition of molecular data.

Methods: Here, we describe the morphology and reproductive anatomy of a species previously reported as "black", and the morphology of a species previously reported as "blue". Based on next generation sequencing, we obtained the complete mitogenome of five species of Bipaliinae, including these two species.

Results: The new species n. sp. (syn: "black" of Justine et al., 2018) is formally described on the basis of morphology, histology and mitogenome, and is assigned to on the basis of its reproductive anatomy. The type-locality is Casier, Italy, and other localities are in the Department of Pyrénées-Atlantiques, France; some published or unpublished records suggest that this species might also be present in Russia, China, and Japan. The mitogenomic polymorphism of two geographically distinct specimens (Italy France) is described; the gene displayed 2.25% difference. The new species n. sp. (syn: "blue" of Justine et al., 2018) is formally described on the basis of external morphology and complete mitogenome and is assigned to on the basis of an absence of information on its reproductive anatomy. The type- and only known locality is the island of Mayotte in the Mozambique Channel off Africa. Phylogenies of bipaliine geoplanids were constructed on the basis of SSU, LSU, mitochondrial proteins and concatenated sequences of , SSU and LSU. In all four phylogenies, was the sister-group to all the other bipaliines. With the exception of which could not be circularised, the complete mitogenomes of , , , and were colinear. The 16S gene in all bipaliine species was problematic because usual tools were unable to locate its exact position.

Conclusion: Next generation sequencing, which can provide complete mitochondrial genomes as well as traditionally used genes such as SSU, LSU and , is a powerful tool for delineating and describing species of Bipaliinae when the reproductive structure cannot be studied, which is sometimes the case of asexually reproducing invasive species. The unexpected position of the new species as sister-group to all other Bipaliinae in all phylogenetic analyses suggests that the species could belong to a new genus, yet to be described.
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http://dx.doi.org/10.7717/peerj.12725DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8815365PMC
February 2022

Marine and brackish D.G.Mann (Bacillariophyta) species from the Java Sea and South China Sea coasts with the description of three new species.

PhytoKeys 2021 22;183:115-142. Epub 2021 Oct 22.

Université de Nantes, EA 2160 Mer - Molécules - Santé 2, Rue de la Houssinière, 44322 Nantes, France.

In this study, samples were collected from the Java Sea coasts, from the South China Sea in Hainan Island coasts and Quảng Yên region and Rú Chá mangrove near Hue in Central Vietnam. In studied samples a total of eight species have been observed. Three of the taxa studied are described herein as species new to science - , and Under light microscopy (LM) and are similar with rhombic-lanceolate to rhombic/ elliptic-lanceolate to elliptic valve shapes and narrowly rounded apices. Both species can be easily distinguished by stria density (higher density in ). Under SEM is characterized by cribrate areola occlusions, a character thus far observed only in three established species. The remaining species of the whole genus known thus far are characterized by hymenate areola. Similar morphology species have been observed from tropical mangrove forests from Madagascar but they all can be easily distinguished based on the lack of grooves in the central area. The third species - has rhombic-elliptic to rhombic-lanceolate valves with broadly rounded to slightly protracted apices in larger specimens. This species has a relatively broad central area. Also unique among brackish-water is the small, rounded stigma positioned almost midway between the valve center and valve margin. In the habitats from which the new species are described we also identified five established taxa including, , , , and . For those species we provide detailed SEM characteristics of valve ultrastructure, as well as the range of environmental conditions and geographic distribution within the study area.
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http://dx.doi.org/10.3897/phytokeys.183.71049DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8556211PMC
October 2021

sp. nov., a cryptic diatom species from the highly alkaline Van Lake (Turkey).

PeerJ 2021 22;9:e12220. Epub 2021 Oct 22.

Institute of Marine and Environmental Sciences, University of Szczecin, Szczecin, Poland.

In this article we describe 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 of its organellar genomes and several molecular phylogenies. This species could easily be overlooked because of its extreme similarity to but molecular phylogenies indicate that they are only distantly related. Furthermore, molecular data suggest that may occur in several alkaline lakes of Asia Minor and Siberia, but was previously misidentified as . It also revealed the very close genetic proximity between and the endosymbiont of the dinotom , providing additional clues on what might have been the original species of diatoms to enter symbiosis.
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http://dx.doi.org/10.7717/peerj.12220DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8544256PMC
October 2021

Mitochondrial and Plastid Genomes of the Monoraphid Diatom .

