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The genomic signatures of adaptation in harmful Sargassum blooms of the Caribbean Sea (CASE studentship)

  • Full or part time

    Dr M Kapralov
  • Application Deadline
    Applications accepted all year round
  • Competition Funded PhD Project (European/UK Students Only)
    Competition Funded PhD Project (European/UK Students Only)

Project Description

Background
This CASE studentship will apply evolutionary genomic approaches to understand environmental adaptation in the Caribbean harmful bloom-forming macroalgae, Sargassum natans. The studentship will be based in Durham and Newcastle (Dr Kapralov); the student will have 3-6 months’ CASE placement with the Grupo Puntacana Fundación, which is responsible for coastal ecotourism in the Dominican Republic. The Dominican Republic is an Overseas Development Aid recipient with the largest economy of any Caribbean Island nation: we focus on it as an exemplar for harmful algal blooms in the Caribbean and western Atlantic.

Aims
Specific aims are:
a) To collect bloom-associated and non-bloom-associated Caribbean S. natans strains and establish long-term cultures at our CASE partner’s research station in Punta Cana, Dominican Republic.
b) To generate draft genome sequences (PacBio) from each of these S. natans strains
c) To combine gene expression (RNAseq) and whole-genome polymorphism data to identify loci under selection in bloom-forming Sargassum seaweeds
d) To develop and encourage the student as an independent researcher

Methodology (and Research Training for the Student)
Work will begin by collecting bloom-forming and non-bloom-forming S. natans strains in conjunction with our CASE partners. Genomic DNA will be extracted and sequenced using PacBio reads to generate a draft genome. RNAseq data will also be collected from each strain under different growth conditions (high nutrient vs. low nutrient) to link genome differences to gene expression. Little is known about adaptation and selection in seaweed genomes, so the student will develop an existing RNAseq bioinformatics pipeline to highlight differentially expressed genes between S. natans strains. Genome-wide association scans (Q-Q plots) will give preliminary links between bloom-formation and genotype before more powerful tests are applied (single point/haplotype analysis). The focus will be on scanning for selection (identifying sweeps, etc.) using well-established genetic tools, combining these with environmental data collected for each sample in collaboration with the CASE partner to highlight associations between haplotypes and the environmental conditions that trigger blooms (e.g. fertiliser leaching from cultivated land in Florida and the Caribbean).

Finally, results will be fed into bloom mitigation plans for the Caribbean region. The Durham PI has already established links with multiple stakeholders in the Dominican Republic and is currently advising the government of the Dominican Republic on responses to Sargassum blooms.

Timetable of Activities
Months 1-12: Induction and training - introduction to seaweed culturing and molecular biology - fieldtrip to CASE partner to collect S. natans strains and establish cultures in the Dominican Republic - gDNA extraction and PacBio sequencing – R coding
Months 13-24: Scans for selection from PacBio reads - Second fieldtrip to carry out RNAseq on cultivated S. natans strains - development of RNAseq analysis pipeline
Months 25-42: - Development of the student’s own research ideas and generation of new NGS data:
a) Competitive growth experiments to use population genomics to test coexistence theory (associating competitive fitness with haplotypes).
b) Acquiring population genomic data (e.g. RADseq) to correlate with satellite imaging data to investigate the dynamics of S. natans bloom formation
Months 42-48: Writing up.

Funding Notes

NOTE: For projects in competition with others if you don’t state how you wish applicants to apply we will use the standard wording “This project is in competition with others for funding. Success will depend on the quality of applications received, relative to those for competing projects. If you are interested in applying, in the first instance contact the supervisor, with a CV and covering letter, detailing your reasons for applying for the project” and request that staff ask only the best applicants to submit an application.

References

Smetacek V, Zingone A (2013) Green and golden seaweed tides on the rise. Nature 504, 84-88.
Amaral-Zettler LA, Dragone NB, Schell J, Slikas B, Murphy LG, Morrall CE, Zettler ER. (2017). Comparative mitochondrial and chloroplast genomics of a genetically distinct form of Sargassum contributing to recent “Golden Tides” in the Western Atlantic. Ecology and Evolution, 7(2), 516–525.
De Clerck O, Kao S-M, Bogaert KA, Blomme J, Foflonker F, Kwantes M, Vancaester E, Vanderstraeten L, Aydogdu E, Boesger J, Califano G, Charrier B, Clewes R, Del Cortona A, D’Hondt S, Fernandez-Pozo N, Gachon CM, Hanikenne M, Lattermann L, Leliaert F, Liu X, Maggs CA, Popper ZA, Raven JA, Van Bel M, Wilhelmsson, PKI, Bhattacharya D, Coates JC, Rensing SA, Van Der Straeten D, Vardi A, Sterck L, Vandepoele K, Van de Peer Y, Wichard T, Bothwell, JH. (2018). Insights into the Evolution of Multicellularity from the Sea Lettuce Genome. Current Biology
Wichard T, Charrier B, Mineur F, Bothwell JH, Clerck OD, Coates JC (2015) The green seaweed
Ulva: a model system to study morphogenesis. Frontiers in Plant Science 6, 1-8.
Hermida-Carrera C, Fares MA, Fernández A, Gil-Pelegrin E, Kapralov MV, Mir A, Molins A, Peguero-Pina JJ, Rocha J, Sancho-Knapik D, Galmes J. Positively selected amino acid replacements within the RuBisCO enzyme of oak trees are associated with ecological adaptations. PLoS ONE 2017, 12(8), e0183970.
Galmés J, Kapralov MV, Copolovici LO, Hermida C, Niinemets Ü. Temperature responses of the Rubisco maximum carboxylase activity across domains of life: phylogenetic signals, trade-offs, and importance for carbon gain.Photosynthesis research 2015, 123, 183-201.

How good is research at Durham University in Biological Sciences?

FTE Category A staff submitted: 39.00

Research output data provided by the Research Excellence Framework (REF)

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