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Marine Genomics

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https://www.readbyqxmd.com/read/29866485/the-north-sea-goes-viral-occurrence-and-distribution-of-north-sea-bacteriophages
#1
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/29754835/identification-and-expression-analysis-of-long-noncoding-rnas-in-embryogenesis-and-larval-metamorphosis-of-ciona-savignyi
#2
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
https://www.readbyqxmd.com/read/29650372/genomic-signatures-of-parasite-driven-natural-selection-in-north-european-atlantic-salmon-salmo-salar
#3
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
https://www.readbyqxmd.com/read/29526397/peptidergic-signaling-in-the-tadpole-shrimp-triops-newberryi-a-potential-model-for-investigating-the-roles-played-by-peptide-paracrines-hormones-in-adaptation-to-environmental-change
#4
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
https://www.readbyqxmd.com/read/29510906/reconstruction-of-the-repetitive-antifreeze-glycoprotein-genomic-loci-in-the-cold-water-gadids-boreogadus-saida-and-microgadus-tomcod
#5
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
https://www.readbyqxmd.com/read/29496460/performance-and-precision-of-double-digestion-rad-ddrad-genotyping-in-large-multiplexed-datasets-of-marine-fish-species
#6
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
https://www.readbyqxmd.com/read/29395623/muscle-and-liver-transcriptome-characterization-and-genetic-marker-discovery-in-the-farmed-meagre-argyrosomus-regius
#7
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
https://www.readbyqxmd.com/read/29673959/a-200k-snp-chip-reveals-a-novel-pacific-salmon-louse-genotype-linked-to-differential-efficacy-of-emamectin-benzoate
#8
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
https://www.readbyqxmd.com/read/29657123/transcriptome-of-the-bivalve-limecola-balthica-l-from-western-pacific-a-new-resource-for-studies-of-european-populations
#9
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
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
#10
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
https://www.readbyqxmd.com/read/29395622/prediction-of-a-peptidome-for-the-ecotoxicological-model-hyalella-azteca-crustacea-amphipoda-using-a-de-novo-assembled-transcriptome
#11
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
https://www.readbyqxmd.com/read/29306571/genomic-analyses-of-five-roseivirga-species-insights-into-marine-adaptation
#12
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
https://www.readbyqxmd.com/read/29275151/coelacanth-specific-adaptive-genes-give-insights-into-primitive-evolution-for-water-to-land-transition-of-tetrapods
#13
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
https://www.readbyqxmd.com/read/29249402/a-phylogenetic-classification-of-gastropod-aquaporins
#14
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
https://www.readbyqxmd.com/read/28870633/de-novo-assembly-and-annotation-of-the-whole-transcriptome-of-oratosquilla-oratoria
#15
Fangrui Lou, Tianxiang Gao, Shanshan Cai, Zhiqiang Han
As the representative species of Stomatopoda, Oratosquilla oratoria can tolerate the complex benthic environment. In this study, our goal was to develop the transcriptomic resource of O. oratoria that would support adaptation mechanism studies. We generated the whole transcriptome of O. oratoria from combined tissues (eyestalk, muscle, sexual and viscus) using Hiseq technology. A total of 51,305,284 high-quality clean reads were assembled to produce 59,054 non-redundant transcripts with a mean length of 987nt using Trinity and CORSET software...
April 2018: Marine Genomics
https://www.readbyqxmd.com/read/28869183/complete-genome-sequence-of-pseudoalteromonas-espejiana-dsm9414-t-an-amino-acid-requiring-strain-from-seawater
#16
Jin-Cheng Rong, Qian-Qian Cha, Xue-Bing Ren, Bin-Bin Xie, Xiao-Yan Song
Strain DSM9414, the type strain of Pseudoalteromonas espejiana, is a Gram-negative, and amino-acid-requiring stain isolated from seawater off the coast of Northern California. In this study, we report the complete genome sequence of Pseudoalteromonas espejiana DSM9414T . The genome (4,500,451bp; 40.3% G+C) is composed of two circular chromosomes: chromosome I is 3,720,756bp with 40.4% G+C content and chromosome II is 779,695bp with 39.8% G+C content. Genomic analysis showed that chromosome I encodes a complete set of ABC transporters responsible for branched-chain amino acids, whose homologous proteins were not discovered in other Pseudoalteromonas genomes released...
April 2018: Marine Genomics
https://www.readbyqxmd.com/read/28843847/skin-transcriptomes-of-common-bottlenose-dolphins-tursiops-truncatus-from-the-northern-gulf-of-mexico-and-southeastern-u-s-atlantic-coasts
#17
Marion G Neely, Jeanine S Morey, Paul Anderson, Brian C Balmer, Gina M Ylitalo, Eric S Zolman, Todd R Speakman, Carrie Sinclair, Melannie J Bachman, Kevin Huncik, John Kucklick, Patricia E Rosel, Keith D Mullin, Teri K Rowles, Lori H Schwacke, Frances M Van Dolah
Common bottlenose dolphins serve as sentinels for the health of their coastal environments as they are susceptible to health impacts from anthropogenic inputs through both direct exposure and food web magnification. Remote biopsy samples have been widely used to reveal contaminant burdens in free-ranging bottlenose dolphins, but do not address the health consequences of this exposure. To gain insight into whether remote biopsies can also identify health impacts associated with contaminant burdens, we employed RNA sequencing (RNA-seq) to interrogate the transcriptomes of remote skin biopsies from 116 bottlenose dolphins from the northern Gulf of Mexico and southeastern U...
April 2018: Marine Genomics
https://www.readbyqxmd.com/read/28803857/mapping-of-quantitative-trait-loci-for-temporal-growth-and-age-at-maturity-in-coho-salmon-evidence-for-genotype-by-sex-interactions
#18
Miyako Kodama, Jeffrey J Hard, Kerry A Naish
Phenotypic differences between males and females are ubiquitous throughout the animal kingdom. Therefore, investigating the extent to which sex-dependent genetic effects contribute to phenotypic variation is important in understanding the evolutionary response of each sex to natural and artificial selection. Sex-specific differences in growth patterns and age at sexual maturity have been observed in a number of anadromous salmonid fishes. In these species, faster growing individuals in a given cohort often mature earlier than conspecifics, and earlier maturing individuals are often males...
April 2018: Marine Genomics
https://www.readbyqxmd.com/read/28601440/a-transcriptomic-resource-for-the-northern-krill-meganyctiphanes-norvegica-based-on-a-short-term-temperature-exposure-experiment
#19
Leocadio Blanco-Bercial, Amy E Maas
The northern krill, Meganyctiphanes norvegica, is an important component of the pelagic food web across the North Atlantic. Widespread from the Mediterranean to the Subarctic Atlantic, populations appear to be strongly adapted to local temperatures, and seem to have very little plasticity. The goal of this study was to create and annotate a de novo transcriptome assembly to allow for comparative and physiological studies and to explore the gene expression response of M. norvegica from the Gulf of Maine to two different temperature conditions...
April 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
#20
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...
February 14, 2018: Marine Genomics
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