Int J Mol Sci 2021 Oct 15;22(20). Epub 2021 Oct 15.

Institute of Marine and Environmental Sciences, University of Szczecin, Mickiewicza 16a, 70-383 Szczecin, Poland.

We provide for the first time the complete plastid and mitochondrial genomes of a monoraphid diatom: The mitogenome is 41,957 bp in size and displays two group II introns in the gene. The 187,029 bp plastid genome features the typical quadripartite architecture of diatom genomes. It contains a group II intron in the gene that overlaps the large single-copy and the inverted repeat region. There is also a group IB4 intron encoding a putative LAGLIDADG homing endonuclease in the gene. The multigene phylogenies conducted provide more evidence of the proximity between and fistula-bearing species of biraphid diatoms.
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http://dx.doi.org/10.3390/ijms222011139DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8541233PMC
October 2021

Complete chloroplast genome of the mixotrophic chrysophyte (Ochromonadales, Synurophyceae) from Van Lake in Eastern Anatolia.

Mitochondrial DNA B Resour 2021 27;6(9):2719-2721. Epub 2021 Aug 27.

Institute of Marine and Environmental Sciences, University of Szczecin, Szczecin, Poland.

We sequenced the chloroplast genome of (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 to its chrysophyte counterparts, the . inverted repeat differs noticeably in gene content and the whole genome is missing 11 protein-coding genes. The maximum likelihood phylogeny inferred from concatenated protein-coding genes positioned among the chrysophytes as sister to the clade containing the Synurales (Synurophyceae) and Chromulinales (Chrysophyceae).
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http://dx.doi.org/10.1080/23802359.2021.1923416DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8405094PMC
August 2021

The complete chloroplast genome of Secale sylvestre (Poaceae: Triticeae).

J Appl Genet 2022 Feb 15;63(1):115-117. Epub 2021 Aug 15.

Institute of Biology, University of Szczecin, PL-71-415, Szczecin, Poland.

Secale sylvestre is a wild species of rye, morphologically distinct from domestic species. To draw comparisons between species based on molecular features, it is important to have high-quality sequences, especially in the case of organellar genomes. For such reason, the complete chloroplast genome of Secale sylvestre Host introd. no. 6047 will provide useful data for ecological, agricultural, and phylogenetic purposes. Here we present the complete, annotated chloroplast genome sequence of Secale sylvestre Host introd. no. 6047. The genome is 137116 base pair (bp) long. It is the first complete chloroplast genome that can be used as a reference genome for further analysis. The genome can be accessed on GenBank with the accession number (MW557517).
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http://dx.doi.org/10.1007/s13353-021-00656-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8755654PMC
February 2022

Extreme Enlargement of the Inverted Repeat Region in the Plastid Genomes of Diatoms from the Genus .

Int J Mol Sci 2021 Jul 2;22(13). Epub 2021 Jul 2.

Institute of Marine and Environmental Sciences, University of Szczecin, Mickiewicza 16a, 70-383 Szczecin, Poland.

We sequenced the plastid genomes of three diatoms from the genus , including two strains formerly designated as . 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 region. Important rearrangements of gene order were identified among the two populations of cf. . The other sequenced chloroplast genome is 1.5 times smaller compared with those of the cf. strains and it features an usual quadripartite structure. The extensive structural changes reported here for the genus are compared with those previously observed for other algae and plants displaying large plastid genomes.
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http://dx.doi.org/10.3390/ijms22137155DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8268801PMC
July 2021

, A Novel Cosmopolitan Species of Blue Diatoms.

Biology (Basel) 2021 Apr 14;10(4). Epub 2021 Apr 14.

Institute of Graduate Studies in Science, Department of Biotechnology, Mersin University, Ciftlikkoy, Mersin 33343, Turkey.

