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Marine Genomics

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https://www.readbyqxmd.com/read/30420273/symbiotic-bacteria-associated-with-ascidian-vanadium-accumulation-identified-by-16s-rrna-amplicon-sequencing
#1
Tatsuya Ueki, Manabu Fujie, Romaidi, Noriyuki Satoh
Ascidians belonging to Phlebobranchia accumulate vanadium to an extraordinary degree (≤ 350 mM). Vanadium levels are strictly regulated and vary among ascidian species; thus, they represent well-suited models for studies on vanadium accumulation. No comprehensive study on metal accumulation and reduction in marine organisms in relation to their symbiotic bacterial communities has been published. Therefore, we performed comparative 16S rRNA amplicon sequence analyses on samples from three tissues (branchial sac, intestine, and intestinal lumen) involved in vanadium absorption, isolated from two vanadium-rich (Ascidia ahodori and Ascidia sydneiensis samea) and one vanadium-poor species (Styela plicata)...
November 9, 2018: Marine Genomics
https://www.readbyqxmd.com/read/30409725/transcriptomic-response-of-the-crassostrea-virginica-gonad-after-exposure-to-a-water-accommodation-fraction-of-hydrocarbons-and-the-potential-implications-in-reproduction
#2
S Tapia-Morales, E A López-Landavery, I Giffard-Mena, N Ramírez-Álvarez, R J E Gómez-Reyes, F Díaz, C E Galindo-Sánchez
The Crassostrea virginica oyster has biological and economic importance in the Gulf of Mexico, an area with a high extraction and production of hydrocarbons. Exposure to hydrocarbons affects the reproductive processes in bivalves. In C. virginica, the effect of hydrocarbons on the gonad of the undifferentiated organism has not been evaluated to determine the possible damage during the maturation process. To evaluate this effect, RNA-seq data was generated from C. virginica gonads exposed to a 200 μg/L of hydrocarbons at different exposure times (7, 14 and 21 days) and a control treatment (without hydrocarbons)...
November 5, 2018: Marine Genomics
https://www.readbyqxmd.com/read/30297161/mechanistic-philosophies-of-development-theodor-boveri-and-eric-h-davidson
#3
Silvia Caianiello
No abstract text is available yet for this article.
October 5, 2018: Marine Genomics
https://www.readbyqxmd.com/read/30293673/transcriptomic-and-metabolic-response-to-chronic-and-acute-thermal-exposure-of-juvenile-geoduck-clams-panopea-globosa
#4
Oscar E Juárez, Fabiola Lafarga-De la Cruz, Ignacio Leyva-Valencia, Edgar López-Landavery, Zaúl García-Esquivel, Fernando Díaz, Denisse Re-Araujo, Brent Vadopalas, Clara E Galindo-Sánchez
The Cortes geoduck Panopea globosa is a large bivalve with a high commercial value distributed from the southern Pacific coast of the Baja California Peninsula to the northern Gulf of California, inhabiting a wide range of subtropical temperatures. A new record of this species in shallower waters suggests that it can tolerate a warmer environment than previously thought. To better understand the whole-body and molecular response mechanisms to different temperatures, we assessed the metabolic rate of juvenile individuals exposed to chronic and acute thermal conditions and analyzed the transcriptomic response in ctenidial tissues...
October 4, 2018: Marine Genomics
https://www.readbyqxmd.com/read/30293672/transcriptome-analysis-of-the-midgut-gland-of-the-brown-shrimp-crangon-crangon-indicates-high-polymorphism-in-digestive-enzymes
#5
Diana Martínez-Alarcón, Lars Harms, Wilhelm Hagen, Reinhard Saborowski
Tolerance of organisms towards heterogeneous and variable environments is highly related to physiological flexibility. An effective strategy to enhance physiological flexibility is the expression of polymorphic enzymes. This seems to be the case in the brown shrimp Crangon crangon. It shows high reproduction rates, feeds opportunistically on endo- and epibenthic organisms, and is apparently well adapted to variable environmental conditions. Previous electrophoretic studies revealed a high level of polymorphism and no consistent phenotype of digestive enzymes between individuals...
