Skip to main content
University of Gothenburg
Image
Laboratoriearbete
Photo: Anna-Lena Lundqvist

Marine Genetic Models

In the project IMAGO, Infrastructure for MArine Genetic model Organisms, we develop marine species into new experimentally amenable genetic models. IMAGO provides reference genomes and additional genomic resources, for example, gene maps and transcriptomes, to interested collaborators. Also, we are happy to share knowledge about how to culture the model species. Further development is ongoing with improved annotations and new versions of reference genomes for some species.

IMAGO Model Species

åtta imagoarter

The IMAGO species represent key-species in North Easts Atlantic coastal ecosystems. Check details for each species below, and get in contact with us for more information.

The species

Brittle star, Amphiura filiformis

Bay barnacle, Balanus improvisus

Marine yeast, Debaryomyces hansenii

Bladderwrack, Fucus vesiculosus

Baltic isopod, Idotea balthica

Rough periwinkle, Littorina saxatilis

Sand goby, Pomatoschistus minutus

Marine diatom, Skeletonema marinoi

Brittle star, Amphiura filiformis

Amphiura filiformis is a burrowing  brittle star with a disc up to 10 mm in diameter with long arms (10 x disc diameter in average) that extend into the water column for suspension feeding, making it an ecosystem engineer and important food item for flatfish, cod and crayfish. It is the dominant species on many sublittoral soft bottoms down to 200 m depth in the North Sea and the Mediterranean. Amphiura filiformis has exceptional adult regenerative abilities and can regenerate fully functional arms in a matter of weeks. A. filiformis has separate sexes and reproduce annually during the summer months (July-September). Adults are at least 3 years old before they are mature and have a life span of 10-20 years.  Larvae is planktotrophic and metamorphose a month later under culture conditions. Both larvae and adults can be cultured in our facilities.

RESEARCH OPPORTUNITIES
Echinoderms offer viable and tractable models for molecular and cellular research on stem cells and regeneration. Genetic information between species of echinoderms is highly conserved, but the nature of the common molecular regulatory pathways that facilitate regeneration is still unclear. A big effort on transcriptomics has been made, but genome information provides key information to fully understand the process. Amphiura filiformis is an emerging model for regeneration and stem cell biology in biomedical research. Major scientific targets include cellular and molecular mechanisms underlying regeneration with important links to neuroscience, stem cell biology and neuropeptide structure and function in the absence of a centralised nervous system. A. filiformis is also a key model on the study of molecular bases of bioluminescence.

GENOME RESOURCES
Genome is still not published, but don't hesitate to contact us for collaboration on the unpublished genome data. 

Estimated Genome size: 2,5 Gbp
Basic information
– Total assembly length: 2436555670 bp
– 85,2 and 86,1 % BUSCO completeness (on eukaryotic and metazoan levels, respectively)
– Number of scaffolds: 96452
– Longest scaffold: 841412
– Number of scaffolds >100kb: 5768
– Number of scaffolds >10kb: 42377
– N50: 75901   

Raw data used for assembly
Illumina libraries, bp - 200, 300, 550, 3000, 5 000-8 000 (paired-ended)

Assembly Annotation
Trimmed datasets were assembled and scaffolded using Soap denovo. 200 genes were   manually curated. 

OTHER RESOURCES
Adult cultures can be set up and maintained all year around. Synchronized larvae cultures can be obtained during the summer months.

KEY REFERENCES
Czarkwiani, A., Ferrario, C., Dylus, D., Sugni, M., & Oliveri, P. (2016, 4 22). Skeletal regeneration in the brittle star Amphiura filiformis. Frontiers in Zoology, 13(1).

Delroisse, J., Mallefet, J., & Flammang, P. (2016, 4 1). De Novo Adult Transcriptomes of Two European Brittle Stars: Spotlight on Opsin-Based Photoreception. PLoS ONE, 11(4).

Delroisse, J., Ullrich-Lüter, E., Blaue, S., Ortega-Martinez, O., Eeckhaut, I., Flammang, P., & Mallefet, J. (2017). A puzzling homology: A brittle star using a putative cnidarian-type luciferase for bioluminescence. Open Biology, 7(4).

