eBangor

Investigating mechanisms of genome expansion in Corydoradinae catfish

Marburger, Sarah (2015) Investigating mechanisms of genome expansion in Corydoradinae catfish. PhD thesis, Prifysgol Bangor Bangor.

[img] Text
Signed Declaration Marburger.pdf
Restricted to Repository staff only

Download (197kB)
[img] Text
Investigating Mechanisms of Genome Expansion in Corydoradina.pdf
Restricted to Repository staff only until 1 December 2018.

Download (2MB)

Abstract

The Corydoradinae catfish are a diverse sub-family of neo-tropical catfishes (order Siluriformes) with more than 170 species described to date. One of the most compelling features of this sub-family is the enormous amount of variation in genome size. With species containing between 0.5 pg and 4.8pg of DNA, variation is comparable to that found across the Teleostei as a whole. Previous phylogenetic analysis identified nine distinct lineages within the Corydoradinae, with more basal lineages possessing smaller genomes and with largest genome sizes found in the most derived lineages. To date, nothing is known about the mechanism that drove this genome expansion in the Corydoradinae, though Whole Genome Duplication (WGD) events have been suggested. Here, the incidence of WGD events has been investigated using a Hox gene and a restriction site associated DNA (RAD) sequencing data set. Both data sets identified a major duplication event at the base of the group, with additional duplication events occurring across the family. These duplication events were shown to have led to relaxed purifying selection and increased functional divergence of HoxA13a copies in the Corydoradinae compared with teleosts that have not undergone additional rounds of WGD. The RAD data set confirmed significant genome-wide shifts in duplicate, multi-haplotype regions across the Corydoradinae, and indicates that several species from lineages 6-9 are functionally polyploid, whereas species that underwent earlier WGDs have largely diploidized and are likely paleopolyploids. An increase in paralogous genes was noted, with Gene Ontology suggesting that gene retention in the Corydoradinae mirrors previously described retention in Tetraodon following the fish-specific genome duplication in the Teleostei. Intriguingly, the RAD data also identified a significant expansion of Transposable Elements (TEs), driven by a DNA TE superfamily (Tc1-Mariner). This expansion significantly contributed to the genome size variation, though to a lesser degree than the WGD events identified within this thesis.

Item Type: Thesis (PhD)
Subjects: Degree Thesis
Departments: College of Natural Sciences > School of Biological Sciences
Degree Thesis
Date Deposited: 27 Apr 2016 15:43
Last Modified: 30 Aug 2017 10:42
URI: http://e.bangor.ac.uk/id/eprint/6562
Administer Item Administer Item

eBangor is powered by EPrints 3 which is developed by the School of Electronics and Computer Science at the University of Southampton. More information and software credits.