October 4, 2018: Marine Genomics
https://www.readbyqxmd.com/read/30279127/gene-expression-profiles-of-pyropia-yezoensis-in-response-to-dehydration-and-rehydration-stresses
#6
Peipei Sun, Xianghai Tang, Guiqi Bi, Kuipeng Xu, Fanna Kong, Yunxiang Mao
Pyropia yezoensis is an economically important marine macroalgae, naturally distributed in the upper intertidal zone. Owing to the nature of its habitat, the thallus will periodically be exposed to seawater or atmosphere, and can lose up to 95% of its cellular water content. This makes the alga an ideal research model to investigate the mechanisms of desiccation tolerance. In this study, we investigated the response mechanisms to dehydration and rehydration stresses at the transcription level in Pyropia yezoensis...
September 29, 2018: Marine Genomics
https://www.readbyqxmd.com/read/30249373/winter-picoplankton-diversity-in-an-oligotrophic-marginal-sea
#7
Maja Mucko, Sunčica Bosak, Raffaella Casotti, Cecilia Balestra, Zrinka Ljubešić
Marine picoplankton, unicellular organisms with cell sizes up to 3 μm in diameter, numerically dominate marine ecosystems, encompassing Archaea, Bacteria, Eukarya (protists and fungi) as well as viruses. Autotrophic and heterotrophic picoplankton abundance and community composition with a focus on picoeukaryotes (PEs) were investigated in the winter of 2016 at three stations along a coast-to-offshore transect in the southern Adriatic Sea. Abundances were estimated by flow cytometry, while community composition by Illumina High-Throughput Sequencing (HTS) of 16S and 18S rRNA genes...
September 21, 2018: Marine Genomics
https://www.readbyqxmd.com/read/30201306/de-novo-transcriptome-assembly-of-the-coral-agaricia-lamarcki-lamarck-s-sheet-coral-from-mesophotic-depth-in-southwest-puerto-rico
#8
Alex J Veglia, Nicholas M Hammerman, Ramón E Rivera-Vicéns, Nikolaos V Schizas
The plating coral, Agaricia lamarcki is a widely distributed species inhabiting reefs across the Caribbean basin and Florida. This species is of interest since it is considered a depth-generalist, found from 10 to 70 m. Given the scope of contemporary studies on this coral's population dynamics and physiology, as well as, the potential of mesophotic reefs to be refuge habitats for deteriorated shallow water reefs, we present the first de novo transcriptome assembly of an important mesophotic coral. Using next-generation paired-end sequencing (Illumina Hiseq4000; 2 × 150 bp), we obtained a total of 82,506,058 raw reads...
September 7, 2018: Marine Genomics
https://www.readbyqxmd.com/read/30197044/the-acute-transcriptomic-response-of-coral-algae-interactions-to-ph-fluctuation
#9
Zhenyue Lin, Liuying Wang, Mingliang Chen, Jianming Chen
Little is known about how the coral host and its endosymbiont interactions change when they are exposed to a sudden nonlinear environmental transformation, yet this is crucial to coral survival in extreme events. Here, we present a study that investigates the transcriptomic response of corals and their endosymbionts to an abrupt change in pH (pH 7.60 and 8.35). The transcriptome indicates that the endosymbiont demonstrates a synchronized downregulation in carbon acquisition and fixation processes and may result in photosynthetic dysfunction in endosymbiotic Symbiodinium, suggesting that the mutualistic continuum of coral-algae interactions is compromised in response to high-CO2 exposure...
September 6, 2018: Marine Genomics
https://www.readbyqxmd.com/read/30195478/comparative-transcriptome-analysis-of-paphia-undulata-with-different-foot-colors
#10
Suzhen Deng, Xiaolin Zhang, Qingchang Li, Jing Zhang, Fang Han, Xiande Liu
Foot color is an important trait in Paphia undulata that influences consumer selection. To elucidate the molecular basis of foot color, six transcriptome libraries of P. undulata with different foot colors were constructed: white (L2, L3 and L4) and orange (D2, D3, D4). There is a significant difference in color index (L⁎ , a⁎ , b⁎ ) between the two groups (P < 0.05). These six paired-end libraries were sequenced using the Illumina HiSeq 2500 platform. In total, 48.22 Gb of clean data were obtained and de novo assembled into 58,159 unigenes with a mean length of 889...