Dupont, S., & Thorndyke, M. (2006, 10). Growth or differentiation? Adaptive regeneration in the brittlestar Amphiura filiformis. The Journal of experimental biology, 209(Pt 19), 3873-81.

Dylus, D., Czarkwiani, A., Blowes, L., Elphick, M., & Oliveri, P. (2018, 2 28). Developmental transcriptomics of the brittle star Amphiura filiformis reveals gene regulatory network rewiring in echinoderm larval skeleton evolution. Genome Biology, 19(1).

Dylus, D., Czarkwiani, A., Stångberg, J., Ortega-Martinez, O., Dupont, S., & Oliveri, P. (2016, 1 11). Large-scale gene expression study in the ophiuroid Amphiura filiformis provides insights into evolution of gene regulatory networks. EvoDevo, 7(1).

Ferrario, C., Czarkwiani, A., Dylus, D., Piovani, L., Candia Carnevali, M., Sugni, M., & Oliveri, P. (2020). Extracellular matrix gene expression during arm regeneration in Amphiura filiformis. Cell and Tissue Research.

Purushothaman, S., Saxena, S., Meghah, V., Swamy, C., Ortega-Martinez, O., Dupont, S., & Idris, M. (2015, 1 1). Transcriptomic and proteomic analyses of Amphiura filiformis arm tissue-undergoing regeneration. Journal of Proteomics, 112, 113-124.

Brittle star
Brittlestar, Amphiura filiformis.
Photo: Fredrik Pleijel

Bay barnacle, Balanus improvisus

The Bay barnacle is a sessile crustacean found in coastal, shallow waters worldwide, especially in estuarine and brackish waters. Being sessile, barnacles experience extreme changes in environmental conditions requiring specific evolutionary adaptations. It is one of few macro-invertebrates that inhabits most of the salinity gradient from the North Sea to the Baltic Sea and is known for its broad salinity tolerance (1.8 – 35‰) The species has a complex life cycle with seven different larval stages, which have been studied both in ecological contexts as well as in antifouling research.

RESEARCH OPPORTUNITIES
The recent and worldwide spread of this species enables studies about rapid evolution of local adaptation to a range of new habitats differing in temperature, salinity and pH etc. Genetic resources provide tools to investigate genes that are involved in the settlement process and responses to environmental change. Several important molecular features of its osmoregulatory machinery have also been unravelled, like gene families for Na+/K+ ATPase and aquaporin. 

The species also has biotechnological implications as a major fouling agent on ships and other marine constructions resulting in large economic and environmental impact. It also has applications in other areas of biotechnological research, e.g. the underwater ”super glue” produced by the larvae at metamorphosis.

GENOME RESOURCES

  • Estimated genome size:  We have shown both experimentally (DNA staining and flow cytometry) and computationally (kmer analysis) that B. improvisus has a haploid genome size of ~ 740 Mbp
  • High genetic diversity: B. improvisus has a very high nucleotide diversity averaging ≈ 5% in coding regions
  • Available sequence information: EST library (cDNA), Transcriptomes adult + cyprids (Illumina+PacBio), complete mitochondrial genome, DNA from several adults, reference one individual genome (PacBio) (ongoing work).
  • Additional related species for which we have transcriptomics and/or genomics data:
    Balanus balanus (Tjärnö, Sweden) *
    Balanus crenatus (Tjärnö, Sweden) *
    Semibalanus balanoides (Tjärnö, Sweden) *
    Balanus perforatus (Roscoff, France)
    Chtalamus montagui (Roscoff, France)
    Elminius modestus (Roscoff, France)
    * = plus DNA sequences from 10x Chromium

OTHER RESOURCES
A culturing technique has been developed providing year-round larvae continuously for >20 years at Tjärnö Marina Laboratory, Sweden.