Specimens of a new species of blue diatoms from the genus 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 combined morphological and genomic approach led to the conclusion that they belong to a single new to science cosmopolitan species, sp. nov. A preliminary characterization of its blue pigment shows similarities to marennine produced by , as evidenced by UV-visible spectrophotometry and Raman spectrometry. Life cycle stages including auxosporulation were also observed, providing data on the cardinal points of this species. For the two most geographically distant populations (North Carolina and East Mediterranean), complete mitochondrial and plastid genomes were sequenced. The mitogenomes of both strains share a rare pseudogene, but the number, nature, and positions of the group II introns inside its gene differ between the two populations. There are also two pairs of genes fused in single ORFs. The plastid genomes are characterized by large regions of recombination with plasmid DNA, which are in both cases located between the and genes, but whose content differs between the strains. The two sequenced strains hosts three plasmids coding for putative serine recombinase protein whose sequences are compared, and four out of six of these plasmids were highly conserved.
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http://dx.doi.org/10.3390/biology10040328DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8070900PMC
April 2021

A gene-rich and compact chloroplast genome of the green alga (N.Carter) Ettl 1982 from the shores of Mersin (Eastern Mediterranean Sea).

Mitochondrial DNA B Resour 2021 Feb 5;6(2):308-310. Epub 2021 Feb 5.

Faculty of Education, Department of Mathematics and Science Education, Mersin University, Ciftlikkoy, Mersin, Turkey.

We report the complete chloroplast genome of the MED1 strain of from the Eastern Mediterranean Sea. At 111,026 bp, this genome is smaller and more compact than those of and , and in contrast to the latter taxa, its inverted repeat contains no complete protein-coding genes. It encodes 3 rRNAs, 33 tRNAs and 94 proteins. Maximum likelihood analysis of a concatenated set of chloroplast genes from green algae belonging to deep-diverging lineages positioned the three species in a strongly supported clade in which is sister to .
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http://dx.doi.org/10.1080/23802359.2020.1866461DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7872528PMC
February 2021

Complete mitogenome of the invasive land flatworm , the second Geoplanidae (Platyhelminthes) to display an unusually long gene.

Mitochondrial DNA B Resour 2020 18;5(3):2115-2116. Epub 2020 May 18.

Institut Systématique Évolution Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France.

We sequenced the complete mitogenome of the invasive flatworm (Platyhelminthes, order Tricladida, family Geoplanidae). The genome is 17,210 bp long, and displays common unusual characteristics shared with , such as its colinearity, an overlap between and genes and an unusually long genes. Both and are members of the subfamily Rhynchodeminae and their close relationships are supported by the maximum likelihood phylogeny inferred from the protein-coding genes.
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http://dx.doi.org/10.1080/23802359.2020.1765709DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7510624PMC
May 2020

The land flatworm (Geoplanidae) in Guadeloupe and Martinique: new reports and molecular characterization including complete mitogenome.

PeerJ 2020 9;8:e10098. Epub 2020 Nov 9.

Life Sciences Department, Natural History Museum, London, UK.

Background: The land flatworm Jones & Sterrer, 2005 (Geoplanidae) was described from two specimens collected in Bermuda in 1963 and 1988 and not recorded since.

Methods: On the basis of a citizen science project, we received observations in the field, photographs and specimens from non-professionals and local scientists in Martinique and Guadeloupe. We barcoded (COI) specimens from both islands and studied the histology of the reproductive organs of one specimen. Based on Next Generation Sequencing, we obtained the complete mitogenome of and some information on its prey from contaminating DNA.

Results: We add records from 2006 to 2019 in two French islands of the Caribbean arc, Guadeloupe (six records) and Martinique (14 records), based on photographs obtained from citizen science and specimens examined. A specimen from Martinique was studied for histology of the copulatory organs and barcoded for the COI gene; its anatomy was similar to the holotype, therefore confirming species identification. The COI gene was identical for several specimens from Martinique and Guadeloupe and differed from the closest species by more than 10%; molecular characterisation of the species is thus possible by standard molecular barcoding techniques. The mitogenome is 14,962 bp in length and contains 12 protein coding genes, two rRNA genes and 22 tRNA genes; for two protein genes it was not possible to determine the start codon. The mitogenome was compared with the few available mitogenomes from geoplanids and the most similar was , a species from South America. An analysis of contaminating DNA in the digestive system suggests that preys on terrestrial molluscs, and citizen science observations in the field suggest that prey include molluscs and earthworms; the species thus could be a threat to biodiversity of soil animals in the Caribbean.
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http://dx.doi.org/10.7717/peerj.10098DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7659627PMC
November 2020

The Taxonomy and Diversity of Proschkinia (Bacillariophyta), A Common But Enigmatic Genus from Marine Coasts.

