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Marine Genomics

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https://www.readbyqxmd.com/read/29223543/metagenomic-sequencing-of-environmental-dna-reveals-marine-faunal-assemblages-from-the-west-antarctic-peninsula
#1
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...
December 6, 2017: Marine Genomics
https://www.readbyqxmd.com/read/29198427/towards-the-identification-of-ancestrally-shared-regenerative-mechanisms-across-the-metazoa-a-transcriptomic-case-study-in-the-demosponge-halisarca-caerulea
#2
Nathan J Kenny, Jasper M de Goeij, Didier M de Bakker, Casey G Whalen, Eugene Berezikov, Ana Riesgo
Regeneration is an essential process for all multicellular organisms, allowing them to recover effectively from internal and external injury. This process has been studied extensively in a medical context in vertebrates, with pathways often investigated mechanistically, both to derive increased understanding and as potential drug targets for therapy. Several species from other parts of the metazoan tree of life, including Hydra, planarians and echinoderms, noted for their regenerative capabilities, have previously been targeted for study...
November 29, 2017: Marine Genomics
https://www.readbyqxmd.com/read/29175002/complete-genome-sequence-of-granulosicoccus-antarcticus-type-strain-imcc3135t-a-marine-gammaproteobacterium-with-a-putative-dimethylsulfoniopropionate-demethylase-gene
#3
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...
November 23, 2017: Marine Genomics
https://www.readbyqxmd.com/read/29074263/novel-subfamilies-of-actin-regulating-proteins
#4
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...
October 23, 2017: Marine Genomics
https://www.readbyqxmd.com/read/29031541/how-to-boost-marine-fungal-research-a-first-step-towards-a-multidisciplinary-approach-by-combining-molecular-fungal-ecology-and-natural-products-chemistry
#5
Marlis Reich, Antje Labes
Marine fungi have attracted attention in recent years due to increased appreciation of their functional role in ecosystems and as important sources of new natural products. The concomitant development of various "omic" technologies has boosted fungal research in the fields of biodiversity, physiological ecology and natural product biosynthesis. Each of these research areas has its own research agenda, scientific language and quality standards, which have so far hindered an interdisciplinary exchange. Inter- and transdisciplinary interactions are, however, vital for: (i) a detailed understanding of the ecological role of marine fungi, (ii) unlocking their hidden potential for natural product discovery, and (iii) designing access routes for biotechnological production...
October 11, 2017: Marine Genomics
https://www.readbyqxmd.com/read/28970064/cross-disciplinarity-in-the-advance-of-antarctic-ecosystem-research
#6
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...
September 29, 2017: 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
#7
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...
September 28, 2017: 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
#8
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...
September 22, 2017: Marine Genomics
https://www.readbyqxmd.com/read/28919018/de-novo-transcriptome-assembly-of-the-calanoid-copepod-neocalanus-flemingeri-a-new-resource-for-emergence-from-diapause
#9
Vittoria Roncalli, Matthew C Cieslak, Stephanie A Sommer, Russell R Hopcroft, Petra H Lenz
Copepods, small planktonic crustaceans, are key links between primary producers and upper trophic levels, including many economically important fishes. In the subarctic North Pacific, the life cycle of copepods like Neocalanus flemingeri includes an ontogenetic migration to depth followed by a period of diapause (a type of dormancy) characterized by arrested development and low metabolic activity. The end of diapause is marked by the production of the first brood of eggs. Recent temperature anomalies in the North Pacific have raised concerns about potential negative effects on N...
September 14, 2017: Marine Genomics
https://www.readbyqxmd.com/read/28899645/transcriptome-based-discovery-of-pathways-and-genes-related-to-reproduction-of-the-black-tiger-shrimp-penaeus-monodon
#10
Tanaporn Uengwetwanit, Pattareeya Ponza, Duangjai Sangsrakru, Duangdao Wichadakul, Supawadee Ingsriswang, Rungnapa Leelatanawit, Sirawut Klinbunga, Sithichoke Tangphatsornruang, Nitsara Karoonuthaisiri
The black tiger shrimp (Penaeus monodon) is an aquatic animal with considerable economic importance. Poor reproductive maturation in captivity impedes sustainable aquaculture production of this species. This study aims to provide transcriptomic information on reproductive organs using 454 pyrosequencing technology. The transcriptome analysis of ovaries and testes revealed 41,136 transcripts with 20,192 contigs. We found novel sets of transcripts completing several important reproductive pathways such as gonadotropin-releasing hormone (GnRH) signaling and progesterone-mediated oocyte maturation...
