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Mitochondrial genome and phylogenetic datasets and trees linked with the abyssal coral Abyssoprimnoa gemina.

Background and aims – Kützing separated the genus Achnanthidium from the genus Achnanthes based on two species: Achnanthes minutissima and Achnanthidium microcephalum. These two genera were distinguished by the presence of stalks in the Achnanthes genus and their absence in Achnanthidium. Before electron microscopy, the difference between Achnanthes and Achnanthidium was not clear, especially in Achnanthidium minustissimum sensu lato. The aim of the study is to describe three new species of Achnanthidium from Lake Salda. Material and methods – Lake Salda is located in southwestern Anatolia, in Turkey. The diatoms were collected seasonally from four stations in the lake between 2016 and 2020, from different substrata (epipelic, epiphytic, and epilithic). Key results – Three new species belonging to the genus Achnanthidium have been found in Lake Salda, Turkey. Based on the morphological observations, all new taxa are part of the Achnanthidium minutissimum complex. Achnanthidium barlasii sp. nov. and A. dumlupinarii sp. nov. show a high degree of similarity to each other, but can be separated based on valve outline and a denser areolation, especially in striae close to the apices of the raphe valve. Both species can be distinguished from A. minutissimum based on more separate apices and less elliptic valves. In the case of A. dumlupinarii sp. nov., large specimens show slight undulations of the valve, which is a unique feature. Achnanthidium anatolicum sp. nov. is the most characteristic based on its valve width, broadly rounded valve apices, and almost straight valves in girdle view. All newly described Achnanthidium species can be found in lentic environments, with alkaline water and high calcium ion content. Conclusion – The newly described taxa occurred in the unique habitat of a soda lake. The environment of the lake is highly alkaline, rich in magnesium and calcium, and derived from limestone and dolomitic limestone rocks.

We present here the first observation of Bipalium admarginatum de Beauchamp, 1933 since its original description 90 years ago. Three specimens were found on Perhentian Kecil Island, off Terengganu State, Malaysia and photographed in the field, and two were collected. This report thus includes the first colour photographs published for this species, from a locality close to the type-locality, Tioman Island (which is ca. 200 km south of the locality in this study, on the east coast of Peninsula Malaysia). We describe the external morphology and colour pattern of the species, which correspond well to the original description, itself based only on two preserved specimens. We performed an in-depth molecular characterisation of the species, including its complete mitochondrial genome, the 18S sequence and elongation 1-alpha (EF1-α) sequence. In addition, EF1-α sequences were also retrieved for 5 additional geoplanid species. No tRNA-Thr could be detected in the mitogenome of B. admarginatum, a lack already reported in several species of geoplanids, but we found a 13 bp sequence that contains the anticodon loop and seems to be conserved among geoplanids and might thus possibly represent a non-canonical undetected tRNA. We discuss the difficulties encountered in trying to reconstruct the cluster of nuclear ribosomal genes, a problem already mentioned for other Triclads. Three phylogenies, based respectively on all mitochondrial proteins, 18S, and EF1-α, were computed; the position of B. admarginatum within the Bipaliinae was confirmed in each tree, as sister-group to various bipaliine species according to the sequences available for each tree. In the mitochondrial proteins tree, which had high support, B. admarginatum was sister to Bipalium kewense and Diversibipalium multilineatum.

We determined the complete mitogenome sequence of the bioluminescent fish Malacosteus niger using long-read sequencing technologies. The 21,263 bp mitogenome features a complex structure with two copies of a 1198-bp inverted-repeat and a region of 2616-bp containing alternating copies of 16 and 26 bp repeat elements. Whole mitogenome phylogenies inferred from both nucleotide and amino-acid datasets place M. niger among Melanostomiinae. The need for additional complete mitogenome sequences from the subfamily Malacosteinae is discussed.