J Phycol 2020 08 23;56(4):953-978. Epub 2020 Apr 23.

Department of Integrative Biology, Biological Laboratories, University of Texas at Austin, Austin, Texas, USA.

Detailed morphological documentation is provided for established Proschkinia taxa, including the generitype, P. bulnheimii, and P. complanata, P. complanatula, P. complanatoides and P. hyalosirella, and six new species. All established taxa are characterized from original material from historical collections. The new species described in this paper (P. luticola, P. staurospeciosa, P. impar, P. modesta, P. fistulispectabilis, and P. rosowskii) were isolated from the Western Pacific (Yellow Sea coast of Korea) and the Atlantic (Scottish and Texas coasts). Thorough documentation of the frustule, valve and protoplast architecture revealed the combination of characters diagnostic of the genus Proschkinia: a single-lobed chloroplast; a broad girdle composed of U-shaped, perforated bands; the position of the conopeate raphe-sternum relative to the external and internal valve surface; and the presence of an occluded process through the valve, termed the "fistula". Seven strains of Proschkinia were grown in culture and five of these were sequenced for nuclear ribosomal SSU and plastid-encoded rbcL. Phylogenetic analysis recovered a clade of Proschkinia with Fistulifera, another fistula-bearing diatom genus, and together these were sister to a clade formed of the Stauroneidaceae; in turn, all of these were sister to a clade composed of Parlibellus and two monoraphid genera Astartiella and Schizostauron. Despite morphological similarities between Proschkinia and the Naviculaceae, these two taxa are distant in our analysis. We document the variation in the morphology of Proschkinia, including significant variability in the fistula, suggesting that fistula ultrastructure might be one of the key features for species identification within the genus.
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http://dx.doi.org/10.1111/jpy.12998DOI Listing
August 2020

Complete chloroplast genome of the tiny marine diatom (Bacillariophyta) from the Adriatic Sea.

Mitochondrial DNA B Resour 2019 Oct 4;4(2):3374-3376. Epub 2019 Oct 4.

Département de biochimie, de microbiologie et de bio-informatique, Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, Canada.

We report the chloroplast genome sequence of , a tiny araphid pennate diatom collected from the Adriatic Sea. The 160,994-bp . genome displays a quadripartite structure and its gene repertoire resembles those of other diatom chloroplast genomes. Besides the genes located in the inverted repeat, is duplicated. A gene-poor region in the large single-copy region contains multiple ORFs sharing sequence similarities with plasmids and chloroplast ORFs found in other diatom species. The genome features a single intron, a group II intron in . Phylogenomic analysis identified at a basal position within the araphid 2 clade.
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http://dx.doi.org/10.1080/23802359.2019.1673245DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7707228PMC
October 2019

Complete mitogenome of the invasive bivalve .

Mitochondrial DNA B Resour 2019 Sep 6;4(2):2794-2795. Epub 2019 Sep 6.

Département de biochimie, de microbiologie et de bio-informatique, Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, Canada.

We sequenced the complete mitogenome of a Baltic Sea specimen of the invasive bivalve . 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 mitogenome is rearranged in gene order relative to previously sequenced mitogenomes of Mactroidea.
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http://dx.doi.org/10.1080/23802359.2019.1659121DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7706547PMC
September 2019

Complete mitochondrial genome of a rare diatom (Bacillariophyta) and its phylogenetic and taxonomic implications.

Mitochondrial DNA B Resour 2019 25;4(1):25-26. Epub 2018 Nov 25.

Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA.

We obtained the complete mitogenome of 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 and three group II introns in 1. Using mitogenomic data, sp. was recovered with , far distant from and , two genera with which has sometimes been associated based on morphology.
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http://dx.doi.org/10.1080/23802359.2018.1535852DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7510632PMC
November 2018

Complete mitogenome of , the red chut-chut snail from the Cần Giờ Mangrove in Vietnam.