September 9, 2017: Marine Genomics
https://www.readbyqxmd.com/read/28899644/transcriptomics-reveals-tissue-organ-specific-differences-in-gene-expression-in-the-starfish-patiria-pectinifera
#11
Chan-Hee Kim, Hye-Jin Go, Hye Young Oh, Yong Hun Jo, Maurice R Elphick, Nam Gyu Park
Starfish (Phylum Echinodermata) are of interest from an evolutionary perspective because as deuterostomian invertebrates they occupy an "intermediate" phylogenetic position with respect to chordates (e.g. vertebrates) and protostomian invertebrates (e.g. Drosophila). Furthermore, starfish are model organisms for research on fertilization, embryonic development, innate immunity and tissue regeneration. However, large-scale molecular data for starfish tissues/organs are limited. To provide a comprehensive genetic resource for the starfish Patiria pectinifera, we report de novo transcriptome assemblies and global gene expression analysis for six P...
September 9, 2017: Marine Genomics
https://www.readbyqxmd.com/read/28923557/a-molecular-approach-towards-taxonomic-identification-of-elasmobranch-species-from-maltese-fisheries-landings
#12
Adriana Vella, Noel Vella, Sarah Schembri
The mitochondrial genome, through the application of DNA barcoding, provides a powerful tool for identifying species even when specimens are either incomplete or belong to species that exhibit cryptic diversity. In fisheries management accurate identification of whole or part of the specimens landed is a fundamental requirement for the conservation of species affected directly or indirectly by the fisheries activities. In this study cytochrome c oxidase subunit I (COI) and NADH dehydrogenase subunit 2 (ND2) sequences were used to genetically distinguish 36 elasmobranch species collected from Maltese (Central Mediterranean) commercial fisheries landings...
September 8, 2017: 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
#13
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...
September 8, 2017: Marine Genomics
https://www.readbyqxmd.com/read/28888836/transcriptome-sequencing-and-characterization-of-symbiodinium-muscatinei-and-elliptochloris-marina-symbionts-found-within-the-aggregating-sea-anemone-anthopleura-elegantissima
#14
Jason C Macrander, James L Dimond, Brian L Bingham, Adam M Reitzel
There is a growing body of literature using transcriptomic data to study how tropical cnidarians and their photosynthetic endosymbionts respond to environmental stressors and participate in metabolic exchange. Despite these efforts, our understanding of how essential genes function to facilitate symbiosis establishment and maintenance remains limited. The inclusion of taxonomically and ecologically diverse endosymbionts will enhance our understanding of these interactions. Here we characterize the transcriptomes of two very different symbionts found within the temperate sea anemone Anthopleura elegantissima: the chlorophyte Elliptochloris marina and the dinoflagellate Symbiodinium muscatinei...
September 6, 2017: 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...
September 1, 2017: 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 DSM9414(T). 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...
August 28, 2017: 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...
August 23, 2017: Marine Genomics
https://www.readbyqxmd.com/read/28811148/metagenomes-from-deep-baltic-sea-sediments-reveal-how-past-and-present-environmental-conditions-determine-microbial-community-composition
#18
Ian P G Marshall, Søren M Karst, Per H Nielsen, Bo Barker Jørgensen
Microbial communities that lived near the sediment surface in the past become slowly buried and are the source of deep subsurface communities thousands of years later. We used metagenomes to analyse how the composition of buried microbial communities may change to conform to altered environmental conditions at depth. Sediment samples were collected from down to 85m below sea floor during the Integrated Ocean Drilling Program Expedition 347, "Baltic Sea Paleoenvironment". The sediments vary in age, organic carbon content, porewater salinity, and other parameters that reflect the changing Baltic environment from the last ice age and throughout the Holocene...
August 12, 2017: 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
#19
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...
August 10, 2017: Marine Genomics
https://www.readbyqxmd.com/read/28802692/de-novo-transcriptome-assembly-and-rna-seq-expression-analysis-in-blood-from-beluga-whales-of-bristol-bay-ak
#20
Jeanine S Morey, Kathy A Burek Huntington, Michelle Campbell, Tonya M Clauss, Caroline E Goertz, Roderick C Hobbs, Denise Lunardi, Amanda J Moors, Marion G Neely, Lori H Schwacke, Frances M Van Dolah
Assessing the health of marine mammal sentinel species is crucial to understanding the impacts of environmental perturbations on marine ecosystems and human health. In Arctic regions, beluga whales, Delphinapterus leucas, are upper level predators that may serve as a sentinel species, potentially forecasting impacts on human health. While gene expression profiling from blood transcriptomes has widely been used to assess health status and environmental exposures in human and veterinary medicine, its use in wildlife has been limited due to the lack of available genomes and baseline data...
August 9, 2017: Marine Genomics
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