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Marine Genomics

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https://www.readbyqxmd.com/read/29754835/identification-and-expression-analysis-of-long-noncoding-rnas-in-embryogenesis-and-larval-metamorphosis-of-ciona-savignyi
#1
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/29673959/a-200k-snp-chip-reveals-a-novel-pacific-salmon-louse-genotype-linked-to-differential-efficacy-of-emamectin-benzoate
#2
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
#3
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
#4
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/29650372/genomic-signatures-of-parasite-driven-natural-selection-in-north-european-atlantic-salmon-salmo-salar
#5
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...
April 9, 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
#6
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...
March 8, 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
#7
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...
March 3, 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
#8
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...
February 27, 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
#9
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
#10
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/29426805/boveri-s-research-at-the-zoological-station-naples-rediscovery-of-his-original-microscope-slides-at-the-university-of-w%C3%A3-rzburg
#11
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
https://www.readbyqxmd.com/read/29273445/selective-pressure-on-the-protein-coding-genes-of-the-pufferfish-is-correlated-with-phenotypic-traits
#12
Hyeonju Ahn, Chul Lee, Bo-Hye Nam, Eun Bae Kim, Kelsey Caetano-Anolles, Heebal Kim
The pufferfish accumulates neurotoxic tetrodotoxin in its body and inflates by filling its stomach with water. These traits are unique to this species, and may be a result of adaptation post-divergence of Tetraodontidae. However, evolution of the protein-coding genes in the pufferfish has not yet been well elucidated. Detection of positive selection on these genes can help us understand the mechanisms associated with functional evolution. We downloaded well-annotated gene information of two pufferfish species, Takifugu rubripes and Tetraodon nigroviridis, from the public ENSEMBL database...
February 2018: Marine Genomics
https://www.readbyqxmd.com/read/29239804/sex-determination-and-differentiation-genes-in-a-functional-hermaphrodite-scallop-nodipecten-subnodosus
#13
Pavel Galindo-Torres, Alejandra García-Gasca, Raúl Llera-Herrera, Cristina Escobedo-Fregoso, Cei Abreu-Goodger, Ana M Ibarra
The lion-paw, Nodipecten subnodosus is one of three scallop species commercially exploited on the west coast of the Peninsula of Baja California. Because nothing is known about sex determination and sexual differentiation in hermaphrodite scallops, in the present work, a global transcriptomic analysis was performed in two early developmental stages, settling eyed-larvae and spat, as well as in three tissues (undifferentiated gonad, digestive gland, and adductor muscle). Over 27 million Illumina paired-end reads were obtained through the MiSeq platform...
February 2018: Marine Genomics
https://www.readbyqxmd.com/read/29223543/metagenomic-sequencing-of-environmental-dna-reveals-marine-faunal-assemblages-from-the-west-antarctic-peninsula
#14
Dominique A Cowart, Katherine R Murphy, C-H Christina Cheng
The West Antarctic Peninsula (WAP) is the fastest warming region in Antarctica where climate impact on the cold-adapted marine ecosystem is already visible. To monitor faunal changes in remote vast bodies of Antarctic waters, efficient and informative tools are essential. High-throughput sequencing of environmental DNA (eDNA) has emerged as one such tool for monitoring biodiversity and ecosystems, as it increases detection sensitivity of taxa, and sampling is often simpler and less costly than traditional collection methods...
February 2018: Marine Genomics
https://www.readbyqxmd.com/read/29175002/complete-genome-sequence-of-granulosicoccus-antarcticus-type-strain-imcc3135-t-a-marine-gammaproteobacterium-with-a-putative-dimethylsulfoniopropionate-demethylase-gene
#15
Ilnam Kang, Yeonjung Lim, Jang-Cheon Cho
Granulosicoccus, the only genus of the family Granulosicoccaceae, occupies a distinct phylogenetic position within the order Chromatiales of the Gammaproteobacteria. The genus has been found in various marine regions, especially associated with diverse marine macroalgae. No genomes have been reported for the genus Granulosicoccus thus far, hampering studies on physiology and lifestyles of this genus. Here we report the complete genome sequence of strain IMCC3135T , the type strain of Granulosicoccus antarcticus isolated from Antarctic coastal seawater...
February 2018: Marine Genomics
https://www.readbyqxmd.com/read/29074263/novel-subfamilies-of-actin-regulating-proteins
#16
A A Morozov, Ye D Bedoshvili, M S Popova, Ye V Likhoshway
Ability of actin to polymerise and depolymerise makes it essential to key functions of eukaryotic cell. The functioning of actin is controlled by a host of regulatory proteins, the repertoire of which in diatoms is known to remarkably differ from other organisms. We have performed a phylogenetic analysis of 521 actin and actin-related proteins' aminoacid sequences, as well as 190 sequences of gelsolin family proteins from various genomic and transcriptomic datasets. Based on the results of this analysis, as well as on the presence of clade-specific indels in some of the actin-related proteins, we describe a novel ARP subfamily, dubbed ARP12, which is specific to heterokonts and related organisms...
