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Asset Tag: Marine biology

April 21, 2020  |  

A hybrid de novo assembly of the sea pansy (Renilla muelleri) genome.

More than 3,000 species of octocorals (Cnidaria, Anthozoa) inhabit an expansive range of environments, from shallow tropical seas to the deep-ocean floor. They are important foundation species that create coral “forests,” which provide unique niches and 3-dimensional living space for other organisms. The octocoral genus Renilla inhabits sandy, continental shelves in the subtropical and tropical Atlantic and eastern Pacific Oceans. Renilla is especially interesting because it produces secondary metabolites for defense, exhibits bioluminescence, and produces a luciferase that is widely used in dual-reporter assays in molecular biology. Although several anthozoan genomes are currently available, the majority of these are hexacorals. Here, we present a de novo assembly of an azooxanthellate shallow-water octocoral, Renilla muelleri.We generated a hybrid de novo assembly using MaSuRCA v.3.2.6. The final assembly included 4,825 scaffolds and a haploid genome size of 172 megabases (Mb). A BUSCO assessment found 88% of metazoan orthologs present in the genome. An Augustus ab initio gene prediction found 23,660 genes, of which 66% (15,635) had detectable similarity to annotated genes from the starlet sea anemone, Nematostella vectensis, or to the Uniprot database. Although the R. muelleri genome may be smaller (172 Mb minimum size) than other publicly available coral genomes (256-448 Mb), the R. muelleri genome is similar to other coral genomes in terms of the number of complete metazoan BUSCOs and predicted gene models.The R. muelleri hybrid genome provides a novel resource for researchers to investigate the evolution of genes and gene families within Octocorallia and more widely across Anthozoa. It will be a key resource for future comparative genomics with other corals and for understanding the genomic basis of coral diversity. © The Author(s) 2019. Published by Oxford University Press.

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April 21, 2020  |  

Chromosome-scale assemblies reveal the structural evolution of African cichlid genomes.

African cichlid fishes are well known for their rapid radiations and are a model system for studying evolutionary processes. Here we compare multiple, high-quality, chromosome-scale genome assemblies to elucidate the genetic mechanisms underlying cichlid diversification and study how genome structure evolves in rapidly radiating lineages.We re-anchored our recent assembly of the Nile tilapia (Oreochromis niloticus) genome using a new high-density genetic map. We also developed a new de novo genome assembly of the Lake Malawi cichlid, Metriaclima zebra, using high-coverage Pacific Biosciences sequencing, and anchored contigs to linkage groups (LGs) using 4 different genetic maps. These new anchored assemblies allow the first chromosome-scale comparisons of African cichlid genomes. Large intra-chromosomal structural differences (~2-28 megabase pairs) among species are common, while inter-chromosomal differences are rare (<10 megabase pairs total). Placement of the centromeres within the chromosome-scale assemblies identifies large structural differences that explain many of the karyotype differences among species. Structural differences are also associated with unique patterns of recombination on sex chromosomes. Structural differences on LG9, LG11, and LG20 are associated with reduced recombination, indicative of inversions between the rock- and sand-dwelling clades of Lake Malawi cichlids. M. zebra has a larger number of recent transposable element insertions compared with O. niloticus, suggesting that several transposable element families have a higher rate of insertion in the haplochromine cichlid lineage.This study identifies novel structural variation among East African cichlid genomes and provides a new set of genomic resources to support research on the mechanisms driving cichlid adaptation and speciation. © The Author(s) 2019. Published by Oxford University Press.

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April 21, 2020  |  

Crustacean Genome Exploration Reveals the Evolutionary Origin of White Spot Syndrome Virus.

