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Marine Genomics

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https://www.readbyqxmd.com/read/28811148/metagenomes-from-deep-baltic-sea-sediments-reveal-how-past-and-present-environmental-conditions-determine-microbial-community-composition
#1
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
#2
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
#3
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
https://www.readbyqxmd.com/read/28802691/the-genome-analysis-of-oleiphilus-messinensis-me102-dsm-13489-t-reveals-backgrounds-of-its-obligate-alkane-devouring-marine-lifestyle
#4
Stepan V Toshchakov, Alexei A Korzhenkov, Tatyana N Chernikova, Manuel Ferrer, Olga V Golyshina, Michail M Yakimov, Peter N Golyshin
Marine bacterium Oleiphilus messinensis ME102 (DSM 13489(T)) isolated from the sediments of the harbor of Messina (Italy) is a member of the order Oceanospirillales, class Gammaproteobacteria, representing the physiological group of marine obligate hydrocarbonoclastic bacteria (OHCB) alongside the members of the genera Alcanivorax, Oleispira, Thalassolituus, Cycloclasticus and Neptunomonas. These organisms play a crucial role in the natural environmental cleanup in marine systems. Despite having the largest genome (6...
August 9, 2017: Marine Genomics
https://www.readbyqxmd.com/read/28734733/diatom-frustule-morphogenesis-and-function-a-multidisciplinary-survey
#5
REVIEW
Edoardo De Tommasi, Johan Gielis, Alessandra Rogato
Diatoms represent the major component of phytoplankton and are responsible for about 20-25% of global primary production. Hundreds of millions of years of evolution led to tens of thousands of species differing in dimensions and morphologies. In particular, diatom porous silica cell walls, the frustules, are characterized by an extraordinary, species-specific diversity. It is of great interest, among the marine biologists and geneticists community, to shed light on the origin and evolutionary advantage of this variability of dimensions, geometries and pore distributions...
July 19, 2017: Marine Genomics
https://www.readbyqxmd.com/read/28689690/genome-analysis-of-three-novel-lytic-vibrio-coralliilyticus-phages-isolated-from-seawater-okinawa-japan
#6
Chitra Ramphul, Beatriz Estela Casareto, Hideo Dohra, Tomohiro Suzuki, Katsuhiko Yoshimatsu, Koichi Yoshinaga, Yoshimi Suzuki
Three novel Vibrio phages were isolated from seawater in Okinawa. The Vibrio phage RYC infected Vibrio coralliilyticus SWA 07, while Vibrio phages CKB-S1 and CKB-S2 infected the coral pathogen V. coralliilyticus P1 (LMG 23696). The Vibrio phages CKB-S1 and CKB-S2 displayed head-tail structures whereas the Vibrio phage RYC showed a tailless non-enveloped capsid. All these Vibrio phages contained linear and double-stranded DNA. The whole genome sequencing revealed that Vibrio phage RYC has a larger genome size compared to Vibrio phages CKB-S1 and CKB-S2, and six tRNAs genes were found only in Vibrio phage RYC...
July 6, 2017: Marine Genomics
https://www.readbyqxmd.com/read/28625778/analysis-of-phytoplankton-assemblage-structure-in-the-mediterranean-sea-based-on-high-throughput-sequencing-of-partial-18s-rrna-sequences
#7
Antonella Penna, Silvia Casabianca, Antonio Fernandez Guerra, Cristiano Vernesi, Michele Scardi
Studying taxonomic and ecological diversity of phytoplankton assemblages is often difficult because morphological analysis cannot provide a complete description of their composition. Therefore, more robust and feasible approaches have to be chosen to elucidate the interactions between environmental and human pressures and phytoplankton assemblages. The Ocean Sampling Day (OSD) allowed collecting seawater samples from a wide range of oceanic regions including the Mediterranean Sea. In this study, a total of 754,167 V4-18S ribosomal DNA (rDNA) metabarcodes derived from 20 plankton samples collected at 19 sampling sites across the coastal areas of the Mediterranean Sea were analyzed to explore the relationships between phytoplankton assemblages' composition, sub-regional environmental features and human pressures...
June 15, 2017: Marine Genomics
https://www.readbyqxmd.com/read/28602510/population-genetics-of-the-deep-sea-bluntnose-sixgill-shark-hexanchus-griseus-revealing-spatial-genetic-heterogeneity
#8
Noel Vella, Adriana Vella
Hexanchus griseus is a globally distributed deep-water shark species. It inhabits tropical and temperate waters throughout the world, including the Mediterranean Sea where it is by-caught by small-scale fisheries in the region. In this study, we analysed the genetic variation of H. griseus specimens collected from different areas within and outside the Mediterranean region, to assess its genetic connectivity. The mitochondrial DNA (mtDNA) sequence analysed in this study ranged from cytochrome b to 16S rRNA genes including the control region, the 12S rRNA gene and the interspersed tRNA genes in the region, covering a total of 3731 to 3914 nucleotides...