February 2018: Marine Genomics
https://www.readbyqxmd.com/read/28970064/cross-disciplinarity-in-the-advance-of-antarctic-ecosystem-research
#17
REVIEW
J Gutt, E Isla, A N Bertler, G E Bodeker, T J Bracegirdle, R D Cavanagh, J C Comiso, P Convey, V Cummings, R De Conto, D De Master, G di Prisco, F d'Ovidio, H J Griffiths, A L Khan, J López-Martínez, A E Murray, U N Nielsen, S Ott, A Post, Y Ropert-Coudert, T Saucède, R Scherer, S Schiaparelli, I R Schloss, C R Smith, J Stefels, C Stevens, J M Strugnell, S Trimborn, C Verde, E Verleyen, D H Wall, N G Wilson, J C Xavier
The biodiversity, ecosystem services and climate variability of the Antarctic continent and the Southern Ocean are major components of the whole Earth system. Antarctic ecosystems are driven more strongly by the physical environment than many other marine and terrestrial ecosystems. As a consequence, to understand ecological functioning, cross-disciplinary studies are especially important in Antarctic research. The conceptual study presented here is based on a workshop initiated by the Research Programme Antarctic Thresholds - Ecosystem Resilience and Adaptation of the Scientific Committee on Antarctic Research, which focussed on challenges in identifying and applying cross-disciplinary approaches in the Antarctic...
February 2018: Marine Genomics
https://www.readbyqxmd.com/read/28964713/circadian-signaling-in-the-northern-krill-meganyctiphanes-norvegica-in-silico-prediction-of-the-protein-components-of-a-putative-clock-system-using-a-publicly-accessible-transcriptome
#18
Andrew E Christie, Andy Yu, Micah G Pascual
The Northern krill Meganyctiphanes norvegica is a significant component of the zooplankton community in many regions of the North Atlantic Ocean. In the areas it inhabits, M. norvegica is of great importance ecologically, as it is both a major consumer of phytoplankton/small zooplankton and is a primary food source for higher-level consumers. One behavior of significance for both feeding and predator avoidance in Meganyctiphanes is diel vertical migration (DVM), i.e., a rising from depth at dusk and a return to depth at dawn...
February 2018: Marine Genomics
https://www.readbyqxmd.com/read/28958500/using-rna-seq-to-determine-patterns-of-sex-bias-in-gene-expression-in-the-brain-of-the-sex-role-reversed-gulf-pipefish-syngnathus-scovelli
#19
Andria P Beal, F Douglas Martin, Matthew C Hale
Sex-bias in gene expression is a widespread mechanism for controlling the development of phenotypes that differ between males and females. Most studies on sex-bias in gene expression have focused on species that exhibit traditional sex-roles (male-male competition and female parental care). By contrast the Syngnathid fishes (sea horses, pipefish, and sea dragons) are a group of organisms where many species exhibit male brooding and sex-role reversal (female-female competition for mates and paternal parental care), and little is known about how patterns of sex-bias in gene expression vary in species with sex-role reversal...
February 2018: Marine Genomics
https://www.readbyqxmd.com/read/28923556/de-novo-assembly-and-transcriptome-characterization-of-the-freshwater-prawn-palaemonetes-argentinus-implications-for-a-detoxification-response
#20
C Fernando García, Nicolas Pedrini, Arturo Sánchez-Paz, Carlos S Reyna-Blanco, Sabrina Lavarias, Adriana Muhlia-Almazán, Analía Fernández-Giménez, Aldana Laino, Enrique de-la-Re-Vega, German Lukaszewicz, Alonso A López-Zavala, Luis G Brieba, Michael F Criscitello, Jesús S Carrasco-Miranda, Karina D García-Orozco, Adrian Ochoa-Leyva, Enrique Rudiño-Piñera, Alejandro Sanchez-Flores, Rogerio R Sotelo-Mundo
Palaemonetes argentinus, an abundant freshwater prawn species in the northern and central region of Argentina, has been used as a bioindicator of environmental pollutants as it displays a very high sensitivity to pollutants exposure. Despite their extraordinary ecological relevance, a lack of genomic information has hindered a more thorough understanding of the molecular mechanisms potentially involved in detoxification processes of this species. Thus, transcriptomic profiling studies represent a promising approach to overcome the limitations imposed by the lack of extensive genomic resources for P...
February 2018: Marine Genomics
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