Short Read Sequencing Reveals Sub-Genome Structure of the Polyploid Pennate Diatom Fragilariopsis cylindrus

Hodgkinson, Kat (2018) Short Read Sequencing Reveals Sub-Genome Structure of the Polyploid Pennate Diatom Fragilariopsis cylindrus. Masters thesis, University of East Anglia.

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Fragilariopsis cylindrus is a species of pennate diatom capable of survival in the extreme,
variable and fluctuating environmental conditions of polar oceans, which hints at genome
plasticity. Here, we use Illumina short-read sequencing and assembly to reveal new
structural details of the F. cylindrus genome. Our assembly methods and analysis based on
k-mer spectra ensures the inclusion of as much content as possible. We highlight the level of
missing content from previous assemblies using the Illumina reads and assembly as a
comparison. We have confirmed this culture of F. cylindrus (Grunow) Krieger CCMP1102 to
have a typical k-mer spectra signature of a polyploid genome. K-mer spectra plots show
three clear peaks created from the frequencies of distinct k-mers found within the reads.
Our sub-genome size estimate of 50.7Mb by k-mer spectra is within a mutually
complimentary range of previous findings based on qPCR of target genes at 57.9Mb (+-
16.9Mb). Estimates based on k-mer frequency suggest a lower-bound 36Mb total diverged
content between A, B and B’ sub-genomes. Local analysis of three fairly contiguous unitigs
show an average of only 92% identity. Our future aim is to produce a fully-phased assembly
of each sub-genome. We will use this fully phased assembly for divergence analysis, as well
as more detailed analysis into gene content and transcriptome expression. We expect the
assembly to be improved with scaffolding using PacBio reads. We have only sequenced one
culture of F. cylindrus, so cannot conclude whether this is a widespread phenomenon or a
product of laboratory culturing. This will become more apparent with future sequencing of
F. cylindrus cultures. The implications of our findings may make F. cylindrus a very
interesting model for evolutionary studies.

Item Type: Thesis (Masters)
Faculty \ School: Faculty of Science > School of Environmental Sciences
Depositing User: Jackie Webb
Date Deposited: 15 Nov 2018 12:20
Last Modified: 31 Aug 2021 00:39


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