Mitochondrial DNA B Resour 2018 Oct 26;3(2):1267-1269. Epub 2018 Oct 26.

Faculty of Geosciences, Natural Sciences Research and Educational Center and Palaeoceanology Unit, University of Szczecin, Szczecin, Poland.

We sequenced the complete mitogenome of the red chut-chut snail , 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 1, 2 and 3 genes of several Caenogastropoda associated all Cerithioidea together inside a strongly supported clade.
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http://dx.doi.org/10.1080/23802359.2018.1532832DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7799742PMC
October 2018

Mitogenome sequence of a Black Sea isolate of the kinetoplastid .

Mitochondrial DNA B Resour 2018 Sep 10;3(2):968-969. Epub 2018 Sep 10.

Natural Sciences Research and Educational Center and Palaeoceanology Unit, Faculty of Geosciences, University of Szczecin, Szczecin, Poland.

We obtained the mitogenome sequence of a Black Sea isolate of the kinetoplastid . This sequence consists of two contigs totaling 24,925 bp and encodes ten protein-coding genes, one conserved ORF and one rRNA gene. Alignment of the Black Sea mitogenome with the limited sequence data currently available in public databases for another strain of revealed significant genetic divergence between the two isolates. Maximum likelihood phylogenetic inference clearly resolved the Bodonidae from the Trypanosomatidae.
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http://dx.doi.org/10.1080/23802359.2018.1507654DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7799735PMC
September 2018

The complete mitochondrial DNA of the tropical oyster from the Cần Giò' mangrove in Vietnam.

Mitochondrial DNA B Resour 2018 Apr 12;3(1):462-463. Epub 2018 Apr 12.

Mer-Molécules-Santé (MMS), FR CNRS 3473 IUML, Le Mans Université, Le Mans, France.

The complete mitochondrial genome of the oyster 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 and sp. DB1, it contains a non-coding region and two ORFs. The mitogenome provides information that could improve the molecular phylogeny of Asian oysters and be useful to the development of oyster aquaculture in South East Asia.
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http://dx.doi.org/10.1080/23802359.2018.1462126DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7800500PMC
April 2018

Ardissonea crystallina has a type of sexual reproduction that is unusual for centric diatoms.

Sci Rep 2017 11 7;7(1):14670. Epub 2017 Nov 7.

Natural Sciences Research and Educational Center and Palaeoceanology Unit, Faculty of Geosciences, University of Szczecin, Mickiewicza 16a, Szczecin, 70-383, Poland.

Molecular phylogenetic analyses place Ardissonea crystallina (C. Agardh) Grunow and all Toxariids among the bi- and multipolar centric diatoms, almost always recovered as a derived lineage sister to Lampriscus. In all centrics where sexual reproduction has been documented, oogamy, with larger immobile eggs and smaller flagellated sperm has been observed. We were able to initiate both homothallic and heterothallic reproduction in A. crystallina. The heterothallic reproduction turned out to be non-oogamous; gametes were more or less equal in size but no flagellated cells were detected. At the same time, two mating types ("male" and "female") were recognized by the distinct morphology and behaviour of the gametes. While no flagella were observed, periodically thin cytoplasmic projections arose on the surface of the "male" gametes. These projections similar to those found in some pennate diatoms facilitated contact with the "female" cells. In each gametangial cell, regardless of the mating type, only one gamete was formed. Thus, the Toxariids may represent a unique evolutionary group, at least in respect to their reproductive biology. The hypothesis discussed is that non-oogamous mode of reproduction could have evolved in Ardissonea (and possibly in other Toxariids) independently of the pennate lineage of diatoms.
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http://dx.doi.org/10.1038/s41598-017-15301-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5676960PMC
November 2017

Antimicrobial Compounds from Eukaryotic Microalgae against Human Pathogens and Diseases in Aquaculture.

Mar Drugs 2016 Sep 2;14(9). Epub 2016 Sep 2.

FR CNRS 3473 IUML Mer-Molécules-Santé (MMS), Université du Maine, Avenue O. Messiaen, Le Mans 72085, France.

