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Marine Genomics

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https://www.readbyqxmd.com/read/28089489/long-non-coding-rnas-are-associated-with-spatiotemporal-gene-expression-profiles-in-the-marine-gastropod-tegula-atra
#1
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
#2
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
#3
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
#4
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
#5
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
https://www.readbyqxmd.com/read/27932275/complete-genome-sequence-of-serinicoccus-sp-jlt9-an-actinomycete-isolated-from-the-shallow-sea-hydrothermal-system
#6
Yu Han, Dan Lin, Liwei Yu, Xiaofeng Chen, Jia Sun, Kai Tang
Serinicoccus sp. JLT9 was a novel rare actinomycete, isolated from the shallow-sea hydrothermal system. Here, we present the complete genome sequence of Serinicoccus sp. JLT9, which consists of 3,610,932bp with a GC content of 72.43%. The genome data provides insight into microbial adaption to the shallow-sea hydrothermal system and facilitates the discovery of natural compounds in the future.
December 5, 2016: Marine Genomics
https://www.readbyqxmd.com/read/27867038/comparative-mitogenomic-analysis-of-three-species-of-periwinkles-littorina-fabalis-l-obtusata-and-l-saxatilis
#7
João P Marques, Graciela Sotelo, Tomas Larsson, Kerstin Johannesson, Marina Panova, Rui Faria
The flat periwinkles, Littorina fabalis and L.obtusata, offer an interesting system for local adaptation and ecological speciation studies. In order to provide genomic resources for these species, we sequenced their mitogenomes together with that of the rough periwinkle L.saxatilis by means of next-generation sequencing technologies. The three mitogenomes present the typical repertoire of 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes and a putative control region. Although the latter could not be fully recovered in flat periwinkles using short-reads due to a highly repetitive fragment, in L...
November 17, 2016: Marine Genomics
https://www.readbyqxmd.com/read/27843115/de-novo-transcriptome-analysis-of-the-red-seaweed-gracilaria-chilensis-and-identification-of-linkers-associated-with-phycobilisomes
#8
María Alejandra Vorphal, Cristian Gallardo-Escárate, Valentina Valenzuela-Muñoz, Jorge Dagnino-Leone, José Aleikar Vásquez, José Martínez-Oyanedel, Marta Bunster
This work reports the results of the Illumina RNA-Seq of a wild population of female haploid plants of Gracilaria chilensis (Bird et al., 1986) (Rhodophyta, Gigartinalis). Most transcripts were de novo assembled in 12,331 contigs with an average length of 1756bp, showing that 96.64% of the sequences were annotated with known proteins. In particular, the identification of linker proteins of phycobilisomes (PBS) is reported. Linker proteins have primary been identified in cyanobacteria but the information available about them in eukaryotic red alga is not complete, and this is the first report in G...
November 11, 2016: Marine Genomics
https://www.readbyqxmd.com/read/27810366/comparative-transcriptome-analyses-of-a-mangrove-tree-sonneratia-caseolaris-and-its-non-mangrove-relatives-trapa-bispinosa-and-duabanga-grandiflora
#9
Jianfang Li, Yuchen Yang, Shuhuan Yang, Zhang Zhang, Sufang Chen, Cairong Zhong, Renchao Zhou, Suhua Shi
Mangroves are a group of unique plants anchoring in and well adapting to the extreme intertidal environment with high salinity, hypoxia and high temperature and ultraviolet (UV) radiation. Sonneratia caseolaris is a major mangrove tree widely distributed across the West-Indo Pacific region, however the genetic mechanisms of its adaptive evolution are still unclear. In the present study, we performed comparative transcriptome analyses between S. caseolaris and its two non-mangrove relatives, Trapa bispinosa and Duabanga grandiflora, to better understand the evolutionary adaptation of S...
October 31, 2016: Marine Genomics
https://www.readbyqxmd.com/read/27988070/marine-genomics-special-issue-genome-powered-perspectives-in-integrative-physiology-and-evolutionary-biology
#10
EDITORIAL
Michael Berenbrink, Cinzia Verde, Andrew R Cossins
No abstract text is available yet for this article.
