312 research outputs found
DNA, Red Tide and the Sea: a new exhibit at Mystic Aquarium & IFE
No full textDNA, Red Tide and the Sea is a new exhibit at Mystic Aquarium & IFE. It was developed by UConn Marine Sciences Professor Senjie Lin, and Mystic Aquarium. Children can extract DNA from fruit and learn about genetic codes and red tides in the ocean
Prorocentrum shikokuense
No full textProrocentrum shikokuense in the Mediterranean Sea Marampouti et al. (2021) listed Prorocentrum shikokuense among the twenty alien harmful microalgae in the Mediterranean Sea. However, the analyses of the available molecular data reveal that the Mediterranean or Atlanto-Mediterranean ribotypes of most of these ‘alien’ microalgae are genetically distinct from the supposed original exotic populations. This suggests that most of the Mediterranean populations of these microalgae are genetically independent populations rather than recent introductions from exotic ocean regions (Gómez and Galil 2021). The port of Brindisi receives a considerable ship traffic from Asia, apparently supporting the hypothesis of the introduction of exotic phytoplankton via ballast waters. Molecular data are needed, however, to resolve the biogeographical affinity of the Mediterranean population of P. shikokuense. The problem is that available rRNA gene sequences show a strong bias towards isolates from the Pacific Ocean. Another problem is the limited genetic divergence between the isolates because their rRNA gene sequences were almost identical even using variable molecular markers such as the ITS rRNA gene sequence. Nearly all the available sequences of P. shikokuense are from the Pacific Ocean (Figs 2–4). An exception in the SSU- and LSU rRNA gene phylogeny is the strain K-1260 of the Norwegian Culture Collection of Algae (accession numbers MK713637-9) that was isolated in a port of the La Gomera Island in the Canary Archipelago (subtropical North Atlantic). This small port does not receive big ships, and the Canary Archipelago is not known as a route of ship traffic from Asia. The LSU and ITS rRNA gene sequences of the strain K-1260 were 100% identical to the Mediterranean ribotype of P. shikokuense. This suggests a distinct population of P. shikokuense exists in the tropical Atlantic and Mediterranean Sea, at odds with the hypothesis of a recent introduction from Asian waters. However, because most of the available sequences are from isolates from the Pacific Ocean, and the resolution of the molecular marker is insufficient, an unequivocal conclusion on the biogeographical affinities of this species remain to emerge. Percopo et al. (2011) reported a scanning electron microscopy (SEM) image of Prorocentrum shikokuense (identified as P. donghaiense) from the offshore waters of the Gulf of Lions, NW Mediterranean Sea. Cell dimensions were 16.5 µm long and 9.5 µm wide. The individual was shorter, and relatively wider (lower length/wide ratio) than the cells of P. shikokuense during a bloom in the port of Brindisi (mean 21.6 µm long, 9.3 µm wide). It should be noted that the drying in the SEM treatment reduces the cell size (Pertola et al. 2003). The robust appearance of the individuals reported in Percopo et al. (2011) matches well with smaller individuals of P. donghaiense in the species original description (16–22 µm long, 9–14 µm wide; Lu and Goebel 2001). This suggests that the morphotype observed in offshore waters differed from the blooming cells in neritic eutrophic waters (Fig. 1 AH). Percopo et al. (2011) hypothesized that Prorocentrum maximum (Gourret) J.Schiller, described from the Gulf of Lions, could be a senior synonym of P. shikokuense. However, the shape of the cell illustrated by Gourret (1883) as Postprorocentrum maximum may correspond to an individual of P. micans without apical spine. Later, Schiller (1931) transferred it into Prorocentrum as P. maximum. Schiller (1931) reported a line drawing of P. maximum that is considered an earlier illustration of P. mexicanum B.F.Osorio (Gómez et al. 2017).Published as part of Gómez, Fernando, Zhang, Huan, Roselli, Leonilde & Lin, Senjie, 2021, Detection of Prorocentrum shikokuense in the Mediterranean Sea and evidence that P. dentatum, P. obtusidens and P. shikokuense are three different species (Prorocentrales, Dinophyceae), pp. 47-59 in Acta Protozoologica 60 on page 53, DOI: 10.4467/16890027AP.21.006.15380, http://zenodo.org/record/835700
Prorocentrum shikokuense
No full textProrocentrum shikokuense in the North Atlantic Ocean The molecular data suggest the presence of P. shikokuense in the European Atlantic (Figs 2, 4), but studies combining molecular and morphological data remain missing. In addition to the sequence from the subtropical Canary Islands, there is other SSU rRNA gene sequence from a strain isolated in the Baltic Sea that clustered in the clade of P. shikokuense (accession number MH976698) (Fig. 2). Monti-Birkenmeier et al. (2019, their fig. 2c) provided a SEM image of this Baltic strain submitted to GenBank as Prorocentrum cordatum. The cell was oval with a length of 10 µm that fit well with P. cordatum (Monti-Birkenmeier et al. 2019), while cells of P. shikokuense are more elongated and ~20 µm long. There is no coherence between the morphology of the illustrated cell and the topology of the sequence MH 976698 in the molecular phylogeny (Fig. 2). According Xu et al. (2010), P. shikokuense showed an optimal growth at 27 ºC in the East China Sea. In the Mediterranean Sea, blooms of P. shikokuense were observed at temperatures of 28–32 ºC (Roselli et al. 2019). The Baltic Sea is characterized by low temperatures, and huge blooms are not expected. Further studies are needed to confirm the occurrence of P. shikokuense in the Baltic Sea. In the