KEY REFERENCES
Fyhn, H. J. (1976) Holeuryhalinity and Its Mechanisms in a Cirriped Crustacean, Balanus-Improvisus. Comparative Biochemistry and Physiology a-Physiology 53:19-30

Lind, U., Alm Rosenblad, M., Wrange, A.-L., Sundell, K.S., Jonsson, P.R., André, C., Havenhand, J., Blomberg, A. (2013) Molecular characterization of the α-subunit of Na+/K+ ATPase from the euryhaline barnacle Balanus improvisus reveals multiple genes and differential expression of alternative splice variants. PLoS One, 8:e77069

 Wrange AL, André C, Lundh T, Lind U, Blomberg A, Jonsson PJ, Havenhand JN. (2014) Importance of plasticity and local adaptation for coping with changing salinity in coastal areas: a test case with barnacles in the Baltic Sea. BMC Evolutionary Biology, 14:156

 Lind, U., M. Järvå, M. Alm Rosenblad, P. Pingitore, E. Karlsson, A.-L. Wrange, E. Kamdal, K. Sundell, C. André, P. R. Jonsson, J. Havenhand, L. A. Eriksson, K. Hedfalk, A. Blomberg (2017) Analysis of aquaporins from the euryhaline barnacle Balanus improvisus reveals differential expression in response to changes in salinity. PLoS One, 12:e0181192

 Jonsson, P.R., A.-L. Wrange, U. Lind, A. Abramova, M. Ogemark, A. Blomberg (2018). The Barnacle Balanus improvisus as a Marine Model - Culturing and Gene Expression. JOVE (Journal of Visualized Experiments), 138:e57825

Abramova, A., Lind U., Blomberg A., Alm Rosenblad M. (2019) The complex barnacle perfume: Identification of waterborne pheromone homologues in Balanus improvisus and their differential expression during settlement. Biofouling, 35:416

Sundell, K., Wrange, A-L., Jonsson, P.R., Blomberg, A. (2019) Osmoregulation in barnacles: An evolutionary perspective of potential mechanisms and future research directions. Frontiers in Physiology, 10:877 

Abramova A., Alm Rosenblad M., Blomberg A., Larsson T.A. (2019) Sensory receptor repertoire in cyprid antennules of the barnacle Balanus improvisus. PLoS One, 14:e0216294

Bay barnacles
Bay barnacles, Balanus improvisus
Photo: Fredrik Pleijel & Kent Berntsson

Contact

Marine yeast, Debaryomyces hansenii

Debaryomyces hansenii is a marine yeast that occurs globally with extreme tolerance to salt/dehydration stress. It is a unicellular free-living organism that mostly occurs in an asexually reproducing haploid state, and it is slightly salt-stimulated and grows best under salt levels in the range of sea-water. Its adaptation to salt also makes it frequently isolated from salt-conserved foods.

RESEARCH OPPORTUNITIES
We will generate a unique genetic resource for experimental work in this marine yeast-species to enable studies that will lead to a better understanding of the mechanistic basis of salinity adaptation. The completed genome from a number of strain isolates opens up for global studies on gene expression and comparative studies of mechanistic differences in its molecular response between strains, but also in relation to the model yeast S. cerevisiae as well as other sequenced yeast species. Studies on D. hansenii will be central in our understanding of the evolution of osmoregulation in marine fungi. 

GENOME RESOURCES

  • Estimated Genome size: 13.8 Mbp
  • Genome sequencing progress: We have conducted resequencing of 17 strains of D. hansenii from various regions and sources to get a better understanding of the species’ genetic diversity. We analyse the data in collaboration with Prof. Gianni Liti (University of Nice, France) with the current goal to establish a pan-genome for the species. 
  • Additional genetic resources:  We are currently establishing the methodology for making gene-deletions in D. hansenii using CRISPR-cas technology.
    The genome for the type strain was completed in 2004. One of the strains, J26, originally isolated by late Prof. Birgitta Norkrans in Kungsbackafjorden 1966, is studied for its physiological responses of glycerol and arabinitol accumulation during salt-stress. D. hansenii strains from different regions and sources have been phenotyped for growth changes under a wide array of conditions, in particular in relation to osmo- and salt-stress. 