September 5, 2018: Marine Genomics
https://www.readbyqxmd.com/read/30154054/on-the-revolution-of-cetacean-evolution
#11
REVIEW
Annalaura Mancia
The order of Cetacea with 88 species including Odontoceti (or toothed whales) and Mysticeti (or baleen whales) is the most specialized and diversified group of mammals. The blue whale with a maximum recorded length of 29.9 m for 173 t of weight is the largest animal known to have ever existed, and any dolphin's brain is most powerful and complex than any other brain in the animal kingdom, second only to primate's. Nevertheless, Cetacea are mammals that re-entered the oceans only a little over 50 million years ago, a relatively short time on the evolutionary scale...
August 25, 2018: Marine Genomics
https://www.readbyqxmd.com/read/30064945/gene-expression-across-tissues-sex-and-life-stages-in-the-sea-urchin-tripneustes-gratilla-toxopneustidae-odontophora-camarodonta
#12
Áki Jarl Láruson, Simon E Coppard, Melissa H Pespeni, Floyd A Reed
The pan-tropical sea urchin Tripneustes gratilla is an ecologically and economically important shallow water algal grazer. The aquaculture of T. gratilla has spurred growing interest in the population biology of the species, and by extension the generation of more molecular resources. To this purpose, de novo transcriptomes of T. gratilla were generated for two adults, a male and a female, as well as for a cohort of approximately 1000 plutei larvae. Gene expression profiles of three adult tissue samples were quantified and compared...
July 28, 2018: Marine Genomics
https://www.readbyqxmd.com/read/30031746/molecular-evidence-for-an-intrinsic-circadian-pacemaker-in-the-cardiac-ganglion-of-the-american-lobster-homarus-americanus-is-diel-cycling-of-heartbeat-frequency-controlled-by-a-peripheral-clock-system
#13
Andrew E Christie, Andy Yu, Vittoria Roncalli, Micah G Pascual, Matthew C Cieslak, Amanda N Warner, Tess J Lameyer, Meredith E Stanhope, Patsy S Dickinson, J Joe Hull
Whether cardiac output in decapod crustaceans is under circadian control has long been debated, with mixed evidence for and against the hypothesis. Moreover, the locus of the clock system controlling cardiac activity, if it is under circadian control, is unknown. However, a report that the crayfish heart in organ culture maintains a circadian oscillation in heartbeat frequency suggests the presence of a peripheral pacemaker within the cardiac neuromuscular system itself. Because the decapod heart is neurogenic, with contractions controlled by the five motor and four premotor neurons that make up the cardiac ganglion (CG), a likely locus for a circadian clock is the CG itself...
July 18, 2018: Marine Genomics
https://www.readbyqxmd.com/read/29754835/identification-and-expression-analysis-of-long-noncoding-rnas-in-embryogenesis-and-larval-metamorphosis-of-ciona-savignyi
#14
Jiankai Wei, Bo Dong
Long noncoding RNAs (lncRNAs) play important roles in diverse developmental and pathological processes through chromatin reprogramming, cis regulation and posttranscriptional modification. They have been extensively studied in both vertebrates and invertebrates. However, the information of lncRNAs in urochordate is still lacking. In this study, we used the RNA-Seq data from three developmental stages (18, 21 and 42 hours post fertilization, hpf) of embryos and larvae in Ciona savignyi to identify candidate lncRNAs and analyze their expression profiles...
July 2018: Marine Genomics
https://www.readbyqxmd.com/read/29673959/a-200k-snp-chip-reveals-a-novel-pacific-salmon-louse-genotype-linked-to-differential-efficacy-of-emamectin-benzoate
#15
Amber M Messmer, Jong S Leong, Eric B Rondeau, Anita Mueller, Cody A Despins, David R Minkley, Matthew P Kent, Sigbjørn Lien, Brad Boyce, Diane Morrison, Mark D Fast, Joseph D Norman, Roy G Danzmann, Ben F Koop
Antiparasitic drugs such as emamectin benzoate (EMB) are relied upon to reduce the parasite load, particularly of the sea louse Lepeophtheirus salmonis, on farmed salmon. The decline in EMB treatment efficacy for this purpose is an important issue for salmon producers around the world, and particularly for those in the Atlantic Ocean where widespread EMB tolerance in sea lice is recognized as a significant problem. Salmon farms in the Northeast Pacific Ocean have not historically experienced the same issues with treatment efficacy, possibly due to the relatively large population of endemic salmonid hosts that serve to both redistribute surviving lice and dilute populations potentially under selection by introducing naïve lice to farms...