The search for novel compounds of marine origin has increased in the last decades for their application in various areas such as pharmaceutical, human or animal nutrition, cosmetics or bioenergy. In this context of blue technology development, microalgae are of particular interest due to their immense biodiversity and their relatively simple growth needs. In this review, we discuss about the promising use of microalgae and microalgal compounds as sources of natural antibiotics against human pathogens but also about their potential to limit microbial infections in aquaculture. An alternative to conventional antibiotics is needed as the microbial resistance to these drugs is increasing in humans and animals. Furthermore, using natural antibiotics for livestock could meet the consumer demand to avoid chemicals in food, would support a sustainable aquaculture and present the advantage of being environmentally friendly. Using natural and renewable microalgal compounds is still in its early days, but considering the important research development and rapid improvement in culture, extraction and purification processes, the valorization of microalgae will surely extend in the future.
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5039530PMC
http://dx.doi.org/10.3390/md14090159DOI Listing
September 2016

Marennine, promising blue pigments from a widespread Haslea diatom species complex.

Mar Drugs 2014 May 28;12(6):3161-89. Epub 2014 May 28.

FR CNRS 3473 IUML, Mer-Molécules-Santé (MMS), Université du Maine, Ave O. Messiaen, 72085 Le Mans cedex 9, France.

In diatoms, the main photosynthetic pigments are chlorophylls a and c, fucoxanthin, diadinoxanthin and diatoxanthin. The marine pennate diatom Haslea ostrearia has long been known for producing, in addition to these generic pigments, a water-soluble blue pigment, marennine. This pigment, responsible for the greening of oysters in western France, presents different biological activities: allelopathic, antioxidant, antibacterial, antiviral, and growth-inhibiting. A method to extract and purify marennine has been developed, but its chemical structure could hitherto not be resolved. For decades, H. ostrearia was the only organism known to produce marennine, and can be found worldwide. Our knowledge about H. ostrearia-like diatom biodiversity has recently been extended with the discovery of several new species of blue diatoms, the recently described H. karadagensis, H. silbo sp. inedit. and H. provincialis sp. inedit. These blue diatoms produce different marennine-like pigments, which belong to the same chemical family and present similar biological activities. Aside from being a potential source of natural blue pigments, H. ostrearia-like diatoms thus present a commercial potential for aquaculture, cosmetics, food and health industries.
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http://dx.doi.org/10.3390/md12063161DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4071570PMC
May 2014

Inheritance of mitochondrial DNA in the Pennate diatom Haslea ostrearia (Naviculaceae) during auxosporulation suggests a uniparental transmission.

Protist 2013 May 7;164(3):340-51. Epub 2013 Mar 7.

MMS EA 2160, Faculté des Sciences et des Techniques, Université du Maine, Avenue Olivier Messiaen, 72085 Le Mans Cedex 9, France.

We present the first study examining mtDNA transmission in diatoms, using sexual progeny of the pennate species Haslea ostrearia (Naviculaceae). A fragment of the cytochrome oxidase subunit I gene (cox1) with 7 nucleic substitutions between parental clones was used as a parental tracer in 16 F1 clones obtained from two pairs of mating crosses. Each cross involved a parental clone isolated from France (Bay of Bourgneuf) and Sweden (Kattegat Bay). We determined that all progeny possessed only one cox1 parental haplotype. These results suggest that the mitochondrial DNA transmission in H. ostrearia is uniparental. Implications and new topics of investigation are discussed.
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http://dx.doi.org/10.1016/j.protis.2013.01.001DOI Listing
May 2013

A (2)H solid-state NMR study of the effect of antimicrobial agents on intact Escherichia coli without mutating.

Biochim Biophys Acta 2013 Feb 16;1828(2):614-22. Epub 2012 Sep 16.

Department of Chemistry, Université du Québec à Montréal, P.O. Box 8888, Downtown Station, Montréal, Québec, Canada H3C 3P8.