KEY REFERENCES
Dujon et al., (2004) Genome evolution in yeasts, Nature 430:35.

Adler, L., Blomberg, A. and Nilsson, A. (1985) Glycerol Metabolism and Osmoregulation in the Salt-tolerant Yeast Debaryomyces hansenii. Journal of Bacteriology. 162:300.

Norkrans, B. (1966) On the occurrence of yeast in an estuary off the Swedish west coast. Svensk botanisk tidskrift 60:4.

Marine yeast, Debramyces
Marine yeast, Debramyces
Photo: CeMEB

Contact

Bladder wrack, Fucus vesiculosus

Bladder wrack is a foundation species in the North Atlantic and is essentially the only perennial species of macroalga present in the northern parts of the Baltic Sea. It provides important habitat for associated flora and fauna, contributing to maintain biodiversity in shallow rocky areas. Bladder wrack reproduces mainly sexually but is also reproducing asexually by fragmentation in the northern and eastern parts of the Baltic Sea.

RESEARCH OPPORTUNITIES
Fucus vesiculosus shows extensive morphological, chemical and ecological variation among populations, and populations are also typically highly genetically differentiated. The species has evolved cell wall modifications to adapt to different levels of the intertidal. It also has an unusually high tolerance to variation in salinity and desiccation. It is used as a model to study the genetic basis of speciation with sibling species, e.g. F. radicans and F. guiryi, as a result of recent speciation events. Given the ability to reproduce asexually, it is also tractable for studies on clonal genome evolution. 

GENOME RESOURCES
Genome assembly is publicly available on NCBI. The raw data from the assembly is not available yet, but feel free to contact us for collaboration on these unpublished genome data. 

  • Genome assembly, basic information
    NG50 = 51.3 kb based on assumed genome length 1.2 Gb
    7,998,267 contigs
    1.2 Gb total length
    2 9 % BUSCO completeness
  • NCBI BioProject: PRJNA629489 
  • Raw data used for assembly 
    Illumina libraries  – 1*180bp, 1*300bp, 1*550bp, 1*2.5 kb (mate-pair), 1*5.5kb (mate-pair)

  • Additional genetic resources
    Transcriptome assembly - Sequence length: 53.750 Mbp, N50: 1206 bp. (PRJNA453106)

  • Population genomic 2b-RAD data from Öresund (Sweden and Denmark) (PRJNA629489)
    RNA-Seq data, gene expression reproductive tissues. (SRR575725)

  • Database resources: albiorix.bioenv.gu.se

KEY REFERENCES
Johannesson et al.(2011) J. Phycol.;

Pereyra et al. (2013) J. Evol. Biol.;

Panova et al. (2016) Marine Genomics;

Rugiu et al. (2020) BMC Genomics;

Kinnby et al. (2020) Front. Mar. Sci. 

 

Fucus
Bladder wrack, Fucus vesiculosus
Photo: CeMEB

Baltic isopod, Idotea balthica

The isopod Idotea balthica is an ecosystem engineer which increases productivity of seagrass beds and seaweed forests by reducing epiphytes. I. balthica is a major part of the diet of many fish species, including cod and, in the Baltic Sea, perch. The species is found both sides the northern Atlantic. It is very common in the Baltic Sea where it lives in association with seagrass and fucoid seaweeds down to salinities of 4 psu. I. balthica has dimorphic sexes and the brooded offspring develop without planktonic stages.

RESEARCH OPPORTUNITIES
Idotea balthica has a short generation time, ca. 3 months in culture, and is very easy to culture. The natural environment is easily reproduced in laboratory experiments and mesocosms, or manipulated in field settings. The species is characterized by its high tolerance to low salinity. As a brooding species, it is an ideal marine model species for evolutionary experimental studies targeting, for example, phenotypic plasticity, local adaptation and response to selection.