White spot syndrome virus (WSSV) is a crustacean-infecting, double-stranded DNA virus and is the most serious viral pathogen in the global shrimp industry. WSSV is the sole recognized member of the family Nimaviridae, and the lack of genomic data on other nimaviruses has obscured the evolutionary history of WSSV. Here, we investigated the evolutionary history of WSSV by characterizing WSSV relatives hidden in host genomic data. We surveyed 14 host crustacean genomes and identified five novel nimaviral genomes. Comparative genomic analysis of Nimaviridae identified 28 “core genes” that are ubiquitously conserved in Nimaviridae; unexpected conservation of 13 uncharacterized proteins highlighted yet-unknown essential functions underlying the nimavirus replication cycle. The ancestral Nimaviridae gene set contained five baculoviral per os infectivity factor homologs and a sulfhydryl oxidase homolog, suggesting a shared phylogenetic origin of Nimaviridae and insect-associated double-stranded DNA viruses. Moreover, we show that novel gene acquisition and subsequent amplification reinforced the unique accessory gene repertoire of WSSV. Expansion of unique envelope protein and nonstructural virulence-associated genes may have been the key genomic event that made WSSV such a deadly pathogen.IMPORTANCE WSSV is the deadliest viral pathogen threatening global shrimp aquaculture. The evolutionary history of WSSV has remained a mystery, because few WSSV relatives, or nimaviruses, had been reported. Our aim was to trace the history of WSSV using the genomes of novel nimaviruses hidden in host genome data. We demonstrate that WSSV emerged from a diverse family of crustacean-infecting large DNA viruses. By comparing the genomes of WSSV and its relatives, we show that WSSV possesses an expanded set of unique host-virus interaction-related genes. This extensive gene gain may have been the key genomic event that made WSSV such a deadly pathogen. Moreover, conservation of insect-infecting virus protein homologs suggests a common phylogenetic origin of crustacean-infecting Nimaviridae and other insect-infecting DNA viruses. Our work redefines the previously poorly characterized crustacean virus family and reveals the ancient genomic events that preordained the emergence of a devastating shrimp pathogen.Copyright © 2019 American Society for Microbiology.

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April 21, 2020  |  

Complete genome sequence and comparative analysis of Synechococcus sp. CS-601 (SynAce01), a cold-adapted cyanobacterium from an olligotrophic Antarctic habitat.

Marine picocyanobacteria belonging to Synechococcus are major contributors to the global carbon cycle, however the genomic information of its cold-adapted members has been lacking to date. To fill this void the genome of a cold-adapted planktonic cyanobacterium Synechococcus sp. CS-601 (SynAce01) has been sequenced. The genome of the strain contains a single chromosome of approximately 2.75 MBp and GC content of 63.92%. Gene prediction yielded 2984 protein coding sequences and 44 tRNA genes. The genome contained evidence of horizontal gene transfer events during its evolution. CS-601 appears as a transport generalist with some specific adaptation to an oligotrophic marine environment. It has a broad repertoire of transporters of both inorganic and organic nutrients to survive in inhospitable environments. The cold adaptation of the strain exhibited characteristics of a psychrotroph rather than psychrophile. Its salt adaptation strategy is likely to rely on the uptake and synthesis of osmolytes, like glycerol or glycine betaine. Overall, the genome reveals two distinct patterns of adaptation to the inhospitable environment of Antarctica. Adaptation to an oligotrophic marine environment is likely due to an abundance of genes, probably acquired horizontally, that are associated with increased transport of nutrients, osmolytes, and light harvesting. On the other hand, adaptations to low temperatures are likely due to prolonged evolutionary changes.

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April 21, 2020  |  

De novo assembly of the goldfish (Carassius auratus) genome and the evolution of genes after whole-genome duplication.

For over a thousand years, the common goldfish (Carassius auratus) was raised throughout Asia for food and as an ornamental pet. As a very close relative of the common carp (Cyprinus carpio), goldfish share the recent genome duplication that occurred approximately 14 million years ago in their common ancestor. The combination of centuries of breeding and a wide array of interesting body morphologies provides an exciting opportunity to link genotype to phenotype and to understand the dynamics of genome evolution and speciation. We generated a high-quality draft sequence and gene annotations of a “Wakin” goldfish using 71X PacBio long reads. The two subgenomes in goldfish retained extensive synteny and collinearity between goldfish and zebrafish. However, genes were lost quickly after the carp whole-genome duplication, and the expression of 30% of the retained duplicated gene diverged substantially across seven tissues sampled. Loss of sequence identity and/or exons determined the divergence of the expression levels across all tissues, while loss of conserved noncoding elements determined expression variance between different tissues. This assembly provides an important resource for comparative genomics and understanding the causes of goldfish variants.

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April 21, 2020  |  

Sensory receptor repertoire in cyprid antennules of the barnacle Balanus improvisus.

