| 1. |
- D'Aniello, Salvatore, et al.
(författare)
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Opsin evolution in the Ambulacraria
- 2015
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Ingår i: Marine Genomics. - : Elsevier BV. - 1874-7787 .- 1876-7478.
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Tidskriftsartikel (refereegranskat)abstract
- Opsins — G-protein coupled receptors involved in photoreception — have been extensively studied in the animal kingdom. The present work provides new insights into opsin-based photoreception and photoreceptor cell evo- lution with a first analysis of opsin sequence data for a major deuterostome clade, the Ambulacraria. Systematic data analysis, including for the first time hemichordate opsin sequences and an expanded echinoderm dataset, led to a robust opsin phylogeny for this cornerstone superphylum. Multiple genomic and transcriptomic resources were surveyed to cover each class of Hemichordata and Echinodermata. In total, 119 ambulacrarian opsin sequences were found, 22 new sequences in hemichordates and 97 in echinoderms (including 67 new sequences). We framed the ambulacrarian opsin repertoire within eumetazoan diversity by including selected reference opsins from non-ambulacrarians. Our findings corroborate the presence of all major ancestral bilaterian opsin groups in Ambulacraria. Furthermore, we identified two opsin groups specific to echinoderms. In conclu- sion, a molecular phylogenetic framework for investigating light-perception and photobiological behaviors in marine deuterostomes has been obtained.
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| 2. |
- Lebret, Karen, et al.
(författare)
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Choice of molecular barcode will affect species prevalence but not bacterial community composition
- 2016
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Ingår i: Marine Genomics. - : Elsevier BV. - 1874-7787 .- 1876-7478. ; 29, s. 39-43
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Tidskriftsartikel (refereegranskat)abstract
- Abstract 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. Significant differences between relative abundances at all taxonomic levels were observed; however, their seasonal dynamics between phyla were largely consistent between methods. This study highlights that care must be taken when comparing datasets generated from different methods.
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| 3. |
- Burns, Gavin, et al.
(författare)
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Transcriptome pyrosequencing of the Antarctic brittle star Ophionotus victoriae
- 2013
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Ingår i: Marine Genomics. - : Elsevier BV. - 1874-7787. ; 9, s. 9-15
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Tidskriftsartikel (refereegranskat)abstract
- Brittle stars are included within a whole range of species, which contribute to knowledge in the medically important area of tissue regeneration. All brittle stars regenerate lose limbs, but the rate at which this occurs is highly variable and species-specific. One of the slowest rates of arm regeneration reported so far is that of the Antarctic Ophionotus victoriae. Additionally, O. victoriae also has an unusual delay in the onset of regeneration of about 5. months. Both processes are of interest for the areas of regeneration biology and adaptation to cold environments. One method of understanding the details of regeneration events in brittle stars is to characterise the genes involved. In the largest transcriptome study of any ophiuroid to date, we describe the results of mRNA pyrosequencing from pooled samples of regenerating arms of O. victoriae. The sequencing reads resulted in 18,000 assembled contiguous sequences of which 19% were putatively annotated by blast sequence similarity searching. We focus on the identification of major gene families and pathways with potential relevance to the regenerative processes including the Wnt/β-catenin pathway, Hox genes, the SOX gene family and the TGF beta signalling pathways. These data significantly increase the amount of ophiuroid sequences publicly available and provide candidate transcripts for the further investigation of the unusual regenerative process in this Antarctic ophiuroid. © 2012 Elsevier B.V.
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| 4. |
- Delroisse, J., et al.
(författare)
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De novo transcriptome of the European brittle star Amphiura filiformis pluteus larvae
- 2015
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Ingår i: Marine Genomics. - : Elsevier. - 1874-7787. ; 23, s. 109-121
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Tidskriftsartikel (refereegranskat)abstract
- Background: In non-classical model species, Next Generation Sequencing increases the ability to analyze the expression of transcripts/genes. In this study, paired-end Illumina HiSeq sequencing technology has been employed to describe a larval transcriptome generated from 64 h post-fertilization pluteus larvae of the brittle star Amphiura filiformis. We focused our analysis on the detection of actors involved in the opsin based light perception, respectively the opsins and the phototransduction actors. Methods & results: In this research, about 47 million high quality readswere generated and 86,572 total unigenes were predicted after de novo assembly. Of all the larval unigenes, 18% show significant matches with reference online databases. 46% of annotated larval unigenes were significantly similar to transcripts from the purple sea urchin. COG, GO and KEGG analyses were performed on predicted unigenes. Regarding the opsin-based photoreception process, even if possible actors of ciliary and rhabdomeric phototransduction cascadeswere detected, no ciliary or rhabdomeric opsinwas identified in these larvae. Additionally, partial non-visual RGR (retinal G protein coupled receptor) opsin mRNAs were identified,possibly indicating the presence of visual cycle reaction in early pluteus larvae. The eye morphogene Pax 6 was also identified in the pluteus transcriptome. Conclusions: Contrary to sea-urchin larvae, brittle star larvae appear to be characterized by an absence of visuallike opsins. These RNA-seq data also provide a useful resource for the echinoderm research community and researchers with an interest in larval biology. © 2015 Elsevier B.V.