ITS rRNA gene phylogeny, a sequence identified as Prorocentrum rostratum with accession number EU244471 clustered in the clade of P. shikokuense among sequences from the Asian Pacific Ocean (Fig. 4). Prorocentrum rostratum is a distinctive species known from tropical waters (Stein 1883). The cells are elongated, 5–6 times as long as broad (~60 µm long), valves ending at anterior end in long pointed process, notched in the side view. Prorocentrum rostratum is easily distinguishable from P. shikokuense that is smaller, ~20 µm long, with an inconspicuous shoulder, and a round posterior margin (Fig. 1 AB, AE–AH). The strain P. rostratum PR 1V (EU244471) was isolated at Vigo, NW Spain. It is not expected to find the tropical species P. rostratum in the cold waters of the Galician Rias. No morphological information of the strain PR1V is available currently. Beyond the problem in the identification associated with the sequences of P. shikokuense in Europe, the presence of P. shikokuense in the European Atlantic Ocean is not unexpected, but a definite conclusion awaits combined morphological and molecular analyses. While the molecular data reveal that P. cordatum is present in the American and European coasts of the North Atlantic Ocean (Figs 2–4), there is no evidence for the presence of P. shikokuense in the American Atlantic coasts.Published as part of Gómez, Fernando, Zhang, Huan, Roselli, Leonilde & Lin, Senjie, 2021, Detection of Prorocentrum shikokuense in the Mediterranean Sea and evidence that P. dentatum, P. obtusidens and P. shikokuense are three different species (Prorocentrales, Dinophyceae), pp. 47-59 in Acta Protozoologica 60 on pages 53-56, DOI: 10.4467/16890027AP.21.006.15380, http://zenodo.org/record/835700
A decade of dinoflagellate genomics illuminating an enigmatic eukaryote cell
No full textAbstract Dinoflagellates are a remarkable group of protists, not only for their association with harmful algal blooms and coral reefs but also for their numerous characteristics deviating from the rules of eukaryotic biology. Genome research on dinoflagellates has lagged due to their immense genome sizes in most species (~ 1-250 Gbp). Nevertheless, the last decade marked a fruitful era of dinoflagellate genomics, with 27 genomes sequenced and many insights attained. This review aims to synthesize information from these genomes, along with other omic data, to reflect on where we are now in understanding dinoflagellates and where we are heading in the future. The most notable insights from the decade-long genomics work include: (1) dinoflagellate genomes have been expanded in multiple times independently, probably by a combination of rampant retroposition, accumulation of repetitive DNA, and genome duplication; (2) Symbiodiniacean genomes are highly divergent, but share about 3,445 core unigenes concentrated in 219 KEGG pathways; (3) Most dinoflagellate genes are encoded unidirectionally and are not intron-poor; (4) The dinoflagellate nucleus has undergone extreme evolutionary changes, including complete or nearly complete loss of nucleosome and histone H1, and acquisition of dinoflagellate viral nuclear protein (DVNP); (5) Major basic nuclear protein (MBNP), histone-like protein (HLP), and bacterial HU-like protein (HCc) belong to the same protein family, and MBNP can be the unifying name; (6) Dinoflagellate gene expression is regulated by poorly understood mechanisms, but microRNA and other epigenetic mechanisms are likely important; (7) Over 50% of dinoflagellate genes are “dark” and their functions remain to be deciphered using functional genetics; (8) Initial insights into the genomic basis of parasitism and mutualism have emerged. The review then highlights functionally unique and interesting genes. Future research needs to obtain a finished genome, tackle large genomes, characterize the unknown genes, and develop a quantitative molecular ecological model for addressing ecological questions
Distinct gene number-genome size relationships for eukaryotes and non-eukaryotes: gene content estimation for dinoflagellate genomes.
No full textThe ability to predict gene content is highly desirable for characterization of not-yet sequenced genomes like those of dinoflagellates. Using data from completely sequenced and annotated genomes from phylogenetically diverse lineages, we investigated the relationship between gene content and genome size using regression analyses. Distinct relationships between log(10)-transformed protein-coding gene number (Y') versus log(10)-transformed genome size (X', genome size in kbp) were found for eukaryotes and non-eukaryotes. Eukaryotes best fit a logarithmic model, Y' = ln(-46.200+22.678X', whereas non-eukaryotes a linear model, Y' = 0.045+0.977X', both with high significance (p0.91). Total gene number shows similar trends in both groups to their respective protein coding regressions. The distinct correlations reflect lower and decreasing gene-coding percentages as genome size increases in eukaryotes (82%-1%) compared to higher and relatively stable percentages in prokaryotes and viruses (97%-47%). The eukaryotic regression models project that the smallest dinoflagellate genome (3x10(6) kbp) contains 38,188 protein-coding (40,086 total) genes and the largest (245x10(6) kbp) 87,688 protein-coding (92,013 total) genes, corresponding to 1.8% and 0.05% gene-coding percentages. These estimates do not likely represent extraordinarily high functional diversity of the encoded proteome but rather highly redundant genomes as evidenced by high gene copy numbers documented for various dinoflagellate species
Mitogen-activated protein kinase in pfiesteria piscicida and its growth rate-related expression
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