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Marine Genomics

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
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
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
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
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
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
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
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
Andrew E Christie, Micah G Pascual, Andy Yu
Peptides are the largest/most diverse class of molecules used by animals for chemical communication, and with their cognate receptors, are key players in modulating physiological/behavioral control systems, including those involved in adaptation to environmental change. Crustaceans have long served as models for investigating peptidergic control of physiology/behavior, and members of Notostraca, an ancient branchiopod order, have recently been proposed as models for investigating the genetic/physiological underpinnings of ecoresponsiveness; nothing is currently known about the genes/proteins underlying peptidergic signaling in any member of this crustacean taxon...
June 2018: Marine Genomics
Xuan Zhuang, Katherine R Murphy, Laura Ghigliotti, Eva Pisano, C-H Christina Cheng
Antifreeze glycoproteins (AFGPs) are a novel evolutionary innovation in members of the northern cod fish family (Gadidae), crucial in preventing death from inoculative freezing by environmental ice in their frigid Arctic and sub-Arctic habitats. However, the genomic origin and molecular mechanism of evolution of this novel life-saving adaptive genetic trait remained to be definitively determined. To this end, we constructed large insert genomic DNA BAC (bacterial artificial chromosome) libraries for two AFGP-bearing gadids, the high-Arctic polar cod Boreogadus saida and the cold-temperate Atlantic tomcod Microgadus tomcod, to isolate and sequence their AFGP genomic regions for fine resolution evolutionary analyses...
June 2018: Marine Genomics
F Maroso, J E J Hillen, B G Pardo, K Gkagkavouzis, I Coscia, M Hermida, R Franch, B Hellemans, J Van Houdt, B Simionati, J B Taggart, E E Nielsen, G Maes, S A Ciavaglia, L M I Webster, F A M Volckaert, P Martinez, L Bargelloni, R Ogden
The development of Genotyping-By-Sequencing (GBS) technologies enables cost-effective analysis of large numbers of Single Nucleotide Polymorphisms (SNPs), especially in "non-model" species. Nevertheless, as such technologies enter a mature phase, biases and errors inherent to GBS are becoming evident. Here, we evaluated the performance of double digest Restriction enzyme Associated DNA (ddRAD) sequencing in SNP genotyping studies including high number of samples. Datasets of sequence data were generated from three marine teleost species (>5500 samples, >2...
June 2018: Marine Genomics
T Manousaki, A Tsakogiannis, J Lagnel, D Kyriakis, N Duncan, A Estevez, C S Tsigenopoulos
Meagre (Argyrosomus regius), a teleost fish of the family Sciaenidae, is part of a group of marine fish species considered new for Mediterranean aquaculture representing the larger fish cultured in the region. Meagre aquaculture started ~25years ago in West Mediterranean, and the supply of juveniles has been dominated by few hatcheries. This fact has raised concerns on possible inbreeding, urging the need for genetic information on the species and for an assessment of the polymorphisms found in the genome. To that end we characterized the muscle and liver transcriptome of a pool of meagre individuals, from different families and phenotypic size, to obtain a backbone that can support future studies regarding physiology, immunology and genetics of the species...
June 2018: Marine Genomics
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...
May 10, 2018: Marine Genomics
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...
April 16, 2018: Marine Genomics
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...
April 12, 2018: Marine Genomics
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...
April 11, 2018: Marine Genomics
Andrew E Christie, Matthew C Cieslak, Vittoria Roncalli, Petra H Lenz, Kaley M Major, Helen C Poynton
Due to its sensitivity to many environmental and anthropogenic stressors, including a wide range of chemical compounds, Hyalella azteca, a freshwater amphipod, has emerged as one of the most commonly used invertebrates for ecotoxicological assessment.Peptidergic signaling systems are key components in the control of organism-environment interactions, and there is a growing literature suggesting that they are targets of a number of aquatic toxicants.Interestingly, and despite its model species status in the field of ecotoxicology, little is known about the peptide hormones of H...
April 2018: Marine Genomics
Chitra Selvaratnam, Suganthi Thevarajoo, Kian Mau Goh, Kok-Gan Chan, Chun Shiong Chong
To date, the genus Roseivirga consists of six species with one subspecies and is one of the least-studied genera among the family Flammeovirgaceae. In order to further explore this genus, the genome sequences of five Roseivirga spp. were compared and described in this study. The Roseivirga genomes have similar sizes in the range of 4.08-4.47Mb with an average of 4.22Mb. Several key proteins related to osmotic stress adaptation were identified in Roseivirga spp. including betaine transporter, choline dehydrogenase, and glutamate synthases...
April 2018: Marine Genomics
Chul Lee, Heesu Jeong, DongAhn Yoo, Eun Bae Kim, Bo-Hye Nam, Heebal Kim
Coelacanth is a group of extant lobe-finned fishes in Sarcopterygii that provides evolutionary information for the missing link between ray-finned fish and tetrapod vertebrates. Its phenotypes, different from actinopterygian fishes, have been considered as primitive terrestrial traits such as cartilages in their fatty fins which are homologous with the humerus and femur. To investigate molecular evolution of coelacanth which led to its divergence into Sarcopterygii, we compared its protein coding sequences with 11 actinopterygian fishes...
April 2018: Marine Genomics
D J Colgan, R P Santos
Successful responses to the multifarious challenges of controlling water balance are critical for snails' survival in the great diversity of habitats they occupy. Advances are being made in understanding how such challenges are approached at the molecular level, including through the study of aquaporins, which are proteins functioning to facilitate the passage of water and other small molecules across cellular membranes. Deduced aquaporin amino acid sequences from partial genomic assemblies of three neritimorph species were added to available gastropod data and sequences from other taxa to make a phylogenetic classification of these proteins using maximum likelihood and Bayesian analyses...
April 2018: Marine Genomics
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