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Marine Genomics

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
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
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
Barbara Picone, Clint Rhode, Rouvay Roodt-Wilding
Aquatic animal diseases are one of the most important limitations to the growth of aquaculture. miRNAs represent an important class of small ncRNAs able to modulate host immune and stress responses. In Mollusca, a large phylum of invertebrates, miRNAs have been identified in several species. The current preliminary study identified known miRNAs from the South African abalone, Haliotis midae. The economic and ecological importance of abalone makes this species a suitable model for studying and understanding stress response in marine gastropods...
October 17, 2016: Marine Genomics
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.
October 13, 2016: Marine Genomics
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...
October 11, 2016: Marine Genomics
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...
October 11, 2016: Marine Genomics
Ratna Prabha, Dhananjaya P Singh, Swati Sinha, Khurshid Ahmad, Anil Rai
With the increasing accumulation of genomic sequence information of prokaryotes, the study of codon usage bias has gained renewed attention. The purpose of this study was to examine codon selection pattern within and across cyanobacterial species belonging to diverse taxonomic orders and habitats. We performed detailed comparative analysis of cyanobacterial genomes with respect to codon bias. Our analysis reflects that in cyanobacterial genomes, A- and/or T-ending codons were used predominantly in the genes whereas G- and/or C-ending codons were largely avoided...
October 9, 2016: Marine Genomics
Genki Ozawa, Shigeru Shimamura, Yoshihiro Takaki, Shin-Ichi Yokobori, Yasuhiko Ohara, Kiyotaka Takishita, Tadashi Maruyama, Katsunori Fujikura, Takao Yoshida
The mitochondrial genomes of bivalves have often been used for comparative genomics and for resolving phylogenetic relationships. More than 100 bivalve complete mitochondrial genomes have been sequenced to date. However, few mitochondrial genomes have been reported for deep-sea chemosymbiotic bivalves, which belong to the subclasses Pteriomorphia and Heterodonta. In the present study, we sequenced the mitochondrial genomes of eight deep-sea chemosymbiotic bivalve species: three species of Bathymodiolus mussels (B...
October 6, 2016: Marine Genomics
J Bethke, R Avendaño-Herrera
Streptococcus phocae is a beta-hemolytic, Gram-positive bacterium that was first isolated in Norway from clinical specimens of harbor seal (Phoca vitulina) affected by pneumonia or respiratory infection, and in 2005, this bacterium was identified from disease outbreaks at an Atlantic salmon farm. A recent comparative polyphasic study reclassified Streptococcus phocae as subsp. phocae and subsp. salmonis, and there are currently two S. phocae NCBI sequencing projects for the type strains ATCC 51973(T) and C-4(T)...
October 5, 2016: Marine Genomics
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...
October 3, 2016: Marine Genomics
Ângela M Ribeiro, Andrew D Foote, Anne Kupczok, Bárbara Frazão, Morten T Limborg, Rosalía Piñeiro, Samuel Abalde, Sara Rocha, Rute R da Fonseca
Marine ecosystems occupy 71% of the surface of our planet, yet we know little about their diversity. Although the inventory of species is continually increasing, as registered by the Census of Marine Life program, only about 10% of the estimated two million marine species are known. This lag between observed and estimated diversity is in part due to the elusiveness of most aquatic species and the technical difficulties of exploring extreme environments, as for instance the abyssal plains and polar waters. In the last decade, the rapid development of affordable and flexible high-throughput sequencing approaches have been helping to improve our knowledge of marine biodiversity, from the rich microbial biota that forms the base of the tree of life to a wealth of plant and animal species...
September 17, 2016: Marine Genomics
Karen Lebret, Joanna Schroeder, Cecilia Balestreri, Andrea Highfield, Denise Cummings, Tim Smyth, Declan Schroeder
The rapid advancement of next generation sequencing protocols in recent years has led to the diversification in the methods used to study microbial communities; however, how comparable the data generated from these different methods are, remains unclear. In this study we compared the taxonomic composition and seasonal dynamics of the bacterial community determined by two distinct 16s amplicon sequencing protocols: sequencing of the V6 region of the 16s rRNA gene using 454 pyrosequencing vs the V4 region of the 16s rRNA gene using the Illumina Hiseq 2500 platform...
October 2016: Marine Genomics
Pankaj Verma, Rangamaran Vijaya Raghavan, Che Ok Jeon, Hyo Jung Lee, Padmanaban Vishnu Priya, Gopal Dharani, Ramalingam Kirubagaran
Deep-sea environments are gaining global attention as potential sources of useful microorganisms, thereby warranting a better understanding of the diversity and genomic potential of the microbes present. To this end, here we provide the first insights into the composition of the bacterial communities in deep-sea sediment samples from the southwestern Bay of Bengal and the geographically distinct volcanic Barren Island in the Andaman Sea. High-throughput 16S rRNA gene sequencing of the sediments revealed the presence of >44,000 operational taxonomic units (OTUs) in each of the samples, suggesting high bacterial diversity...
August 25, 2016: Marine Genomics
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...
August 24, 2016: Marine Genomics
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...
August 15, 2016: Marine Genomics
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...
August 15, 2016: Marine Genomics
Francesco Maroso, Rafaella Franch, Giulia Dalla Rovere, Marco Arculeo, Luca Bargelloni
Dolphinfish is an important fish species for both commercial and sport fishing, but so far limited information is available on genetic variability and pattern of differentiation of dolphinfish populations in the Mediterranean basin. Recently developed techniques allow genome-wide identification of genetic markers for better understanding of population structure in species with limited genome information. Using restriction-site associated DNA analysis we successfully genotyped 140 individuals of dolphinfish from eight locations in the Mediterranean Sea at 3324 SNP loci...
August 2016: Marine Genomics
Jens N Lohscheider, Carolina Río Bártulos
Plastoglobules (PG) are lipophilic droplets attached to thylakoid membranes in higher plants and green algae and are implicated in prenyl lipid biosynthesis. They might also represent a central hub for integration of plastid signals under stress and therefore the adaptation of the thylakoid membrane under such conditions. In Arabidopsis thaliana, PG contain around 30 specific proteins of which Fibrillins (FBN) and Activity of bc1 complex kinases (ABC1K) represent the majority with respect to both number and protein mass...
August 2016: Marine Genomics
Lu Fang, Yuchen Yang, Wuxia Guo, Jianfang Li, Cairong Zhong, Yelin Huang, Renchao Zhou, Suhua Shi
Aegiceras corniculatum (L.) Blanco is one of the most salt tolerant mangrove species and can thrive in 3% salinity at the seaward edge of mangrove forests. Here we sequenced the transcriptome of A. corniculatum used Illumina GA platform to develop its genomic resources for ecological and evolutionary studies. We obtained about 50 million high-quality paired-end reads with 75bp in length. Using the short read assembler Velvet, we yielded 49,437 contigs with the average length of 625bp. A total of 32,744 (66...
August 2016: Marine Genomics
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