The complete chloroplast genome of Secale cereale ssp. segetale (Zhuk.) Roshev. (Poaceae: Triticeae) was sequenced and analyzed to better use its genetic resources to enrich rye and wheat breeding. The study was carried out using the following methods: DNA extraction, sequencing, assembly and annotation, comparison with other complete chloroplast genomes of the five Secale species, and multigene phylogeny. As a result of the study, it was determined that the chloroplast genome is 137,042 base pair (bp) long and contains 137 genes, including 113 unique genes and 24 genes which are duplicated in the IRs. Moreover, a total of 29 SSRs were detected in the Secale cereale ssp. segetale chloroplast genome. The phylogenetic analysis showed that Secale cereale ssp. segetale appeared to share the highest degree of similarity with S. cereale and S. strictum. Intraspecific diversity has been observed between the published chloroplast genome sequences of S. cereale ssp. segetale. The genome can be accessed on GenBank with the accession number (OL688773).

Mitochondrial genome of Bipalium admarginatum. EF1 gene complete CDS of several species of Bipaliinae. Putative clusters of rRNA of Bipalium admarginatum.

Raw fasta file, annotated genbank file and fastq file containing the mongest read obtained of the mitochondrial genome of Malacosteus niger.

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 has been long considered a cosmopolitan diatom, but recent studies provided evidence for cryptic diversity and the existence of several other blue species, some of them inhabiting places where diatoms described as H. ostrearia had previously been observed. Recently, a marine diatom with blue tips was isolated into clonal culture from a plankton net sample from Kei Mouth on the Indian Ocean coast of South Africa. It was identified as H. ostrearia through a combination of LM/SEM microscopy and molecular analysis. This constitutes the first established record of this species from South Africa and the Indian Ocean and the second record for the southern hemisphere. Molecular barcoding clearly discriminated the South African strain from an Australian strain and cox1 based molecular phylogeny associated it instead with strains from the French Atlantic Coast, raising questions about the dispersal of this species. The complete mitochondrial and plastid genomes were compared to those of Haslea nusantara and Haslea silbo. Multigene phylogenies performed with all protein-coding genes of the plastome and the mitogenome associated H. ostrearia with H. silbo. In addition, complete sequences of circular plasmids were obtained and one of them showed an important conservation with a plasmid found in H. silbo.

The large hemi-discoid diatom Palmerina ostenfeldii was common in subtropical Moreton Bay, Australia, following a flood in January 2011. All diatom cells exhibited diagnostic subapical folds settled by loricate peritrich ciliates, but which readily abandoned stressed diatom cells. We characterized both diatoms and ciliates by morphological and molecular analyses, including careful video observations on non-preserved cells immediately after collection. The fold in the diatom cell wall comprises a narrow shelf upon which the ciliates attach (on average seven per fold, and similar for the two folds of a single diatom cell) but without penetrating the diatom wall itself. Folds were fully developed in newly formed internal valves, indicating that the ciliates play no role in their morphogenesis. SSU rRNA sequences of P. ostenfeldii from Moreton Bay (with ciliates) differed by 25 bp (1.5%) from those of P. hardmaniana from Texas (without ciliates), but surprisingly rbcL chloroplast sequences for both diatom species were indistinguishable. The ciliate species epiphytic on P. ostenfeldii, previously referred to as the cold-water tintinnid Amphorella borealis could not be assigned to any known species. We formally describe it here as Vaginicola collariforma sp. nov. within the crown clade of peritrichs which also includes the closely related genus Cothurnia (but distinguished as having an external stalk). Beating of the peritrich oral cilia was observed to drive rotational movement of the large discoid diatoms as in a ferris wheel. The observed diatom-ciliate symbiosis may represent a unique evolutionary adaptation in which the ciliate is host-specific and attaches in a specific locality on the host cell.