Barnacle settlement involves sensing of a variety of exogenous cues. A pair of antennules is the main sensory organ that the cyprid larva uses to explore the surface. Antennules are equipped with a number of setae that have both chemo- and mechanosensing function. The current study explores the repertoire of sensory receptors in Balanus improvisus cyprid antennules with the goal to better understand sensory systems involved in the settling behavior of this species. We carried out transcriptome sequencing of dissected B. improvisus cyprid antennules. The generated transcriptome assembly was used to search for sensory receptors using HMM models. Among potential chemosensory genes, we identified the ionotropic receptors IR25a, IR8a and IR93a, and several divergent IR candidates to be expressed in the cyprid antennules. We found one gustatory-like receptor but no odorant receptors, chemosensory or odorant-binding proteins. Apart from chemosensory receptors, we also identified 13 potential mechanosensory genes represented by several transient receptor potential channels (TRP) subfamilies. Furthermore, we analyzed changes in expression profiles of IRs and TRPs during the B. improvisus settling process. Several of the sensory genes were differentially expressed during the course of larval settlement. This study gives expanded knowledge about the sensory systems present in barnacles, a taxonomic group for which only limited information about receptors is currently available. It furthermore serves as a starting point for more in depth studies of how sensory signaling affects settling behavior in barnacles with implications for preventing biofouling.

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April 21, 2020  |  

The genetic architecture underlying diapause termination in a planktonic crustacean.

Diapause is a feature of the life cycle of many invertebrates by which unfavourable environmental conditions can be outlived. The seasonal timing of diapause allows organisms to adapt to seasonal changes in habitat suitability and thus is key to their fitness. In the planktonic crustacean Daphnia, various cues can induce the production of diapause stages that are resistant to heat, drought or freezing and contain one to two embryos in developmental arrest. Daphnia is a keystone species of many freshwater ecosystems, where it acts as the main link between phytoplankton and higher trophic levels. The correct seasonal timing of diapause termination is essential to maintain trophic interactions and is achieved via a genetically based interpretation of environmental cues like photoperiod and temperature. Field monitoring and modelling studies raised concerns on whether populations can advance their seasonal release from diapause to advances in spring phenology under global change, or if a failure to adapt will cause trophic mismatches negatively affecting ecosystem functioning. Our capacity to understand and predict the evolution of diapause timing requires information about the genetic architecture underlying this trait. In this study, we identified eight quantitative trait loci (QTLs) and four epistatic interactions that together explained 66.5% of the variation in diapause termination in Daphnia magna using QTL mapping. Our results suggest that the most significant QTL is modulating diapause termination dependent on photoperiod and is involved in three of the four detected epistatic interactions. Candidate genes at this QTL could be identified through the integration with genome data and included the presynaptic active zone protein bruchpilot. Our findings contribute to understanding the genomic control of seasonal diapause timing in an ecological relevant species. © 2019 John Wiley & Sons Ltd.

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April 21, 2020  |  

The genome of the jellyfish Aurelia and the evolution of animal complexity.

We present the genome of the moon jellyfish Aurelia, a genome from a cnidarian with a medusa life stage. Our analyses suggest that gene gain and loss in Aurelia is comparable to what has been found in its morphologically simpler relatives-the anthozoan corals and sea anemones. RNA sequencing analysis does not support the hypothesis that taxonomically restricted (orphan) genes play an oversized role in the development of the medusa stage. Instead, genes broadly conserved across animals and eukaryotes play comparable roles throughout the life cycle. All life stages of Aurelia are significantly enriched in the expression of genes that are hypothesized to interact in protein networks found in bilaterian animals. Collectively, our results suggest that increased life cycle complexity in Aurelia does not correlate with an increased number of genes. This leads to two possible evolutionary scenarios: either medusozoans evolved their complex medusa life stage (with concomitant shifts into new ecological niches) primarily by re-working genetic pathways already present in the last common ancestor of cnidarians, or the earliest cnidarians had a medusa life stage, which was subsequently lost in the anthozoans. While we favour the earlier hypothesis, the latter is consistent with growing evidence that many of the earliest animals were more physically complex than previously hypothesized.