GENOME RESOURCES

  • Genome assembly, basic information
    NG50 = 12.9 kb based on assumed haploid genome length 1 Gb
    338 k contigs
    1.54 Gb total length
    80 % BUSCO completeness (using Metazoa reference)
  • NCBI BioProject: PRJNA599581 (data not public yet)
  • Raw data used for assembly
    Illumina libraries  – 2*300bp (125 & 150 bp reads, paired-end), 2*550bp (300bp reads, paried-end).
    PacBio data – 25 Mb, Mean read length 8 kb.
    10 x Chromium data – 690 Mreads, read length 150 bp (mean fragment length 10 kb).
  • Assembly Annotation
    MAKER automated annotation (two iterations). No manual curation.
  • Additional genetic resources
    Transcriptome assembly - Sequence length: 78 Mbp, N50: 1132 bp. (PRJNA451082)
    RNA-Seq data, gene expression due to dietary change. (PRJNA451082)
    Population genomic 2b-RAD data from the Baltic Sea (PRJNA551577)

KEY REFERENCES

Population structure in the Baltic Sea: De Wit et al. 2020

Metabolite detoxification mechanisms: De Wit et al. 2018

Idotea phylogeny: Panova et al. 2016

Plasticity to salinity changes: Wood et al. 2014

Ecology and Distribution in the Baltic Sea: Leidenberger et al. 2012

Host exploitation: Vesakoski et al. 2008

Food and habitat choice: Orav-Kotta & Kotta 2004

Sexual behavioural differences: Jormalainen & Tuomi 1989

Idotea baltica
Baltic isopod, Idotea baltica
Photo: Pierre DeWit

Contact

Rough periwinkle, Littorina saxatilis

The rough periwinkle Littorina saxatilis is a dominant grazer on filamentous and microalgae on rocky shores. It has a wide distribution in the North Atlantic from Greenland to Portugal, and from Baffin Island to Delaware Bay. It commonly reaches densities of several hundred snails per square meter and its removal completely changes the ecosystem of rocky shores. It is an important food source for crabs, and in some areas birds and fishes. Unlike many marine invertebrates, L. saxatilis lacks larval stages and females give birth to small shelled juveniles. This greatly limits dispersal of the snails; however, occasional long-range dispersal occurs by rafting. The species exhibits an exceptional morphological variation, which confused taxonomists for centuries, and received the title of the “Champion of taxonomic redundancy” from the World Register of Marine Species.

RESEARCH OPPORTUNITIES
The species is strongly polymorphic and distinct ecotypes evolve repeatedly in contrasting microhabitats both at the regional and local scales. The "Crab" and "Wave" ecotypes differ in their shell size, shape, color and behaviour. Reproductive barriers between ecotypes appear in contact zones and make the species very suitable for studies of the evolution of local adaptation and reproductive isolation under gene flow.

GENOME RESOURCES
Genome assembly v.1 is produced by Tomas Larsson with help from Mats Töpel and Magnus Alm Rosenblad. The fasta file is publicly available on dryad: https://doi.org/10.5061/dryad.bp25b65. The raw data from the assembly will be available at NCBI. 

  • Genome assembly, basic information
    NG50 = 55.4 kb 
    116,262 scaffolds, gap content 4,8 % 
    1.6 Gb total length (estimated genome size 1.3 Gb)
    Complete BUSCOs: 80%, fragmented BUSCOs: 11%, missing BUSCOs: 9 %
  • Raw data used for assembly
    Illumina libraries  – 1*180bp, 4*300bp, 2*350 bp, 2*550bp, 1*1.5 kb (mate-pair), 1*2.5 kb (mate-pair), 1*5.5kb (mate-pair); PacBio data: 25 Gb, Mean insert size 3 kb.
  • Assembly Annotation
    MAKER automated annotation (two iterations). No manual curation.
  • Additional genetic resources
    Transcriptome assemblies for male (37.8 Mbp), female (36.6 Mbp) and combined (32.8 Mbp) are available at NCBI BioProject PRJNA550990.