The aim of the study was sequencing of the mitogenome of Hygrobates turcicus Pešić, Esen & Dabert, 2017 to expand knowledge of the polymorphism and cryptic or pseudocryptic diversity within Hydrachnidia. The samples originated from Bulgaria, Vidima River near Debnewo, 42°56′41.4′′N, 24°48′44.6′′E, depth 0.4 m, stones on the bottom, water flow 0.71 m/s, temperature 10 °C, pH 8.53, oxygen 110%, conductivity 279 µS/cm, hardness 121 CaO mg/l; 11 males, 27 females, 2 deutonymphs 12.x.2019 leg. Zawal, Michoński & Bańkowska; one male and one female dissected and slides mounted. The study was carried out using the following methods: DNA extraction, sequencing, assembly and annotation, comparison with other populations of H. turcicus, and multigene phylogeny. As a result of the study, it was determined that the mitogenome is 15,006 bp long and encodes for 13 proteins, 2 rRNAs, and 22 tRNAs. The genome is colinear with those of H. longiporus and H. taniguchii, the difference in size originating from a non-coding region located between protein-coding genes ND4L and ND3. Five genes have alternative start-codon, and four display premature termination. The multigene phylogeny obtained using all mitochondrial protein-coding genes unambiguously associates H. turcicus with the cluster formed by H. longiporus and H. taniguchii.

International audience; The land flatworm Obama nungara, a species originating from South America and already invasive in many European countries, is recorded from La Réunion, a French island in the Indian Ocean. This is the first record of O. nungara from this locality and also the first record of the species for Africa. Three specimens were collected in 2021 and 2022, in the communes of Saint Paul, Saint Joseph and Le Tampon, respectively; the three localities are widely separated, with two in the Western part and one in the Southeastern part of the island. This suggests that the species is already present in several locations in La Réunion, and it is likely that the species is already present since 2020. The specimen from Saint Paul had the same cox1 haplotype as specimens previously recorded from several countries of Europe; it is hypothesized that the species was imported from Europe, probably from France. We mapped climatic suitability of the species in La Réunion and found that O. nungara could potentially invade a large part of the island. One record was apparently associated with the transport of plates of travertine, a construction material which has numerous cavities thus suitable for the transport and survival of adult or cocoons of land flatworms.; Le Plathelminthe terrestre Obama nungara, une espèce originaire d'Amérique du Sud et déjà envahissante dans de nombreux pays européens, est signalé à La Réunion, une île française de l'Océan Indien. Ceci est le premier signalement d’O. nungara dans cette localité et aussi le premier signalement de l'espèce pour l'Afrique. Trois spécimens ont été collectés en 2021 et 2022, respectivement dans les communes de Saint Paul, Saint Joseph et Le Tampon ; les trois localités sont largement séparées, avec deux dans la partie occidentale et une dans la partie sud-est de l'île. Ceci suggère que l'espèce est déjà présente dans plusieurs localités de La Réunion, et il est probable que l'espèce soit déjà présente depuis 2020. Le spécimen de Saint Paul avait le même haplotype du cox1 que les spécimens précédemment récoltés dans plusieurs pays d'Europe ; nous faisons l’hypothèse que l'espèce a été importée d'Europe, probablement de France. Nous avons cartographié l'adéquation climatique de l'espèce à La Réunion et constaté qu’O. nungara pourrait potentiellement envahir une grande partie de l'île. Un signalement était apparemment associé au transport de plaques de travertin, un matériau de construction qui possède de nombreuses cavités, donc adapté au transport et à la survie des adultes ou des cocons de vers plats terrestres.

(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 bacilladnavir...