June 8, 2017: 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
#9
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...
June 7, 2017: Marine Genomics
https://www.readbyqxmd.com/read/28595872/distribution-and-diversity-of-marine-picocyanobacteria-community-targeting-of-prochlorococcus-ecotypes-in-winter-conditions-southern-adriatic-sea
#10
Ivana Babić, Ines Petrić, Sunčica Bosak, Hrvoje Mihanović, Iris Dupčić Radić, Zrinka Ljubešić
Adriatic, the northernmost part of the Mediterranean Sea, due its oligotrophy, topography, and hydrology dynamics, and complex circulation patterns, was suggested as an important study site for rapid climatology impacts. Its southern part is mainly oligotrophic and dominated by picophytoplankton, with cyanobacteria as main representatives. Diversity and distribution patterns of different Prochlorococcus ecotypes were investigated by molecular tools and flow cytometry during the winter convection event in the southern Adriatic (BIOTA winter cruise; February/March 2015)...
June 5, 2017: Marine Genomics
https://www.readbyqxmd.com/read/28578827/a-phylogenetic-framework-for-the-kingdom-fungi-based-on-18s-rrna-gene-sequences
#11
Pablo Yarza, Pelin Yilmaz, Katrin Panzer, Frank Oliver Glöckner, Marlis Reich
The usage of molecular phylogenetic approaches is critical to advance the understanding of systematics and community processes in the kingdom Fungi. Among the possible phylogenetic markers (or combinations of them), the 18S rRNA gene appears currently as the most prominent candidate due to its large availability in public databases and informative content. The purpose of this work was the creation of a reference phylogenetic framework that can serve as ready-to-use package for its application on fungal classification and community analysis...
May 31, 2017: Marine Genomics
https://www.readbyqxmd.com/read/28566222/tissue-specific-transcriptomic-profiling-provides-new-insights-into-the-reproductive-ecology-and-biology-of-the-iconic-seagrass-species-posidonia-oceanica
#12
Laura Entrambasaguas, Marlene Jahnke, Elio Biffali, Marco Borra, Remo Sanges, Lázaro Marín-Guirao, Gabriele Procaccini
Seagrasses form extensive meadows in shallow coastal waters and are among the world's most productive ecosystems. Seagrasses can produce both clonally and sexually, and flowering has long been considered infrequent, but important for maintaining genetically diverse stands. Here we investigate the molecular mechanisms involved in flowering of the seagrass Posidonia oceanica, an iconic species endemic to the Mediterranean. We generated a de novo transcriptome of this non-model species for leaf, male and female flower tissue of three individuals, and present molecular evidence for genes that may be involved in the flowering process and on the reproductive biology of the species...
May 26, 2017: Marine Genomics
https://www.readbyqxmd.com/read/28648476/constraint-based-metabolic-modelling-of-marine-microbes-and-communities
#13
REVIEW
Marco Fondi, Renato Fani
Constraint-based metabolic modelling (CBMM) consists in the use of computational methods and tools to perform genome-scale simulations and predict metabolic features at the whole cellular level. This approach is rapidly expanding in microbiology, as it combines reliable predictive abilities with conceptually and technically simple frameworks. Among the possible outcomes of CBMM, the capability to i) guide a focused planning of metabolic engineering experiments and ii) provide a system-level understanding of (single or community-level) microbial metabolic circuits also represent primary aims in present-day marine microbiology...
August 2017: Marine Genomics
https://www.readbyqxmd.com/read/28545861/characterization-of-autonomous-families-of-tc1-mariner-transposons-in-neoteleost-genomes
#14
Bo Gao, Wei Chen, Dan Shen, Saisai Wang, Cai Chen, Li Zhang, Wei Wang, Xiaoyan Wang, Chengyi Song
We report the comprehensive analysis of Tc1/mariner transposons in six species of neoteleost (cod, tetraodon, fugu, medaka, stickleback, and tilapia) for which draft sequences are available. In total, 33 Tc1/mariner families were identified in these neoteleost genomes, with 3-7 families in each species. Thirty of these are in full length and designed as autonomous families, and were classified into the DD34E (Tc1) and DD×D (pogo) groups. The DD34E (Tc1) group was further classified into five clusters (Passport-like, SB-like, Frog Prince-like, Minos-like, and Bari-like)...
August 2017: Marine Genomics
https://www.readbyqxmd.com/read/28476580/comparative-profiling-of-microbial-community-of-three-economically-important-fishes-reared-in-sea-cages-under-tropical-offshore-environment
#15
M K Rasheeda, Vijaya Raghavan Rangamaran, Senthilkumar Srinivasan, Sendhil Kumar Ramaiah, Rajaprabhu Gunasekaran, Santhanakumar Jaypal, Dharani Gopal, Kirubagaran Ramalingam
The present study was undertaken to evaluate the microbial composition of farmed cobia pompano and milkfish, reared in sea-cages by culture-independent methods. This study would serve as a basis for assessing the general health of fish, identifying the dominant bacterial species present in the gut for future probiotic work and in early detection of potential pathogens. High-throughput sequencing of V3-V4 hyper variable regions of 16S rDNA on Illumina MiSeq platform facilitated unravelling of composite bacterial population...