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April 21, 2020  |  

The Draft Genome of an Octocoral, Dendronephthya gigantea.

Coral reefs composed of stony corals are threatened by global marine environmental changes. However, soft coral communities of octocorallian species, appear more resilient. The genomes of several cnidarians species have been published, including from stony corals, sea anemones, and hydra. To fill the phylogenetic gap for octocoral species of cnidarians, we sequenced the octocoral, Dendronephthya gigantea, a nonsymbiotic soft coral, commonly known as the carnation coral. The D. gigantea genome size is ~276?Mb. A high-quality genome assembly was constructed from PacBio long reads (29.85 Gb with 108× coverage) and Illumina short paired-end reads (35.54 Gb with 128× coverage) resulting in the highest N50 value (1.4?Mb) reported thus far among cnidarian genomes. About 12% of the genome is repetitive elements and contained 28,879 predicted protein-coding genes. This gene set is composed of 94% complete BUSCO ortholog benchmark genes, which is the second highest value among the cnidarians, indicating high quality. Based on molecular phylogenetic analysis, octocoral and hexacoral divergence times were estimated at 544 MYA. There is a clear difference in Hox gene composition between these species: unlike hexacorals, the Antp superclass Evx gene was absent in D. gigantea. Here, we present the first genome assembly of a nonsymbiotic octocoral, D. gigantea to aid in the comparative genomic analysis of cnidarians, including stony and soft corals, both symbiotic and nonsymbiotic. The D. gigantea genome may also provide clues to mechanisms of differential coping between the soft and stony corals in response to scenarios of global warming. © The Author(s) 2019. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

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April 21, 2020  |  

Biphasic cellular adaptations and ecological implications of Alteromonas macleodii degrading a mixture of algal polysaccharides.

Algal polysaccharides are an important bacterial nutrient source and central component of marine food webs. However, cellular and ecological aspects concerning the bacterial degradation of polysaccharide mixtures, as presumably abundant in natural habitats, are poorly understood. Here, we contextualize marine polysaccharide mixtures and their bacterial utilization in several ways using the model bacterium Alteromonas macleodii 83-1, which can degrade multiple algal polysaccharides and contributes to polysaccharide degradation in the oceans. Transcriptomic, proteomic and exometabolomic profiling revealed cellular adaptations of A. macleodii 83-1 when degrading a mix of laminarin, alginate and pectin. Strain 83-1 exhibited substrate prioritization driven by catabolite repression, with initial laminarin utilization followed by simultaneous alginate/pectin utilization. This biphasic phenotype coincided with pronounced shifts in gene expression, protein abundance and metabolite secretion, mainly involving CAZymes/polysaccharide utilization loci but also other functional traits. Distinct temporal changes in exometabolome composition, including the alginate/pectin-specific secretion of pyrroloquinoline quinone, suggest that substrate-dependent adaptations influence chemical interactions within the community. The ecological relevance of cellular adaptations was underlined by molecular evidence that common marine macroalgae, in particular Saccharina and Fucus, release mixtures of alginate and pectin-like rhamnogalacturonan. Moreover, CAZyme microdiversity and the genomic predisposition towards polysaccharide mixtures among Alteromonas spp. suggest polysaccharide-related traits as an ecophysiological factor, potentially relating to distinct ‘carbohydrate utilization types’ with different ecological strategies. Considering the substantial primary productivity of algae on global scales, these insights contribute to the understanding of bacteria-algae interactions and the remineralization of chemically diverse polysaccharide pools, a key step in marine carbon cycling.

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April 21, 2020  |  

Morphology and genome of a snailfish from the Mariana Trench provide insights into deep-sea adaptation.

It is largely unknown how living organisms-especially vertebrates-survive and thrive in the coldness, darkness and high pressures of the hadal zone. Here, we describe the unique morphology and genome of Pseudoliparis swirei-a recently described snailfish species living below a depth of 6,000?m in the Mariana Trench. Unlike closely related shallow sea species, P. swirei has transparent, unpigmented skin and scales, thin and incompletely ossified bones, an inflated stomach and a non-closed skull. Phylogenetic analyses show that P. swirei diverged from a close relative living near the sea surface about 20?million?years ago and has abundant genetic diversity. Genomic analyses reveal that: (1) the bone Gla protein (bglap) gene has a frameshift mutation that may cause early termination of cartilage calcification; (2) cell membrane fluidity and transport protein activity in P. swirei may have been enhanced by changes in protein sequences and gene expansion; and (3) the stability of its proteins may have been increased by critical mutations in the trimethylamine N-oxide-synthesizing enzyme and hsp90 chaperone protein. Our results provide insights into the morphological, physiological and molecular evolution of hadal vertebrates.