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 BoegerKritsky (1993) of Hexostomatidae as sister-group to the Mazocraeidea and suggests the demise of the suborder Hexostomatinea BoegerKritsky, 1993. We insist on the usefulness of depositing parts of specimens used for molecular analyses, prepared on permanent slides, in a curated collection.Redescription, génome mitochondrial complet et relations phylogénétiques d’Hexostoma thynni (Delaroche, 1811) Rafinesque, 1815 (Monogenea, Hexostomatidae).Des spécimens d’Hexostoma thynni (Delaroche, 1811) Rafinesque, 1815 ont été collectés sur leur hôte-type, le thon rouge Thunnus thynnus, capturé au large de l’Algérie, c’est-à-dire près de la localité-type, au large de Majorque, qui se trouve également en Méditerranée. L’espèce est brièvement redécrite et comparée aux descriptions précédentes, sous le même nom ou sous son synonyme Plagiopeltis duplicata Diesing, 1858, pour vérifier l’identité des spécimens. Les trois genres au sein des Hexostomatidae (Hexostoma Rafinesque, 1815, Neohexostoma Price, 1961 et Homostoma Unnithan, 1965) sont brièvement discutés, avec des commentaires sur la fragilité des caractères utilisés pour les distinguer. En utilisant le séquençage de nouvelle génération, le mitogénome complet et le groupe de gènes ribosomiques (SSU, LSU, ITS1, ITS2, 5.8S) ont été obtenus. Le mitogénome a une longueur de 14 649 pb et code pour 12 gènes codant pour des protéines, 2 gènes d’ARN ribosomal et 22 gènes d’ARN de transfert, et sa taille est similaire à celle des autres mitogénomes obtenus de monogènes Polyopisthocotylea. Une phylogénie basée sur les gènes codant pour les protéines concaténées du mitogénome de 9 espèces de monogènes Polyopisthocotylea a produit un arbre dans lequel l’Hexostomatidae H. thynni était associé à d’autres Mazocraeidea tels que les Chauhaneidae et les Diclidophoridae. Ceci réfute l’hypothèse de BoegerKritsky (1993) des Hexostomatidae comme groupe-frère des Mazocraeidea et suggère la disparition du sous-ordre Hexostomatinea BoegerKritsky, 1993. Nous insistons sur l’intérêt de déposer dans une collection entretenue des parties des spécimens utilisées pour les analyses moléculaires, préparées sur des lames microscopiques permanentes.

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.

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 to its chrysophyte counterparts, the P. malhamensis 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 P. malhamensis among the chrysophytes sensu lato as sister to the clade containing the Synurales (Synurophyceae) and Chromulinales (Chrysophyceae). © 2021 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.

The marine pennate diatom

Capsalids are monopisthocotylean monogenean parasites found on the skin and gills of fish. Capsalines (subfamily Capsalinae) are large-sized capsalids, parasitic on highly prized gamefish, and species of Tristoma parasitise only the gills of swordfish (Xiphias gladius). We obtained specimens of Tristoma integrum Diesing, 1850 from swordfish collected off Algeria in the Mediterranean Sea. Here, we describe the specimens, including the key systematics characters of dorsolateral body sclerites. One specimen was used for a next generation sequencing analysis but a part of it, including the sclerites, was mounted on a permanent slide, drawn, and deposited in a curated collection. We characterised the complete mitogenome, the ribosomal cluster (including 18S and 28S) and additional genes such as Elongation factor 1 alpha (EF1α) and Histone 3. We also retrieved molecular information from the host tissue present in the gut of the monogenean and provide the sequence of the complete rRNA cluster of the host, X. gladius. The mitogenome of T. integrum is 13 968 bp in length and codes for 12 protein, 2 rRNA and 22 tRNA. Phylogenies of capsalids were generated from 28S sequences and concatenated mitochondrial protein-coding genes, respectively. In the 28S phylogeny, most subfamilies based on morphology were not found to be monophyletic, but the Capsalinae were monophyletic. In both phylogenies, the closest member to Tristoma spp. was a member of the Capsaloides. In an Appendix, we report the complex nomenclatural history of Tristoma Cuvier, 1817 and its species.

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 Neph...

