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Marine Genomics

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https://www.readbyqxmd.com/read/28522160/complete-genome-of-a-metabolically-diverse-marine-bacterium-shewanella-japonica-kctc-22435-t
#1
Kyung Mo Kim, Hanna Choe, Byung Kwon Kim, Arshan Nasir
Shewanella japonica KCTC 22435(T) is a facultatively anaerobic, Gram-negative, mesophilic, rod-shaped bacterium isolated from sea water at the Pacific Institute of Bio-organic Chemistry of the Marine Experimental Station, Troitza Bay, Gulf of Peter the Great, Russia. Here, we report the complete genome of S. japonica KCTC 22435(T), which consists of 4,975,677bp (G+C content of 40.80%) with a single chromosome, 4036 protein-coding genes, 97 tRNAs and 8 rRNA operons. Genes detected in the genome reveal that the strain possesses a type II secretion system, cytochrome c family proteins with various numbers of heme-binding motifs, and metabolic pathways for utilizing diverse carbon sources, supporting the potential of KCTC 22435(T) to generate electricity in salinity culture conditions...
May 15, 2017: Marine Genomics
https://www.readbyqxmd.com/read/28479280/pelagic-and-benthic-communities-of-the-antarctic-ecosystem-of-potter-cove-genomics-and-ecological-implications
#2
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...
May 4, 2017: Marine Genomics
https://www.readbyqxmd.com/read/28478932/transcriptome-response-of-previtellogenic-ovary-in-anguilla-japonica-after-artificial-hormone-injection
#3
Shang-Chien Lee, Chung-Der Hsiao, Yung-Song Wang, Show-Wan Lou
In this study we investigate the intra-ovarian pathways underlying early follicle development in Japanese eels, Anguilla japonica. We conducted high-throughput transcriptome analyses in the initial development of the ovary via the next-generation sequencing (NGS). Japanese eels were treated with three weekly salmon pituitary homogenate (SPH) injections. Using RNA-seq, we obtained 29,117,237 and 41,867,557 reads from the control and the SPH-injected groups, respectively. Combining these RNA-seq datasets, we acquired a total of 101,711 unigenes (N50=1,517bp) after performing de novo assembly...
May 3, 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
#4
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...
May 2, 2017: Marine Genomics
https://www.readbyqxmd.com/read/28395865/metabolism-of-branched-chain-amino-acids-revealed-by-transcriptome-analysis-in-vibrio-alginolyticus
#5
Yiqin Deng, Xiongqi Ding, Xiaochun Huang, Yiying Yang, Chang Chen
Branched-chain amino acids (BCAAs) play important roles in nitrogen metabolism. However, little is known about the metabolism of BCAAs in the fish pathogen Vibrio alginolyticus. In this study, the global gene expression patterns of V. alginolyticus ZJ-T cultured in M63 minimal medium supplemented with ammonium sulfate or with three BCAAs (isoleucine, leucine and valine) as nitrogen source were evaluated by transcriptome analysis. The results revealed that 311 genes are up-regulated (|log2(Fold Change)|>1), which are involved in the pathways of flagellar assembly, bacterial chemotaxis and oxidative phosphorylation etc, and meanwhile 251 genes are down-regulated, which are involved in the pathways of BCAAs biosynthesis, selenocompound metabolism and C5-branced dibasic acid metabolism etc...
April 5, 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
#6
E E Malandrakis, O Dadali, M Kavouras, T Danis, P Panagiotaki, H Miliou, F C Kuepper, 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...
April 4, 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
#7
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...
April 3, 2017: Marine Genomics
https://www.readbyqxmd.com/read/28283424/modelling-plankton-ecosystems-in-the-meta-omics-era-are-we-ready
#8
REVIEW
Krzysztof Franciszek Stec, Luigi Caputi, Pier Luigi Buttigieg, Domenico D'Alelio, Federico Matias Ibarbalz, Matthew B Sullivan, Samuel Chaffron, Chris Bowler, Maurizio Ribera d'Alcalà, Daniele Iudicone
Recent progress in applying meta-omics approaches to the study of marine ecosystems potentially allows scientists to study the genetic and functional diversity of plankton at an unprecedented depth and with enhanced precision. However, while a range of persistent technical issues still need to be resolved, a much greater obstacle currently preventing a complete and integrated view of the marine ecosystem is the absence of a clear conceptual framework. Herein, we discuss the knowledge that has thus far been derived from conceptual and statistical modelling of marine plankton ecosystems, and illustrate the potential power of integrated meta-omics approaches in the field...