December 2016: Marine Genomics
https://www.readbyqxmd.com/read/27746103/genome-sequence-of-an-inducible-phage-in-rhodovulum-sp-p5-isolated-from-the-shallow-sea-hydrothermal-system
#11
Dan Lin, Kai Tang, Yu Han, Chenlan Li, Xiaofeng Chen
A prophage namely vB_RhkS_P1 was induced by mitomycin C from Rhodovulum sp. P5 in the shallow-sea hydrothermal systems. The vB_RhkS_P1 had siphovirus-like morphology, and the average particle had a head size of approximately 61nm, and the tail length approximately 93nm. The genome of vB_RhkS_P1 was a size of 38.8kbp, 67.5% GC content, and 59 open reading frames. The genome contained Mu-like head structural genes but its genomic content was distinct from Mu or Mu-like phages.
December 2016: Marine Genomics
https://www.readbyqxmd.com/read/27742405/having-a-blast-searchable-transcriptome-resources-for-the-gilthead-sea-bream-and-the-european-sea-bass
#12
Bruno Louro, João Pedro Marques, Deborah M Power, Adelino V M Canário
The gilthead sea bream (Sparus aurata) and the European sea bass (Dicentrarchus labrax) are the most important aquaculture species in the Mediterranean Sea and since the last decade it has been seen an exponential increase in their available molecular resources. In order to improve accessibility to transcriptome resources, Expressed Sequence Tags (ESTs), mRNA sequences and raw read sequences were assembled and deposited in BLAST queryable databases. The publicly available sea bream and sea bass sequences (6...
December 2016: Marine Genomics
https://www.readbyqxmd.com/read/27742404/diving-into-marine-genomics-with-crispr-cas9-systems
#13
Tsuyoshi Momose, Jean-Paul Concordet
More and more genomes are sequenced and a great range of biological questions can be examined at the genomic level in a growing number of organisms. Testing the function of genome features, from gene networks, genome organization, conserved non-coding sequences to microRNAs, and, more generally, experimentally addressing the genotype-phenotype relationship is now possible owing to the clustered, regularly interspaced, short palindromic repeats (CRISPR)-Cas9 revolution of genome editing. In the present review, we give a brief overview of the CRISPR/Cas9 toolbox and different strategies for genome editing currently available...
December 2016: Marine Genomics
https://www.readbyqxmd.com/read/27720170/a-transcriptome-resource-for-the-deep-sea-bacterium-shewanella-piezotolerans-wp3-under-cold-and-high-hydrostatic-pressure-shock-stress
#14
Huahua Jian, Shengkang Li, Xixiang Tang, Xiang Xiao
Low temperature and high hydrostatic pressure (HHP) are two of the most remarkable environmental factors influencing deep-sea ecosystem. The adaptive mechanisms of microorganisms which live in these extreme environments to low temperature and high pressure warrant investigation. In this study, the global gene expression patterns of the deep-sea bacterium Shewanella piezotolerans WP3 in response to cold (0 °C) and HHP (50 MPa) shock were evaluated through DNA microarray analysis. Results revealed that 22, 66, and 106 genes were differentially expressed after WP3 was respectively exposed to cold shock for 30, 60, and 90 min...
December 2016: Marine Genomics
https://www.readbyqxmd.com/read/27567592/global-transcriptome-analysis-of-the-heat-shock-response-of-the-deep-sea-bacterium-shewanella-piezotolerans-wp3
#15
Huahua Jian, Shengkang Li, Xiaoyuan Feng, Xiang Xiao
For microorganisms, heat shock is a major stressful condition. Heat shock is characterized by sudden temperature increases that damage important protein structures and interfere with essential cellular functions. In this study, global gene expression patterns of the deep-sea bacterium Shewanella piezotolerans WP3 in response to heat shock were studied by DNA microarray analysis. Overall, 438, 573, and 627 genes were found to be differentially expressed after heat shock for 30, 60, and 90min, respectively. Functional classification of differentially transcribed genes was performed using the Clusters of Orthologous Groups of Proteins database...
