Dr Iain Perry

(he/him)

BSc (Hons), PhD

Publication

• Date
• Type

Research

While the majority of my work focuses on developing pipelines to more efficiently and reproducably perform Bioinformatics, I remain engaged in a variety of reseach areas, including that of my PhD.

Living the high life: high altitude adaptation in earthworms
To date few have looked into how earthworms have adapted or acclimatised to the harsh and
dynamic environment of high altitude. In this work, I explore the terrestrial invertebrates,
earthworms that were found at high altitude on the volcanic island of Pico in the Azores
(Portugal) and at Les Deux Alpes in the French Alps. I initially identify species presence along an
altitudinal transect compare species diversity and lineage, before investigating gene regulatory
control and genomic adaptation between high and low altitude populations to identify if high
altitude populations have acquired a genetic advantage to their low altitude cousin or if all
worms have it within them to survive if given time to acclimatise.
Altitudinal transects of two temperate-zone mountains were conducted, at Les Deux Alpes and
Pico, to identify presence and abundance of species. The two most abundant species, Lumbricus
terrestris and Aporrectodea caliginosa, were investigated to identify diversity and species
lineage to determine which species better allowed for adaption and acclimatisation
investigations, that are not heavily influenced by deeply rooted species diversity. Having
identified A. caliginosa in Pico as the most suitable candidate for investigating adaption and
acclimatisation with its low population diversity, an de novo genome assembly was developed
and annotated.
Live individuals of A. caliginosa from a high and a low altitude site on Pico were acclimatised to
standard laboratory conditions for six months prior to experimental exposure to conditions
simulating six climatic conditions for two weeks with temperature and oxygen as variables.
RNAseq was performed on the RNA taken from a body transect (including muscular, nerve and
gut tissues) of the exposed experimental worms, and differential gene expression was
calculated and explored between the high and low altitude populations. Despite both
populations normalising in identical soils for 6 months, high altitude individuals had a lower
response in gene expression than the Low altitude individuals and suggested an element of
epigenetic conditioning or adaption allowing a more plastic response to the changes in
conditions. In particular, HMGB1, a gene that is known for its roles in regulating environmental
responses, had a comparatively lower expression in the high altitude population than the low
altitude population when exposed to simulated high altitude climatic stressors. SNP analysis
from transcriptomic sequences revealed the high altitude individuals had SNPs associated with
genes that linked to directly to this gene indicating a level of adaption through SNPs and
acclimatisation through potential epigenetic priming within the high altitude population.

Teaching

I have given lecures and training on a wide range of Bioinformatics including:

RNASeq experiments

Differential gene expression anlaysis

SNP analysis in de novo organisms

E-DNA analysis

Biography

2020: Senior Bioinformatician - Wales Gene Park, Cardiff University

2016: PhD Molecular Genomics - School of Biosciences, Cardiff University

2014: Reseach associate - School of Biosciences, Cardiff University

2012: Research studentship - DMPK, Vernalis

2010: BSc Biochemistry - School of Bioscience, Cardiff University