The paper reports a process of sexual reproduction in the Black Sea diatom Climaconeis scalaris (Brebisson) E.J. Cox, 1982, initiated in laboratory conditions. A crossing system of this species allows both homo- and heterothallic reproduction. The fertilization is allogamous. Diploid mother gametangial cells secreted mucilage, forming a mucilage track, while actively gliding relative to each other. Each gametangium in a pair produced two elongated, cylindrical round-ended haploid gametes, which were largely morphologically and behaviorally isogamous. The division of the protoplast of the gametangial cell occurred in the transapical plane without the rearrangement of gametes. Growing auxospores were located parallel to the parent frustules. The research produced data on changes in the cell size, number of chloroplasts, and the position of cardinal points in the life cycle of the examined species.

Background and aims – The diatom genus Simonsenia has been considered for some time a minor taxon, limited in its distribution to fresh and slightly brackish waters. Recently, knowledge of its diversity and geographic distribution has been enhanced with new species described from brackish-marine waters of the southern Iberian Peninsula and from inland freshwaters of South China, and here we report novel Simonsenia from fully marine waters. Methods – New isolates of Simonsenia species were obtained from marine waters, the littoral zone of the Korean Yellow Sea coast and the Gulf of Mexico in Corpus Christi (Texas), and documented in LM, SEM and with DNA sequence data (plastid-encoded rbcL and psbC). Phylogenetic trees of raphid diatoms were constructed to assess the relationships of the new species and of the genus as a whole. Key results and conclusions – Two novel species of Simonsenia (S. eileencoxiae and S. paucistriata) are described and a further putative taxon is characterized morphologically. The molecular phylogeny of the new Simonsenia species and previously sequenced species supports both the monophyly of the genus and its place within the Bacillariaceae. The Simonsenia clade clusters with clades composed of Cylindrotheca, Denticula and some Nitzschia spp. (including N. amphibia, N. frustulum, N. inconspicua). Hence Simonsenia is firmly positioned within the Bacillariaceae by molecular phylogenies, confirming its position within this group based on the possession of a canal raphe and its ultrastructure, and rejecting its classification within the Surirellaceae. Morphological data from the new Simonsenia species is typical for the genus, with a “simonsenioid” canal raphe type supported over the valve face with fenestral braces, alar canals connecting the canal raphe with the cell lumen, and the presence of fenestrae between the alar canals externally. Our results indicate unequivocally that the biogeography and the biodiversity of Simonsenia remain highly underestimated. info:eu-repo/semantics/publishedVersion

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 molecular techniques. The morphological characteristics of H. nusantara have been described, illustrated and compared to other morphologically similar blue Haslea taxa, distributed worldwide. Additionally, molecular characterization was achieved by sequencing plastidial and mitochondrial genomes. Key results – This new species, named Haslea nusantara, cannot be discriminated by its morphology (stria density) but it is characterized by its gene sequences (rbcL chloroplast gene and cox1 mitochondrial gene). Moreover, it differentiates from other blue Haslea species by the presence of a thin central bar, which has been previously reported in non-blue species like H. pseudostrearia. The complete mitochondrion (36,288 basepairs, bp) and plastid (120,448 bp) genomes of H. nusantara were sequenced and the gene arrangements were compared with other diatom genomes. Phylogeny analyses established using rbcL indicated that H. nusantara is included in the blue Haslea cluster and close to a blue Haslea sp. found in Canary Islands (H. silbo sp. ined.). Conclusions – All investigations carried out in this study show that H. nusantara is a new blue-pigmented species, which belongs to the blue Haslea clade, with an exceptional geographic distribution in the Southern Hemisphere.

We describe the new species Gomphonemopsis sieminskae from brackish waters of the East China Sea littoral near Ningbo, China. Two diatom strains isolated from Ulva sp. were successfully grown, then analyzed by light (LM) and scanning electron (SEM) microscopy. The new species is compared to known Gomphonemopsis species, and similarities to G. pseudoexigua and G. obscurum are emphasized. Although the size metric data overlap and the external views are fairly similar, the two taxa differ in their valve interior. Molecular barcoding strongly discriminated G. sieminskae from G. cf. exigua, while rbcL gene-based phylogeny showed G. sieminskae to be sister to Phaeodactylum tricornutum. In this respect our results confirm the recent discovery, based on molecular data, that Gomphonemopsis is a close-relative taxon to Phaeodactylum, and place it in Phaeodactylaceae instead of Rhoicospheniaceae as inferred solely from morphology.