March 7, 2017: Marine Genomics
https://www.readbyqxmd.com/read/28258924/in-depth-transcriptome-analysis-of-larimichthys-polyactis-de-novo-assembly-functional-annotation
#9
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...
February 28, 2017: Marine Genomics
https://www.readbyqxmd.com/read/28237778/genome-of-a-giant-bacteriophage-from-a-decaying-trichodesmium-bloom
#10
Ulrike Pfreundt, Dina Spungin, Shengwei Hou, Björn Voß, Ilana Berman-Frank, Wolfgang R Hess
De-novo assembly of a metagenomic dataset obtained from a decaying cyanobacterial Trichodesmium bloom from the New Caledonian lagoon resulted in a complete giant phage genome of 257,908bp, obtained independently with multiple assembly tools. Noteworthy, gammaproteobacteria were an abundant fraction in the sequenced samples. Mapping of the raw reads with 99% accuracy to the giant phage genome resulted in an average coverage of 262X. The closest sequenced relatives, albeit still distant, are the Pseudomonas phages PaBG from Lake Baikal and Lu11 isolated from a soil sample from the Philippines...
February 22, 2017: Marine Genomics
https://www.readbyqxmd.com/read/28188115/differential-mantle-transcriptomics-and-characterization-of-growth-related-genes-in-the-diploid-and-triploid-pearl-oyster-pinctada-fucata
#11
Yunyan Guan, Maoxian He, Houbo Wu
To explore the molecular mechanism of triploidy effect in the pearl oyster Pinctada fucata, two RNA-seq libraries were constructed from the mantle tissue of diploids and triploids by Roche-454 massive parallel pyrosequencing. The identification of differential expressed genes (DEGs) between diploid and triploid may reveal the molecular mechanism of triploidy effect. In this study, 230 down-regulated and 259 up-regulated DEGs were obtained by comparison between diploid and triploid libraries. The gene ontology and KEGG pathway analysis revealed more functional activation in triploids and it may due to the duplicated gene expression in transcriptional level during whole genome duplication (WGD)...
February 7, 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
#12
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...
February 6, 2017: Marine Genomics
https://www.readbyqxmd.com/read/28169128/population-genomics-reveals-high-gene-flow-in-grass-rockfish-sebastes-rastrelliger
#13
Edith Martinez, Vincent Buonaccorsi, John R Hyde, Andres Aguilar
Variation at the genomic level is important for understanding a species' demographic and phylogenetic history, in addition to identifying candidate regions that may be under selection and important to local adaptation. We used restriction-site associated DNA (RAD) sequencing to sample single nucleotide polymorphisms (SNPs) from the grass rockfish genome (Sebastes rastrelliger) to assess range-wide patterns of population structure and test for signatures of selection (i.e. outlier loci). Two different filtering criteria yielded 6572 and 10,393 SNPs that were genotyped in over 70% of 110 individuals from six sampling areas using RAD loci...
February 4, 2017: Marine Genomics
https://www.readbyqxmd.com/read/27330039/nfat5-genes-are-part-of-the-osmotic-regulatory-system-in-atlantic-salmon-salmo-salar
#14
Marlene Lorgen, Even H Jorgensen, William C Jordan, Samuel A M Martin, David G Hazlerigg
The anadromous Atlantic salmon utilizes both fresh and salt water (FW and SW) habitats during its life cycle. The parr-smolt transformation (PST) is an important developmental transition from a FW adapted juvenile parr to a SW adapted smolt. Physiological changes in osmoregulatory tissues, particularly the gill, are key in maintaining effective ion regulation during PST. Changes are initiated prior to SW exposure (preparative phase), and are completed when smolts enter the sea (activational phase) where osmotic stress may directly stimulate changes in gene expression...
February 2017: Marine Genomics
https://www.readbyqxmd.com/read/28111206/de-novo-assembly-and-characterization-of-the-transcriptome-of-the-newly-described-dinoflagellate-ansanella-granifera-spotlight-on-flagellum-associated-genes
#15
Se Hyeon Jang, Hae Jin Jeong, Jae Kyung Chon, Sung Yeon Lee
Many dinoflagellates are known to cause red tides and often outgrow non-motile diatoms and motile small flagellates through active vertical migration between well-lit surface and eutrophic deep waters and/or by locating and ingesting prey cells. Their flagella play important roles in these two critical behaviors. However, the structural and functional genes of dinoflagellate flagella are very little known. Thus, a de novo assembly and characterization of the transcriptome of the fast-swimming dinoflagellate Ansanella granifera were conducted and its flagellum genes were compared with those of other dinoflagellates, motile small flagellates, and non-motile protist species...
