Computational analysis of eukaryotic metatranscriptomes from diverse marine environments

Toseland, Andrew (2013) Computational analysis of eukaryotic metatranscriptomes from diverse marine environments. Doctoral thesis, University of East Anglia.

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Phytoplankton are photosynthetic microbes that form the basis of the marine
food web and are estimated to produce over half of all oxygen in the Earth's
atmosphere. Recent advances in high-throughput DNA sequencing technologies
have allowed scientists to sample the set of genes actively transcribed from communities
of microbes in-situ. This set of transcripts (the metatranscriptome)
provides a snapshot of actively transcribed genes at the time of sampling, and
can provide insights into microbial metabolism and their relationship with their
environment. In this thesis we present the computational analysis of eukaryotic
phytoplankton metatranscriptome data sampled from representative marine
environments; the simulation of metatranscriptome data for benchmarking
computational tools; and analysis carried out on a newly sequenced eukaryotic
phytoplankton genome.
Transcripts a�liated with ribosomal proteins and associated with translation
dominated in all but the Equatorial Paci�c metatranscriptome sample.
Hierarchical clustering of the metatranscriptome samples by taxa produced two
groups: the diatom dominated and the alveolate dominated. However, clustering
by Gene Ontology terms clustered the samples by environment type (tropical,
temperate and polar), producing a gradient of translation-associated transcripts
which increased as the in-situ temperature of the samples decreased. A strong
correlation (R = 0:9) was detected between the relative proportion of transcripts
associated with temperature and the in-situ temperature. Laboratory
experiments on model diatom species under control conditions con�rmed that
as the in-situ temperature decreases, these model diatoms produce more transcripts
and consequently more ribosomal proteins.
A translational e�ciency experiment demonstrated that the rate of translation
decreased under low temperatures for a model diatom species. This suggested
that the increased production of ribosomes acts as a compensatory mechanism
under low temperatures. As more ribosomes require more phosphate-rich
rRNAs we hypothesised that this could have an impact on biogeochemical cycles
(E.g. the Red�eld ratio of Nitrate (N) to Phosphate (P)). This was modelled
by our collaborators from the University of Exeter, who produced a global phytoplankton
cell model of resource allocation. They showed how the N:P ratio
di�ers across latitudinal temperature zones and predicted the impact of increasing
temperature on global N:P.

Item Type: Thesis (Doctoral)
Faculty \ School: Faculty of Science > School of Computing Sciences
Depositing User: Users 2259 not found.
Date Deposited: 12 Jun 2014 14:32
Last Modified: 12 Jun 2014 14:32

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