August 2017: Marine Genomics
https://www.readbyqxmd.com/read/28389176/identification-of-the-abiotic-stress-related-transcription-in-little-neptune-grass-cymodocea-nodosa-with-rna-seq
#16
E Malandrakis, O Dadali, M Kavouras, T Danis, P Panagiotaki, H Miliou, S Tsioli, S Orfanidis, F C Küpper, A Exadactylos
Seagrasses exhibit vital ecological roles in the marine environment. Nevertheless, the genomic resources available for seagrasses are still scarce. In the present study, the transcriptome of Cymodocea nodosa was sequenced with a view to study the molecular mechanisms underlying abiotic stress responses. The sequenced transcriptome for the species was near-complete and a high percentage of the transcripts was computationally annotated. An experimental simulation of marine plant exposure to extreme temperature (34°C), salinity (50psu) and their combination was conducted...
August 2017: Marine Genomics
https://www.readbyqxmd.com/read/28385518/assembly-of-a-reference-transcriptome-for-the-gymnosome-pteropod-clione-limacina-and-profiling-responses-to-short-term-co2-exposure
#17
Ali A Thabet, Amy E Maas, Samy A Saber, Ann M Tarrant
The gymnosome (unshelled) pteropod Clione limacina is a pelagic predatory mollusc found in polar and sub-polar regions. It has been studied for its distinctive swimming behavior and as an obligate predator on the closely related thecosome (shelled) pteropods. As concern about ocean acidification increases, it becomes useful to compare the physiological responses of closely-related calcifying and non-calcifying species to acidification. The goals of this study were thus to generate a reference transcriptome for Clione limacina, to expose individuals to CO2 for a period of 3days, and to explore differential patterns of gene expression...
August 2017: Marine Genomics
https://www.readbyqxmd.com/read/28185799/exploring-single-nucleotide-polymorphism-snp-microsatellite-ssr-and-differentially-expressed-genes-in-the-jellyfish-rhopilema-esculentum-by-transcriptome-sequencing
#18
Yunfeng Li, Zunchun Zhou, Meilin Tian, Yi Tian, Ying Dong, Shilei Li, Weidong Liu, Chongbo He
In this study, single nucleotide polymorphism (SNP), microsatellite (SSR) and differentially expressed genes (DEGs) in the oral parts, gonads, and umbrella parts of the jellyfish Rhopilema esculentum were analyzed by RNA-Seq technology. A total of 76.4 million raw reads and 72.1 million clean reads were generated from deep sequencing. Approximately 119,874 tentative unigenes and 149,239 transcripts were obtained. A total of 1,034,708 SNP markers were detected in the three tissues. For microsatellite mining, 5088 SSRs were identified from the unigene sequences...
August 2017: Marine Genomics
https://www.readbyqxmd.com/read/28479280/pelagic-and-benthic-communities-of-the-antarctic-ecosystem-of-potter-cove-genomics-and-ecological-implications
#19
REVIEW
D Abele, S Vazquez, A G J Buma, E Hernandez, C Quiroga, C Held, S Frickenhaus, L Harms, J L Lopez, E Helmke, W P Mac Cormack
Molecular technologies are more frequently applied in Antarctic ecosystem research and the growing amount of sequence-based information available in databases adds a new dimension to understanding the response of Antarctic organisms and communities to environmental change. We apply molecular techniques, including fingerprinting, and amplicon and metagenome sequencing, to understand biodiversity and phylogeography to resolve adaptive processes in an Antarctic coastal ecosystem from microbial to macrobenthic organisms and communities...
June 2017: Marine Genomics
https://www.readbyqxmd.com/read/28258924/in-depth-transcriptome-analysis-of-larimichthys-polyactis-de-novo-assembly-functional-annotation
#20
Lian-Wei Liu, You-Zhen Sui, Wen-Bin Zhu, Ai Guo, Kai-Da Xu, Yong-Dong Zhou
Larimichthys polyactis (small yellow croaker) is a commercially important marine benthic fish, and is the main catching target of fisheries in China, Japan and Korea. Researches across different fields have progressed the understanding of this species; however, no genomics studies of this fish have been reported so far. In this study, we performed de novo transcriptome sequencing of eight cDNA libraries from brain, gill, heart, intestine, liver, muscle, ovary, and testis tissues of L. polyactis. A total of 182,227,948 paired-end reads (>200bp) were generated, from which 134,439 transcripts were assembled...
June 2017: Marine Genomics
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