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April 21, 2020  |  

Morphotypes of the common beadlet anemone Actinia equina (L.) are genetically distinct

Anemones of the genus Actinia are ecologically important and familiar organisms on many rocky shores. However, this genus is taxonomically problematical and prior evidence suggests that the North Atlantic beadlet anemone, Actinia equina, may actually consist of a number of cryptic species. Previous genetic work has been largely limited to allozyme electrophoresis and there remains a dearth of genetic resources with which to study this genus. Mitochondrial DNA sequencing may help to clarify the taxonomy of Actinia. Here, the complete mitochondrial genome of the beadlet anemone Actinia equina (Cnidaria: Anthozoa: Actinaria: Actiniidae) is shown to be 20,690?bp in length and to contain the standard complement of Cnidarian features including 13 protein coding genes, two rRNA genes, two tRNAs and two Group I introns, one with an in-frame truncated homing endonuclease gene open reading frame. However, amplification and sequencing of the standard mtDNA barcoding region of the cytochrome oxidase I gene revealed only two haplotypes, differing by a single base pair, in widely geographically separated A. equina and its congener A. prasina. COI barcoding shows that whilst A. equina and A. prasina share the common mtDNA haplotype, haplotype frequency differed significantly between A. equina with red/orange pedal discs and those with green pedal discs, consistent with the hypothesis that these morphotypes represent incipient species.

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April 21, 2020  |  

Characterization of the whole transcriptome of whelk Rapana venosa by single-molecule mRNA sequencing

The veined rapa whelk (Rapana venosa) is an important commercial gastropod in China but is also an important invasive pest worldwide. Lack of genome information restricts investigation of this species. Here we report the first full-length transcriptome database derived from six different developmental stages of the whelk obtained using the PacBio Iso-Seq. As a result, 88,162 high-quality and full-length unigenes were obtained with average length of 2895?bp, among which 70,496 unigenes were successfully annotated, and 192,951 CDS regions, 1182 transcription factors, 284,387 microsatellite loci, and 27,222 lncRNAs were indentified. This study provides a valuable resource for characterizing the R. venosa transcriptome and for future analyses of gene expression profiles.

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April 21, 2020  |  

Complete genome sequence of Euzebya sp. DY32-46, a marine Actinobacteria isolated from the Pacific Ocean

Euzebya sp. DY32-46 was isolated from seawater collected at the depth of 150?m in the eastern Pacific Ocean. The genome was sequenced and consisted of one chromosome and one plasmid pEDY32-46I with sizes of 5,799,875 and 571,580?bp as well as DNA G?+?C contents of 70.7 and 69.6%, respectively. Genomic annotation showed that fifty biosynthetic gene clusters of secondary metabolites were located in the chromosome of Euzebya sp. DY32-46, indicating that a wide variety of its natural products need to be explored. Besides, dozens of biogeochemically relevant genes found in the genome of Euzebya sp. DY32-46 revealed its ecological roles in marine carbon, nitrogen, phosphorus and sulfur cycles including transporting ammonium, phosphate and methylammonium, cleaving dimethylsulfoniopropionate and phosphate, reducing nitrite, etc. Based on genomic similarity analysis, Euzebya sp. DY32-46 represents a novel genospecies of the genus Euzebya, with average nucleotide identity and digital DNA-DNA hybridization values of 73.1-87.1% and 20.2-32.4% compared with the closely related type strains Euzebya rosea DSW09T and E. tangerina F10T. Comparative genomic analysis revealed that 97.1% of coding sequences were exclusively present in the plasmid pEDY32-46I contributing the speciation of Euzebya sp. DY32-46. This study widens our knowledge about industrial potential as well as ecological roles of the genus Euzebya and provides a great candidate for investigating nascent speciation of marine Actinobacteria.

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