Cultivation of diatom algae is associated with many problems, one of which concerns the contamination of cultures with various microorganisms. A representative of kinetoplastids, the free-living bacteriotroph Bodo saltans Ehrenberg, 1832, can often be found among contaminants. In the case when B. saltans reaches a high abundance, diatom cells cease to divide, some of them die, becoming a substrate for the development of bacteria, and then the substrate for the next trophic link: kinetoplastids. For the decontamination of diatom cultures, we used amphotericin B, a polyene macrocyclic antibiotic active against some protozoa and fungi. The effect of the drug on B. saltans in cultures of eight species of diatoms, including Ardissonea crystallina (C. Agardh) Grunow, Climaconeis scalaris (Brebisson) E.J. Cox, Entomoneis paludosa (W. Smith) Reimer, Haslea karadagensis Davidovich, Gastineau & Mouget, Pleurosigma aestuarii (Brebisson ex Kutzing) W. Smith, Pleurosigma sp., Pseudo-nitzschia calliantha Lundholm, Moestrup & Hasle, and P. pungens (Grunow ex P.T. Cleve) Hasle, was investigated. The rate of division of diatom cells exposed to amphotericin B, depending on the dose and duration of exposure, was experimentally determined. Recommendations on the use of amphotericin B for the decontamination of diatom cultures from B. saltans are given.

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 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 Nephroselmis species in a strongly supported clade in which N. pyriformis is sister to N. astigmatica.

Complete chloroplast genome of Secale sylvestre.

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-coding region and two ORFs. The C. belcheri 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.

Annotated chloroplast genome of Poterioochromonas malhamensis, as fasta and gbk files.

Fasta and gbk files for the chloroplast genome of Nephroselmis pyriformis.

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 Diversibipalium “black”, and the morphology of a species previously reported as Diversibipalium “blue”. Based on next generation sequencing, we obtained the complete mitogenome of five species of Bipaliinae, including these two species. Results The new species Humbertium covidum n. sp. (syn: Diversibipalium “black” of Justine et al., 2018) is formally described on the basis of morphology, histology and mitogenome, and is assigned to Humbertium 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 vs France) is described; the cox1 gene displayed 2.25% difference. The new species Diversibipalium mayottensis n. sp. (syn: Diversibipalium “blue” of Justine et al., 2018) is formally described on the basis of external morphology and complete mitogenome and is assigned to Diversibipalium 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 cox1, SSU and LSU. In all four phylogenies, D. mayottensis was the sister-group to all the other bipaliines. With the exception of D. multilineatum which could not be circularised, the complete mitogenomes of B. kewense, B. vagum, B. adventitium, H. covidum and D. mayottensis 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 cox1, 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 D. mayottensis 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.

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 petB 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 rnl gene. The multigene phylogenies conducted provide more evidence of the proximity between S. trachyderma and fistula-bearing species of biraphid diatoms.

We sequenced the complete mitogenome of a specimen of Cymbiola nobilis (Neogastropoda, Volutidae) from Phu Quốc Island in Vietnam. The mitogenome of this predatory sea snail is 16,314-bp long and c...

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. info:eu-repo/semantics/acceptedVersion

Haslea ostrearia is a marine diatom that synthesizes and releases marennine, a water-soluble blue-green pigment responsible for the greening of the gills and labial palps of bivalves. The present study evaluated the effect of different marennine concentrations (0, 0.5, 1.0 and 2.0 mg l− 1) on the behavior (valve opening), physiology (clearance rates, oxygen consumption, assimilation efficiency and scope for growth) and biochemistry (fatty acid composition of neutral and polar lipids) of two commercially important bivalves, the blue mussel Mytilus edulis and the eastern oyster Crassostrea virginica. Under short-term (

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 microscopy and next generation sequencing. The diatoms identified are opportunistic and cosmopolitan species with known tolerances to organic pollution and variations in salinities, often found in meso- and polysaprobic zones in Europe. Their complete organellar genomes have been sequenced and some exhibit features never observed among diatoms before. To our knowledge this is the first time that living specimens of diatoms from the deep Sahara are identified using modern taxonomical tools in the frame of a study which also demonstrates the possibility to cultivate such material in laboratories for further experiments on biogeography and bioindication. Our study also suggests that European identification keys can be effective when employed on diatoms from the Sahara.