December 2016: Marine Genomics
https://www.readbyqxmd.com/read/27538735/complete-genome-sequence-of-astaxanthin-producing-bacterium-altererythrobacter-ishigakiensis-nbrc-107699
#16
Xiao-Lai Shi, Yue-Hong Wu, Hong Cheng, Xin-Qi Zhang, Chun-Sheng Wang, Xue-Wei Xu
Altererythrobacter ishigakiensis NBRC 107699 was isolated from marine sediment collected from a site on the coast of Ishigaki Island, Japan and deposited to the NITE Biological Resource Center. This strain is able to produce astaxanthin, which can be used as a food supplement. Here we describe the genome sequence and annotation, as well as the features of the organism. The genome of strain NBRC 107699 comprises 2,673,978bp and contains 2618 protein-coding genes (1966 with predicted functions), 42 tRNA genes and 3 rRNA genes...
December 2016: Marine Genomics
https://www.readbyqxmd.com/read/27538734/transcriptional-and-metabolomic-characterization-of-spontaneous-metabolic-cycles-in-mytilus-californianus-under-subtidal-conditions
#17
Andrew Y Gracey, Kwasi Connor
Intertidal mussels are often used to understand how life is orchestrated under tidal regimes of submergence and aerial emersion. The California ribbed mussel, Mytilus californianus, occurs predominantly in the rocky intertidal and is generally studied in the context of intertidal adaptation. We monitored M. californianus under conditions of constant submergence and observed spontaneous episodes of normal versus reduced cardiac activity. Complementary transcriptome and metabolome data indicated that these episodes were correlated with large-scale changes in the physiological state of the mussel, with periods of low cardiac activity indicative of a switch to anaerobic metabolism...
December 2016: Marine Genomics
https://www.readbyqxmd.com/read/27435301/complete-genome-sequence-of-bacillus-oceanisediminis-2691-a-reservoir-of-heavy-metal-resistance-genes
#18
Jaejoon Jung, Haeyoung Jeong, Hyun Ju Kim, Dong-Woo Lee, Sang Jun Lee
Ocean sediments are commonly subject to the pollution of various heavy metals. Intracellular heavy metal concentrations in marine microorganisms should be kept within allowable concentrations. Here, we report redundant heavy metal resistance related genes encoding heavy metal-sensing transcriptional regulators (i.e. cadC), heavy metal efflux pumps, and detoxifying enzymes in the complete genome sequence of Bacillus oceanisediminis 2691. By comparing CadC sequences of strain 2691 with those from other bacterial genomes, we demonstrated that each cadC gene located in the chromosome or plasmid of 2691 cells are similar to those of various near or distant microbes, which might shed light on evolutionary trajectories of redundant heavy metal resistance genes...
December 2016: Marine Genomics
https://www.readbyqxmd.com/read/27346185/targeted-sequencing-for-high-resolution-evolutionary-analyses-following-genome-duplication-in-salmonid-fish-proof-of-concept-for-key-components-of-the-insulin-like-growth-factor-axis
#19
Fiona M Lappin, Rebecca L Shaw, Daniel J Macqueen
High-throughput sequencing has revolutionised comparative and evolutionary genome biology. It has now become relatively commonplace to generate multiple genomes and/or transcriptomes to characterize the evolution of large taxonomic groups of interest. Nevertheless, such efforts may be unsuited to some research questions or remain beyond the scope of some research groups. Here we show that targeted high-throughput sequencing offers a viable alternative to study genome evolution across a vertebrate family of great scientific interest...
December 2016: Marine Genomics
https://www.readbyqxmd.com/read/27189439/genomic-conservation-of-erythropoietic-micrornas-erythromirs-in-white-blooded-antarctic-icefish
#20
Thomas Desvignes, H William Detrich, John H Postlethwait
White-blooded Antarctic crocodile icefish are the only vertebrates known to lack functional hemoglobin genes and red blood cells throughout their lives. We do not yet know, however, whether extinction of hemoglobin genes preceded loss of red blood cells or vice versa, nor whether erythropoiesis regulators disappeared along with hemoglobin genes in this erythrocyte-null clade. Several microRNAs, which we here call erythromiRs, are expressed primarily in developing red blood cells in zebrafish, mouse, and humans...
December 2016: Marine Genomics
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