KEY REFERENCES
Parallel evolution of the Crab and Wave L. saxatilis ecotypes in Spain, UK and Sweden: Butlin et al. (2014) Evolution 68-4: 935–949

DNA extraction protocols for whole genome sequencing in L. saxatilis and other marine organisms: Panova et al. (2016) In: Bourlat S (ed.) Marine genomics: Methods and Protocols. Springer, New York

Shared and non-shared genomic divergence in parallel ecotypes of L. saxatilis at a local scale in Sweden: Ravinet et al. (2016) Molecular Ecology 25: 287-305

Integration of ecology and genomics in studies of the L. saxatilis ecotypes: Johannesson et al. (2017) In: Oleksiak MF, Rajora OP (eds.), Population Genomics: Marine Organisms. Springer, New York

Cline zone analysis reveals genomic architecture underlying rapid divergence of L. saxatilis ecotypes: Westram et al. (2018) Evolution Letters 2: 297-309

Genomic architecture of divergence in L. saxatilis along several environmental gradients: Morales et al. (2019) Science Advances 5: 13

Multiple chromosomal rearrangements in L. saxatilis ecotypes: Faria et al. (2019) Molecular Ecology 28: 375-1393

Krabbsnäcka och vågsnäcka.
Rough periwinkle, Littorina saxatilis
Photo: Fredrik Pleijel

Contact

Sand goby, Pomatoschistus minutus

The Sand goby inhabits shores of the North East Atlantic and the Baltic Sea. Its behaviours and reproductive strategies include exclusive paternal care with males building nests under mussel shells. The Sand goby is euryhaline, i.e. it is able to adapt to a wide range of salinities, however, not to fresh water. Sand goby life stages from pelagic fry to adults are staple food for cod and other large commercial fishes.

RESEARCH OPPPORTUNITIES
The sand goby is a small and experimentally tractable fish, which is exceptionally well-studied when it comes to reproductive biology and behavioural ecology. It is also interesting from the perspective of adaptive evolution to different seawater environments. Phylogenetically it has an interesting position with respect to teleost evolution and the family of gobies has a worldwide distribution with 2000 species of gobies making generalizations and comparative studies possible. Additionally, they can be kept in the laboratory and will pair, build nests, and begin breeding and thus can be useful for toxicology studies and other anthropogenic impacts involving behaviour. However, feeding larvae has proven to be an obstacle to completion of the life cycle from juvenile to adult in captivity.

GENOME RESOURCES

  • Estimated Genome size: 1.0 Gbp
  • Available sequence information in Dryad assembled scaffolds and adult transcriptomes (5 tissues: brain, liver, spleen, ovary, testes)
  • Genome sequencing progress: (last updated 2020-09-02)
    204,891 scaffolds/contigs from 100 – 2,618,418 bases
    21,093 contigs >500 bases
    NG50 is 127 739 bases
    BUSCO score (actinopterygii_odb9 database) 90, 2% complete genes (87,9 % complete and single-copy), 4,5 % fragmented genes and 5,3 % missing genes.​

  • Additional genetic resources:
    Microsatellite markers,
    22 000 SNP markers
  • Database resources: albiorix.bioenv.gu.se

OTHER RESOURCES
Population genetics and phylogenies of the sand goby and the monophyletic Eastern Atlantic-Mediterranean ‘sand goby’ group (Pomatoschistus, Gobiusculus, Knipowitschia and Economidichthys).

Well-described parasite faunas of several species of the ‘sand goby’ group including P. minutus.

KEY REFERENCES

The nuclear genome and local adaptation: Leder EH, André C, Töpel M, Le Moan A, Blomberg A, Havenhand JN, Lindström K, Volckaert FAM, Kvarnemo C, Johannesson K, Svensson O. A postglacial establishment of locally adapted fish populations over a steep salinity gradient. Journal of Evolutionary Biology. 

Larvae behaviour and ecotoxicology: Asnicar D, Ašmonaitė G, Birgersson L, Kvarnemo C, Svensson O, Sturve J, 2018. Sand goby—an ecologically relevant species for behavioural ecotoxicology. Fishes 2018, 3: 13. doi:10.3390/fishes3010013.