Haslea ostrearia is a marine diatom known to produce marennine, a water-soluble blue-green pigment responsible for the greening of oysters in ponds along the French Atlantic coast. This phenomenon occurs seasonally when H. ostrearia blooms in oyster ponds, and it increases the economic value of cultured oysters. From an ecological perspective, H. ostrearia blooms are accompanied by a decrease in the abundance of other microalgae, suggesting that this diatom produces allelochemicals. Recent studies showed that purified marennine has other biological activities, for instance antioxidant, antibacterial, and antiviral activities, which could be used in aquaculture to promote this pigment as a natural antipathogen agent. One important issue regarding the possible use of H. ostrearia in aquaculture as a mixed algal diet, however, is the importance of marennine allelopathy. In this study, we investigated the allelopathic effect of H. ostrearia on the growth of five microalgal species relevant to aquaculture: Chaetoceros calcitrans, Skeletonema costatum, Phaeodactylum tricornutum, Tetraselmis suecica, and Tisochrysis lutea. Allelopathic tests were realized by co-culturing these microalgae with H. ostrearia in batch and in semi-continuous mode, based on initial biovolume ratios. Our findings showed that inhibition of the growth of microalgae due to the presence of H. ostrearia and marennine was species dependent. Skeletonema costatum, C. calcitrans, and T. lutea were significantly more sensitive, whereas T. suecica and P. tricornutum appeared to be more resistant. Growth irradiance significantly influenced the allelopathic effect against the sensitive species S. costatum, and the H. ostrearia production of marennine increases with irradiance. Data presented in this study partly support the hypothesis that marennine released into the culture medium possibly acts as an allelochemical compound, thus explaining the dominance of H. ostrearia and the loss of sensitive algae in oyster ponds, but also that some species are insensitive, which allows co-culturing and use in a mixed algal diet in aquaculture.

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 from Navicula and Nitzschia, two genera with which Proschkinia has sometimes been associated based on morphology. info:eu-repo/semantics/publishedVersion

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 phylogeny, based on all protein-coding genes, weakly resolved the position of M. neglecta, as it tended to asssociate it with species representing the basal lineage of Annelids. This result underlines the need for more mitogenomes of Spionidae in order to improve the accuracy of their phylogeny.

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 gene...

We obtained the mitogenome sequence of a Black Sea isolate of the kinetoplastid Bodo saltans. 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 B. saltans revealed significant genetic divergence between the two isolates. Maximum likelihood phylogenetic inference clearly resolved the Bodonidae from the Trypanosomatidae.

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.

Algae have traditionally been included in the group Cryptogamae ('hidden reproduction'), as opposed to Phanerogamae or Spermatophyta, the Seed Plants. Cryptogamae encompassed both macro- and microalgae, lichens, mosses, and ferns, and have also been referred to as 'Thallophyta', 'non-vascular plants', 'spore plants', seedless or flowerless plants, depending on the criteria used for classification. Microalgae have long been considered among the more primitive and less important organisms representing the plant-like characters of autotrophy and immobility. Reproduction in macroalgae was only observed in the 18th century, but the ability of microalgae to reproduce sexually was not demonstrated until the 19th century in microscopic green filamentous algae. In this chapter, we summarise up-to-date information on sexual reproduction in three major groups of microalgae, the diatoms, dinoflagellates and haptophytes, and discuss its relationship to biodiversity and ecological life cycle strategies. Microalgae obviously constitute the microscopic part of the 'plant-like' world, but they do not deserve being considered lower 'plants', as they exhibit a perplexing diversity of modalities of sexual reproduction (haplontic, haplo-diplontic, diplontic life cycles), compared to the 'higher plants' which appear strikingly uniform and rather limited in their life cycle options.