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| 5. |
- Gabre, Jonatan L., 1988, et al.
(författare)
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The coelomic epithelium transcriptome from a clonal sea star, Coscinasterias muricata
- 2015
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Ingår i: Marine Genomics. - : Elsevier BV. - 1874-7787. ; 24, s. 245-248
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Tidskriftsartikel (refereegranskat)abstract
- Coscinasterias is a cosmopolitan genus of large asteroid sea stars with the ability of somatic fission as a clonal reproductive strategy. During fission, the animals tear themselves apart across their central disc, where the lost body parts are regenerated afterwards. Here, we have sequenced and subsequently analysed the transcriptome of the coelomic epithelium of a clonal Coscinasterias muricata specimen from New Zealand. Out of the total 389,768 raw reads, 11,344 contigs were assembled and grouped into functions. Raw read and assembled contig sequences are available at NCBI (BioSample: SAMN03371637), while the annotated assembly can be accessed through the project transcriptome browser (compgen.bio.ub.edu/gbrowse/starfish_transcriptome/). Our data is valuable for future detailed exploration of the coelomic epithelium functions as well as for a better understanding of sea star physiology. (c) 2015 Elsevier B.V. All rights reserved.
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| 6. |
- Marques, João P, et al.
(författare)
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Comparative mitogenomic analysis of three species of periwinkles: Littorina fabalis, L.obtusata and L. saxatilis.
- 2017
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Ingår i: Marine Genomics. - : Elsevier BV. - 1874-7787. ; 32, s. 41-47
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Tidskriftsartikel (refereegranskat)abstract
- 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.saxatilis this problem was overcome with additional long-reads and we were able to assemble the complete mitogenome. Both gene order and nucleotide composition are similar between the three species as well as compared to other Littorinimorpha. A large variance in divergence was observed across mitochondrial regions, with six- to ten-fold difference between the highest and the lowest divergence rates. Based on nucleotide changes on the whole molecule and assuming a molecular clock, L.fabalis and L. obtusata started to diverge around 0.8 Mya (0.4-1.1 Mya). The evolution of the mitochondrial protein-coding genes in the three Littorina species appears mainly influenced by purifying selection as revealed by phylogenetic tests based on dN/dS ratios that did not detect any evidence for positive selection, although some caution is required given the limited power of the dataset and the implemented approaches.
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| 7. |
- Michalek, K., et al.
(författare)
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Mytilus hybridisation and impact on aquaculture: A minireview
- 2016
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Ingår i: Marine Genomics. - : Elsevier BV. - 1874-7787. ; 27, s. 3-7
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Tidskriftsartikel (refereegranskat)abstract
- The three species in the blue mussel complex (Mytilus edulis, Mytilus galloprovincialis and Mytilus trossulus) show varying levels of hybridisation wherever they occur sympatrically. The spatial variation in hybridisation patterns is potentially governed by environmental conditions, larval dispersal and aquaculture practices. Commercial mussel cultivation has been shown to increase hybridisation through introduction of non-native species or spat transfer. There is evidence that mussel cultivation may promote commercially less desirable phenotypes (e.g. fragile shells), however, to what extent hybridisation impacts aquaculture is currently not clear. The aim of this review is to summarize the available information on Mytilus hybridisation patterns in Europe and their promotion through aquaculture practices in order to shed light on the overall implications for the aquaculture industry.
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| 8. |
- Powell, Daniel, et al.
(författare)
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Transcriptomic responses of saline-adapted Nile tilapia (Oreochromis niloticus) to rearing in both saline and freshwater
- 2021
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Ingår i: Marine Genomics. - : Elsevier BV. - 1874-7787. ; 60
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Tidskriftsartikel (refereegranskat)abstract
- The Nile tilapia, Oreochromis niloticus, is an important species for global aquaculture. Recently, a single genetic line of Nile tilapia was developed using estimated breeding values (EBVs) for body weight under moderately saline water that showed significant improvement in growth performance. To explore the molecular mechanisms underlying this enhanced growth capacity, RNA-Seq was used to profile differences in gene expression in the liver and pituitary gland of high- and low-growth performance families of male Nile tilapia progeny, reared in either saline or freshwater environments. Comparisons of tissues from high- and low-EBV families, and also between fish reared in either saline or freshwater, revealed 142 and 2208 differentially expressed genes (DEGs), respectively. DEGs identified between the EBV groups comprised a number of genes involved in the regulation of growth and reproduction. We found an overexpression of hormone genes involved in growth-inhibition in the pituitary of Low-EBV tilapia including 2 somatostatin genes (GHIH), corticoliberin (CRH) and tachykinin-3-like protein. Furthermore, several genes associated with the cAMP pathway were underexpressed in low-EBV tilapia pituitary together with several early response genes. This study provides insight into the transcriptomic factors associated with growth performance in saline-adapted Nile tilapia reared in environments with high and low salinity levels and provides valuable knowledge for the future development of selection strategies to improve growth performance in this species.