The mitochondrial genome: Adrian-Kalchhauser I, Svensson O, Kutschera VE, Alm Rosenblad M, Pippel M, Winkler S, Schloissnig S, Blomberg A, Burkhardt-Holm P, 2017. The mitochondrial genome sequences of the round goby and the sand goby reveal patterns of recent evolution in gobiid fish. BMC Genomics 201718:177. doi: 10.1186/s12864-017-3550-8

Immigrant reproductive dysfunction: Svensson O, Gräns J, Celander MC, Havenhand J, Leder EH, Lindström K, Schöld S, van Oosterhout C, Kvarnemo C, 2017a. Immigrant reproductive dysfunction facilitates ecological speciation. Evolution 71: 2510-2521. doi: 10.1111/evo.13323

Marine light regimes and rhodopsin: Larmuseau, M.H.D., Vancampenhout, K., Raeymaekers, J.A.M., Van Houdt, J.K.J., & Volckaert, F.A.M. (2010) Differential modes of selection on the rhodopsin gene in coastal Baltic and North Sea populations of the sand goby, Pomatoschistus minutus. Molecular Ecology, 19, 2256-2268.

Sexual behaviour and ecotoxicology: Saaristo M, Craft JA, Lehtonen KK, Björk H, Lindström K, 2009b. Disruption of sexual selection in sand gobies (Pomatoschistus minutus) by 17α-ethinyl estradiol, an endocrine disruptor. Horm Behav 55: 530-537, doi:10.1016/j.yhbeh.2009.01.006.

Parasitic spawning and paternity: Svensson O, Kvarnemo C, 2007. Parasitic spawning in sand gobies: an experimental assessment of nest-opening size, sneaker male cues, paternity, and filial cannibalism. Behav Ecol 18: 410-419.

Fine-scale population genetic structure: Pampoulie C, Gysels ES, Maes GE, Hellemans B, Leentjes V, Jones AG, Volckaert FA, 2004. Evidence for fine-scale genetic structure and estuarine colonisation in a potential high gene flow marine goby (Pomatoschistus minutus). Heredity 92: 434-45.

Microsatellites and paternity in the field: Jones, A. G., Walker, D., Kvarnemo, C., Lindström, K., & Avise, J. C. (2001a). How cuckoldry can decrease the opportunity for sexual selection: data and theory from a genetic parentage analysis of the sand goby, Pomatoschistus minutus. Proceedings of the National Academy of Sciences, 98, 9151-9156.

Sexual selection – a review: Forsgren E. 1999. Sexual selection and sex roles in the sand goby. In Behaviour and conservation of littoral fishes (ed: Almada VC, Oliveira RF, Gonçalves EJ), pp. 249-274. Lisboa: ISPA. Download pdf (900 k).

Sexual selection and resource abundance: Forsgren E, Kvarnemo C, Lindstrom K, 1996. Mode of sexual selection determined by resource abundance in two sand goby populations Evolution 50: 646-654. doi: 10.2307/2410838

--------------------------
Forsgren et al. 1996 Evolution,

Jones et al. 2001 Proceedings of the National Academy of Sciences of the USA,

Larmuseau et al. 2010 Molecular Ecology,

Larmuseau et al. 2010 Molecular Phylogenetics and Evolution,

Saaristo et al. 2009 Hormones and Behavior,

Pampoulie et al. 2004 Heredity,

Svensson and Kvarnemo 2007 Behavioral Ecology,

Adrian-Kalchhauser et al. 2017 BMC Genomics,

Svensson et al. 2017 Evolution,

Asnicar et al. 2018 Fishes.

Sand goby
Sand goby, Pomatoschistus minutus
Photo: Anders Salesjö

Marine diatom, Skeletonema marinoi

The chain-forming marine species Skeletonema marinoi is an important primary producer in the North Atlantic. It is especially abundant during spring bloom, when it reaches densities of millions of cells per litre. The predominant means of propagation is through vegetative division, but sexual reproduction occur and resting spores are formed under some conditions . 