July 2018: Marine Genomics
https://www.readbyqxmd.com/read/29657123/transcriptome-of-the-bivalve-limecola-balthica-l-from-western-pacific-a-new-resource-for-studies-of-european-populations
#16
Andrey A Yurchenko, Nataliia Katolikova, Dmitrii Polev, Irina Shcherbakova, Petr Strelkov
The Baltic clam Limecola balthica L. (Tellinidae) is broadly used in ecophysiological, toxicological, evolutionary and environmental monitoring studies. However, it is poorly studied in respect of genome and gene functions. We obtained a transcriptome of Limecola b. balthica from Kamchatka (Western Pacific) generated with the use of Illumina high-throughput sequencing. We annotated 11,374 proteins, including 53 from the oxidative phosphorylation pathway and a number of pollution-stress biomarkers, recovered 254,540 single nucleotide variants within two annotated transcriptomes including 25,330 scorable in the previously published European data...
July 2018: Marine Genomics
https://www.readbyqxmd.com/read/29655930/circadian-signaling-in-homarus-americanus-region-specific-de-novo-assembled-transcriptomes-show-that-both-the-brain-and-eyestalk-ganglia-possess-the-molecular-components-of-a-putative-clock-system
#17
Andrew E Christie, Andy Yu, Micah G Pascual, Vittoria Roncalli, Matthew C Cieslak, Amanda N Warner, Tess J Lameyer, Meredith E Stanhope, Patsy S Dickinson, J Joe Hull
Essentially all organisms exhibit recurring patterns of physiology/behavior that oscillate with a period of ~24-h and are synchronized to the solar day. Crustaceans are no exception, with robust circadian rhythms having been documented in many members of this arthropod subphylum. However, little is known about the molecular underpinnings of their circadian rhythmicity. Moreover, the location of the crustacean central clock has not been firmly established, although both the brain and eyestalk ganglia have been hypothesized as loci...
July 2018: Marine Genomics
https://www.readbyqxmd.com/read/29426805/boveri-s-research-at-the-zoological-station-naples-rediscovery-of-his-original-microscope-slides-at-the-university-of-w%C3%A3-rzburg
#18
REVIEW
Ulrich Scheer
Eric Davidson once wrote about Theodor Boveri: "From his own researches, and perhaps most important, his generalized interpretations, derive the paradigms that underlie modern inquiries into the genomic basis of embryogenesis" (Davidson, 1985). As luck would have it, the "primary data" of Boveri's experimental work, namely the microscope slides prepared by him and his wife Marcella during several stays at the Zoological Station in Naples (1901/02, 1911/12 and 1914), have survived at the University of Würzburg...
July 2018: Marine Genomics
https://www.readbyqxmd.com/read/29866485/the-north-sea-goes-viral-occurrence-and-distribution-of-north-sea-bacteriophages
#19
Alexa Garin-Fernandez, Emiliano Pereira-Flores, Frank Oliver Glöckner, Antje Wichels
Marine viruses are dominated by phages and have an enormous influence on microbial population dynamics, due to lysis and horizontal gene transfer. The aim of this study is to analyze the occurrence and diversity of phages in the North Sea, considering the virus-host interactions and biogeographic factors. The virus community of four sampling stations were described using virus metagenomics (viromes). The results show that the virus community was not evenly distributed throughout the North Sea. The dominant phage members were identified as unclassified phage group, followed by Caudovirales order...
June 1, 2018: Marine Genomics
https://www.readbyqxmd.com/read/29650372/genomic-signatures-of-parasite-driven-natural-selection-in-north-european-atlantic-salmon-salmo-salar
#20
Ksenia J Zueva, Jaakko Lumme, Alexey E Veselov, Matthew P Kent, Craig R Primmer
Understanding the genomic basis of host-parasite adaptation is important for predicting the long-term viability of species and developing successful management practices. However, in wild populations, identifying specific signatures of parasite-driven selection often presents a challenge, as it is difficult to unravel the molecular signatures of selection driven by different, but correlated, environmental factors. Furthermore, separating parasite-mediated selection from similar signatures due to genetic drift and population history can also be difficult...
June 2018: Marine Genomics
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