Solid-state nuclear magnetic resonance (NMR) is a useful tool to probe the organization and dynamics of phospholipids in bilayers. The interactions of molecules with membranes are usually studied with model systems; however, the complex composition of biological membranes motivates such investigations on intact cells. We have thus developed a protocol to deuterate membrane phospholipids in Escherichia coli without mutating to facilitate (2)H solid-state NMR studies on intact bacteria. By exploiting the natural lipid biosynthesis pathway and using perdeuterated palmitic acid, our results show that 76% deuteration of the phospholipid fatty acid chains was attained. To verify the responsiveness of these membrane-deuterated E. coli, the effect of known antimicrobial agents was studied. (2)H solid-state NMR spectra combined to spectral moment analysis support the insertion of the antibiotic polymyxin B lipid tail in the bacterial membrane. The use of membrane-deuterated bacteria was shown to be important in cases where antibiotic action of molecules relies on the interaction with lipopolysaccharides. This is the case of fullerenol nanoparticles which showed a different effect on intact cells when compared to dipalmitoylphosphatidylcholine/dipalmitoylphosphatidylglycerol membranes. Our results also suggest that membrane rigidification could play a role in the biocide activity of the detergent cetyltrimethyammonium chloride. Finally, the deuterated E. coli were used to verify the potential antibacterial effect of a marennine-like pigment produced by marine microalgae. We were able to detect a different perturbation of the bacteria membranes by intra- and extracellular forms of the pigment, thus providing valuable information on their action mechanism and suggesting structural differences.
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http://dx.doi.org/10.1016/j.bbamem.2012.09.011DOI Listing
February 2013

Biological activities of purified marennine, the blue pigment responsible for the greening of oysters.

J Agric Food Chem 2012 Apr 29;60(14):3599-605. Epub 2012 Mar 29.

MMS Le Mans, Université du Maine, Le Mans, France.

Marennine, the blue pigment produced by the diatom Haslea ostrearia , exists in two different forms, the intra- and extracellular forms. We investigated the antibacterial, antiviral, and antiproliferative properties of both of these forms. Both forms of marennine inhibited the development of marine bacteria, in particular the pathogenic organism Vibrio aesturianus , at concentrations as low as 1 μg/mL, but they did not display any effect on a wide range of pathogenic bacteria that are relevant for food safety. Both forms of the pigment produced by H. ostrearia also exhibited antiviral activity against the HSV1 herpes virus, with intra- and extracellular marennine having EC(50) values of 24.0 and 27.0 μg/mL, respectively. These values are 2 orders of magnitude higher than the value for the reference drug, Zovirax. Moreover, both forms of marennine were effective in slowing or inhibiting the proliferation of cancer cells. This study confirms the potential of marennine as a biologically active organic molecule, which could have a protective effect on bivalves, which filter seawater and fix the pigment on their gills. Moreover, marennine could be used in food engineering and chemistry as a natural blue pigment. However, despite that it is eaten and possibly assimilated by green oyster consumers, it also deserves in depth evaluation before being considered for use as a nutraceutical.
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http://dx.doi.org/10.1021/jf205004xDOI Listing
April 2012

Light is a key factor in triggering sexual reproduction in the pennate diatom Haslea ostrearia.

FEMS Microbiol Ecol 2009 Aug 6;69(2):194-201. Epub 2009 May 6.

Laboratoire de Physiologie, Université du Maine, Le Mans, France.

Sexual reproduction is an obligatory phase in the life cycle of most diatoms, as cell size decreases with successive vegetative divisions and the maximal cell size is only restored by a specialized cell, the auxospore, which follows zygote formation as a result of sexual reproduction. While in pennate diatoms the induction of sexual reproduction depends primarily on cell-cell interactions, the importance of different external factors for the induction of sexual reproduction is less well known. Here, we investigated the effects of light on sexualization in the marine benthic pennate diatom Haslea ostrearia (Gaillon) R. Simonsen. Compatible clones were crossed and exposed to different combinations of light levels, qualities, and photoperiods. Light was found to be a key factor for sexualization, and to a certain extent, to control auxosporulation in H. ostrearia. The light conditions most favorable for sexual reproduction were low irradiances (<50 micromolphotons m(-2) s(-1)) and short photoperiods (6-10 h), conditions that prevail during winter, and to a lesser extent, the higher irradiances and longer photoperiods that correspond to the spring and fall, when blooms of this organism form in the natural environment. Auxospore formation was very rare in continuous light, and maximum in presence of red radiation, while it was never observed in darkness or in radiation other than red.
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http://dx.doi.org/10.1111/j.1574-6941.2009.00700.xDOI Listing
August 2009
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