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| 9. |
- Sillanpaa, J. K., et al.
(författare)
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Calcium mobilisation following shell damage in the Pacific oyster, Crassostrea gigas
- 2016
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Ingår i: Marine Genomics. - : Elsevier BV. - 1874-7787. ; 27, s. 75-83
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Tidskriftsartikel (refereegranskat)abstract
- Shell growth of oysters requires calcium uptake from the environment and transport to the area of shell formation. A shell regeneration assay in combination with radiolabelled calcium was used to investigate uptake and distribution of calcium to different tissues and hemolymph fractions in Pacific oysters, Crassostrea gigas (Bivalvia, Ostreoida). Oysters were notched at the shell margin and subsequently sampled for hemolymph and grading of shell regeneration during a two week experimental period. Half of the oysters were additionally exposed to Ca-45 and sampled for hemolymph and tissues. Total plasma calcium concentrations increased in notched oysters compared to controls on 1, 2 and 7 days after notching. A decrease in plasma calcium levels was apparent on day 4, for both total and ionic calcium. The shell regeneration assay in the notched oysters resulted in a visible deposition of CaCO3 onto the regenerate from day 7 onwards. This was coinciding with an increased uptake of total calcium on days 11 and 14 as well as free, i.e. ionic and ligand-bound calcium, on day 14. At day 1, notching also increased calcium uptake into the mantle tissues, in areas above the notch and near the hinge. During the experiment, both the total hemocyte count and the number of granulocytes increased in notched compared to control oysters. The present study suggests that induced shell damage results in a dynamic regulation of the calcium uptake from the environment and the distribution of calcium within the body, starting directly after notching. Increases in both total calcium concentrations and uptake rates coincided with the visible depositions of CaCO3 on the regenerate shell. C. gigas was found to transport calcium mainly in the ionic form in the hemolymph, with only minor parts being bound to proteins or smaller ligands. Hemolymph measurement also revealed that C. gigas is able to regulate the extracellular concentrations of calcium and potassium. The changes in plasma calcium concentrations and speciation, concomitant with increases in granulocytes indicate that multiple calcium transport processes are activated after induced shell damage.
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| 10. |
- Stjelja Arvelius, Suzana
(författare)
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Evolutionary history and adaptive significance of the polymorphic Pan I in migratory and stationary populations of Atlantic cod (Gadus morhua)
- 2015
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Ingår i: Marine Genomics. - : Elsevier BV. - 1874-7787. ; 22, s. 45-54
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Tidskriftsartikel (refereegranskat)abstract
- The synaptophysin (SYP) family comprises integral membrane proteins involved in vesicle-trafficking events, but the physiological function of several members has been enigmatic for decades. The presynaptic SYP protein controls neurotransmitter release, while SYP-like 2 (SYPL2) contributes to maintain normal Ca2+-signaling in the skeletal muscles. The polymorphic pantophysin (Pan I) of Atlantic cod shows strong genetic divergence between stationary and migratory populations, which seem to be adapted to local environmental conditions. We have investigated the functional involvement of Pan I in the different ecotypes by analyzing the 1) phylogeny, 2) spatio-temporal gene expression, 3) structure-function relationship of the Pan I-A and I-B protein variants, and 4) linkage to rhodopsin (rho) recently proposed to be associated with different light sensitivities in Icelandic populations of Atlantic cod. We searched for SYP family genes in phylogenetic key species and identified a single syp-related gene in three invertebrate chordates, while four members, Syp, Sypl1, Sypl2 and synaptoporin (Synpr), were found in tetrapods, Comoran coelacanth and spotted gar. Teleost fish were shown to possess duplicated syp, sypl2 and synpr genes of which the sypl2b paralog is identical to Pan I. The ubiquitously expressed cod Pan I codes for a tetra-spanning membrane protein possessing five amino acid substitutions in the first intravesicular loop, but only minor structural differences were shown between the allelic variants. Despite sizable genomic distance (>2.5 Mb) between Pan land rho, highly significant linkage disequilibrium was found by genotyping shallow and deep water juvenile settlers predominated by the Pan I-A-rho(A) and Pan I-B-rho(B) haplotypes, respectively. However, the predicted rhodopsin protein showed no amino add changes, while multiple polymorphic sites in the upstream region might affect the gene expression and pigment levels in stationary and migratory cod. Alternatively, other strongly linked genes might be responsible for the sharp settling stratification of juveniles and the different vertical behavior patterns of adult Atlantic cod. (C) 2015 Elsevier B.V. All rights reserved.
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