A new species of raphid pennate diatom producing a blue pigment, Haslea karadagensis Davidovich, Gastineau & Mouget, sp. nov., was recently isolated from the Crimean coast of the Black Sea (Ukraine). This organism is very similar to the well-known Haslea ostrearia, the first described ‘blue’ diatom, which produces marennine, the pigment involved in the greening of oysters. The Ukrainian diatom, H. karadagensis, differs slightly from H. ostrearia in the structure of its frustule, and the two organisms are unable to interbreed. Two molecular markers, rbcL and the ITS1–5.8S–ITS2 sequences, showed 2% and >50% differences, respectively, between the two species. UV-visible spectrophotometry and in vivo confocal micro-Raman spectroscopy were used to compare the pigment of H. karadagensis with marennine. Both pigments showed absorption bands in the UV and red regions, but the positions of the maxima differ between the pigments. Significant differences were observed by micro-Raman spectroscopy in the 1000–1700 cm−...

For decades, the diatom genus Haslea has been known to comprise both "colorless" species and one species containing a blue pigment, the latter being known as H. ostrearia. Recently, a new blue diatom named H. karadagensis has been isolated from the Black Sea. The mating compatibility of the two species has been tested, and their reproductive isolation confirmed. We provide a detailed description of the heterothallic sexual reproduction process in this new species. Cells from clones which are sexually compatible arrange gametangial pairs. Each gametangium in the pair produces two gametes, which to a large extent are morphologically and behaviorally isogamous. No mucilage or mucilage structures are observed. Zygotes and auxospores have no contact with parental frustules, and their orientation is rather irregular though they tend to lie parallel to each other. Evaluation of the position of cardinal points in the life cycle of the species, and the rate of cell size decrease in culture are presented. In the breeding system of this species both homo- and heterothallic ways of reproduction are realized. The latter is basic and predominant. Among the 36 clones investigated, 16 were sexually compatible with the other 20. Homothallic behavior was extremely rare; only one clone displayed a homothallic mode of reproduction.

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 (

Diatoms are usually referred to as golden-brown microalgae, due to the colour of their plastids and to their pigment composition, mainly carotenoids (fucoxanthin, diadinoxanthin, diatoxanthin), which mask chlorophylls a and c. The species Haslea ostrearia Gaillon/Bory (Simonsen) appears unique because of its extraplastidial bluish colour, a consequence of the presence of a water-soluble blue pigment at cell apices, marennine. When released in seawater, marennine can be fixed on gills of oysters and other bivalves, which turn green. This greening phenomenon is economically exploited in Southwestern France, as it gives an added value to oysters. For decades, this singularity ascribed a worldwide distribution to H. ostrearia, first as Vibrio ostrearius, then Navicula ostrearia, last as H. ostrearia, when the genus Haslea was proposed by R. Simonsen (1974). Indeed, this ‘birthmark’ (presence of blue apices) made H. ostrearia easily recognisable without further scrutiny and identification of the microalga as well as its presence easily deduced from the greening of bivalves. Consequently, the widely admitted cosmopolitan character of H. ostrearia has only been questioned recently, following the discovery in 2008, of a new species of blue diatom in the Black Sea, Haslea karadagensis. The biodiversity of blue diatoms suddenly increased with the finding of other blue species in the Mediterranean Sea, the Canary Islands, etc., the taxonomic characterization of which is in progress. This review thus focuses on the unsuspected biodiversity of blue diatoms within the genus Haslea. Methods for species determination (morphometrics, chemotaxonomy, genomics), as well as a new species, are presented and discussed.

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 2H 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. 2H 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.