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Marine Genomics

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https://www.readbyqxmd.com/read/28689690/genome-analysis-of-three-novel-lytic-vibrio-coralliilyticus-phages-isolated-from-seawater-okinawa-japan
#1
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/28648476/constraint-based-metabolic-modelling-of-marine-microbes-and-communities
#2
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...
June 22, 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
#3
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
#4
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
#5
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
#6
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
#7
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
#8
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/28545861/characterization-of-autonomous-families-of-tc1-mariner-transposons-in-neoteleost-genomes
#9
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)...
May 22, 2017: Marine Genomics
https://www.readbyqxmd.com/read/28545860/de-novo-transcriptome-assembly-and-annotation-for-the-desert-rainbowfish-melanotaenia-splendida-tatei-with-comparison-with-candidate-genes-for-future-climates
#10
Katie Gates, Jonathan Sandoval-Castillo, Louis Bernatchez, Luciano B Beheregaray
Transcriptomics via RNA-seq has rapidly emerged as a powerful tool for ecological and evolutionary studies, enabling genome-scale studies of adaptation via regulation of global gene expression. Here we present a de novo transcriptome for the desert rainbowfish (Melanotaenia splendida tatei) based on individuals sampled in the Lake Eyre Basin, Australia's arid zone river system. Recently developed methods in RNA-seq and bioinformatics were used for sequencing, assembling and annotating a high-quality liver transcriptome suitable for studies of ecology and adaptation in desert rainbowfish...
May 22, 2017: Marine Genomics
https://www.readbyqxmd.com/read/28528769/complete-genome-sequence-and-analysis-of-three-kinds-of-%C3%AE-agarase-of-cellulophaga-lytica-dau203-isolated-from-marine-sediment
#11
Yong-Suk Lee, Yong-Lark Choi
Cellulophaga lytica DAU203 (KACC 19187), isolated from the marine sediment in Korea, has a strong ability to degrade agar. The genome of C. lytica DAU203 contains a single chromosome that is 3,952,957bp in length, with 32.02% G+C contents. The genomic information predicted that the DAU203 has the potential to be utilized in various enzymatic industries.
May 18, 2017: Marine Genomics
https://www.readbyqxmd.com/read/28522160/complete-genome-of-a-metabolically-diverse-marine-bacterium-shewanella-japonica-kctc-22435-t
#12
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/28478932/transcriptome-response-of-previtellogenic-ovary-in-anguilla-japonica-after-artificial-hormone-injection
#13
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
#14
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/28389176/identification-of-the-abiotic-stress-related-transcription-in-little-neptune-grass-cymodocea-nodosa-with-rna-seq
#15
E 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...
April 25, 2017: Marine Genomics
https://www.readbyqxmd.com/read/28479280/pelagic-and-benthic-communities-of-the-antarctic-ecosystem-of-potter-cove-genomics-and-ecological-implications
#16
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
#17
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
https://www.readbyqxmd.com/read/28237778/genome-of-a-giant-bacteriophage-from-a-decaying-trichodesmium-bloom
#18
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...
June 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
#19
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)...
June 2017: Marine Genomics
https://www.readbyqxmd.com/read/28169128/population-genomics-reveals-high-gene-flow-in-grass-rockfish-sebastes-rastrelliger
#20
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...
June 2017: Marine Genomics
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