January 19, 2017: Marine Genomics
https://www.readbyqxmd.com/read/28089489/long-non-coding-rnas-are-associated-with-spatiotemporal-gene-expression-profiles-in-the-marine-gastropod-tegula-atra
#16
Camille Détrée, Gustavo Núñez-Acuña, Fabian Tapia, Cristian Gallardo-Escárate
Increasing evidence suggests that long non-coding RNAs (lncRNAs) play diverse roles in cellular processes, including in the regulation of embryogenesis and growth. However, little is known about the role of lncRNAs in marine invertebrates inhabiting changing environments. Therefore, the aim of this study was to present the first characterization of lncRNAs in an intertidal marine gastropod. Specifically, Tegula atra individuals were sampled in four sites of the central-northern Chilean coastline (28-31°) during summer and winter...
January 12, 2017: Marine Genomics
https://www.readbyqxmd.com/read/28089131/transcriptome-wide-identification-and-functional-investigation-of-circular-rna-in-the-teleost-large-yellow-croaker-larimichthys-crocea
#17
Shuangbin Xu, Shijun Xiao, Changliang Qiu, Zhiyong Wang
Circular RNA (circRNA) was first reported over thirty years ago. With the development of high-throughput sequencing technologies, circRNA has been identified in an increasing number of species. However, few studies on circRNA have been reported in teleost fish. Accumulating transcriptome and phenotype data enable us to probe the biological functions of circRNA in fish species. Here, we report the identification of circRNAs from RNA sequencing (RNA-seq) data in large yellow croaker (Larimichthys crocea), a commercially important marine fish in China and East Asia...
January 6, 2017: Marine Genomics
https://www.readbyqxmd.com/read/28063828/genome-wide-computational-analysis-of-the-secretome-of-brown-algae-phaeophyceae
#18
Makoto Terauchi, Takahiro Yamagishi, Takeaki Hanyuda, Hiroshi Kawai
Brown algae have evolved complex multicellularity in the heterokont lineage. They are phylogenetically distant to land plants, fungi and animals. Especially, the members of Laminariales (so-called kelps) have developed highly differentiated tissues. Extracellular matrix (ECM) plays pivotal roles in a number of essential processes in multicellular organisms, such as cell adhesion, cell and tissue differentiations, cell-to-cell communication, and responses to environmental stimuli. In these processes, a set of extracellular secreted proteins called the secretome operates remodeling of the physicochemical nature of ECM and signal transduction by interacting with cell surface proteins and signaling molecules...
January 4, 2017: Marine Genomics
https://www.readbyqxmd.com/read/28063827/taxonomic-and-functional-diversity-of-a-coastal-planktonic-bacterial-community-in-a-river-influenced-marine-area
#19
Stefan Thiele, Michael Richter, Cecilia Balestra, Frank Oliver Glöckner, Raffaella Casotti
The Gulf of Naples is a dynamical area with intense exchanges between offshore oligotrophic and coastal eutrophic waters with frequent freshwater inputs. The Sarno River, one of the most polluted rivers in Europe, strongly contributes to the pollution of the area, discharging high amounts of heavy metals and organic wastes from heavily cultivated and industrial areas. This paper reports on the diversity and community structure of the marine residential Bacteria and Archaea of the Gulf of Naples in an area close to the river Sarno plume and investigates their small-scale taxonomic diversity and expression patterns as a proxy of potential metabolic activity using metagenomics and metatranscriptomics...
January 4, 2017: Marine Genomics
https://www.readbyqxmd.com/read/28007524/microbial-metatranscriptomes-from-the-thermally-stratified-gulf-of-aqaba-eilat-during-summer
#20
Dan R Miller, Ulrike Pfreundt, Hila Elifantz, Wolfgang R Hess, Ilana Berman-Frank
The water column in the oligotrophic Gulf of Aqaba/Eilat experiences distinct seasonal cycles with the cooling air and water temperatures of late fall and winter destabilizing the thermocline and forming mixed layer depths reaching 300 to 700m. As air temperatures warm thermal re-stratification results in a stable thermocline throughout the summer which physically separates a photic, nutrient-poor surface layer from an aphotic, nutrient-rich deep layer. Here we present the first metatranscriptome dataset, and its taxonomic assignments, sampled from three depths of the 700m deep Station A in the Gulf of Aqaba during the summer stratification (surface - 10m, deep chlorophyll maximum (DCM) - 85m, deep aphotic zone -500m)...
December 19, 2016: Marine Genomics
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