RESEARCH OPPORTUNITIES
Skeletonema marinoi has a benthic resting stage and up to 50 000 propagules per gram of substrate can generally be found in the sediment. The resting cells can survive for at least one hundred years and thereby provide an evolutionary archive in the sediment. These cells can be easily collected, isolated and maintained in culture – generation time is 24 hours. Skeletonema marinoi is an ideal species for resurrection ecology studies, such as the investigation of phenotypic and genotypic responses to environmental change, as both the ancestral and the derived population can be cultured and treated experimentally side-by-side.

GENOME RESOURCES

  • Genome assembly
    A reference genome of one highly characterised strain (R05AC) is available, assembled using Falcon (19 RSII PacBio SMRT cells), with correction performed using Quiver (PacBio data) and Pilon (Illumina HiSeq X data).
  • Estimated genome size: 55Mbp (based on kmer analysis).
    Version 1.1.1 of the reference genome consists of:
    385 primary contigs
    - Length of primary contigs: 77,6 Mbp
    - 2 440 gene models (some manually curated)
    211 associated contigs
    - Length of associated contigs: 19.7 Mbp
    - 5 418 gene models
    2 circularised organellar genomes - plastid (127,2 kbp) + mitochondrion (43,6 kbp)

    Version 1.1.2 of the reference genome consists of:
    (no associated contigs included in this version)
    81 primary contigs 
    - Manual curation performed to remove associated contigs incorrectly labelled as primary contigs, and those which consisted entirely of repeats
    - Length of primary contigs: 54,8 Mbp
    - NG50: 1,2 Mbp.
    - 17 203 gene models (some manually curated)
    2 circularised organellar genomes - plastid (127,2 kbp) + mitochondrion (43,6 kbp)
  • Available resources
    Gothenburg University Marine Algae Culture Collection (GUMACC)
    The strain R05AC used for the reference genome can be ordered from GUMACC. New strains are mainly established from Scandinavian waters, and S. marinoi is currently (2020-05-18) represented in GUMACC by 173 strains isolated from the Kattegat-Skagerrak area, as well as 78 strains from the brackish water Baltic Sea. 

    Bioprojects on NCBI
    Skeletonema marinoi genome project: BioProject PRJNA493755
    Skeletonema marinoi eutrophication project: BioProject PRJNA525337
    Skeletonema marinoi microbiome project: BioProject PRJNA380207

    Albiorix
    Genome browser and BLAST server available to collaborators at the computer cluster Albiorix.

    Mutant collection
    The Skeletonema Marinoi Mutant Collection (SMMC) is under construction, using electroporation to randomly insert a construct containing a bleomycin/zeocin resistance gene in the genome of the reference strain R05AC. Several hundred mutants have so far been generated in this way (2020-05-18).
  • Associated bacteria
    Several bacteria from the S. marinoi microbiome have been isolated, and their genomes have been sequenced.

KEY REFERENCES
Description of S. marinoi: Sarno D et al. (2005) Journal of Phycology 41:151-176

Diversity in the genus Skeletonema: Kooistra WHCF et al. (2008) Protist 159:177-193 

Production of toxic polyunsaturated aldehydes (PUAs): Taylor RL et al. (2009) Journal of Phycology 45:46-53

Genetic structure of S. marinoi in Gullmar Fjord: Godhe A & Härnström K (2010) Molecular Ecology 19:4478-4490 

Genetic structure of revived S. marinoi over a century: Härnström K et al. (2011) PNAS 108:4252-4257

Microsatellites: Almany GR et al. (2009) Molecular Ecology Resources 9:1460-1466

Characterization of life cycle: Godhe A et al. (2014) Protist 165:401-416

Cryopreservation protocol: Day JG et al. (2017) Biopreservation and Biobanking 15:191-202

Method for high-throughput phenotyping: Gross S et al. (2017) Limnology and Oceanography: Methods 16:57-67

Growth on solid medium: Kourtchenko O et al. (2018) Scientific Reports 8:9757

Microbiome and associated bacterial species: Johansson ON et al. (2019) Frontiers in Microbiology 10:1828 

Skeletonema marinoi Mutant Collection: Johansson ON et al. (2019) Scientific Reports 9:5391

 

 

Skeletonema
Skeltonema
Photo: CeMEB