I’m currently part of Prof. Rob Ness’s lab at the University of Toronto Mississauga, investigating the genome of the model organism Chlamydomonas reinhardtii in trying to answer fundamental questions about genome evolution and recombination rate variation. Most if not all of my work is done in Python, R (I am an unapologetic tidyverse enthusiast), and the Unix shell/bash.
About Chlamydomonas reinhardtii
C. reinhardtii has been an important model organism for decades now in a variety of subfields within biology. A unicellular, facultatively sexual (i.e. capable of reproducing clonally or sexually), photosynthetic organism with two flagella, C. reinhardtii has been used in studies of organelle inheritance, cell motility, photosynthesis, and evolutionary genetics. In 2007, its genome was sequenced in its entirety and released to the world, bringing the alga into the ever-growing world of genomics.
Recombination in the MT locus of C. reinhardtii and consequences for selection efficacy
‘Sex’ in C. reinhardtii is determined by a dimorphic, crossover-suppressed mating type locus, which encodes an individual as either MT+ or MT-. C. reinhardtii is isogamous (equal sized gametes) which means there are no sex differences; hence the term ‘mating type’. The two alleles of the MT locus can be thought of as ‘X and Y chromosomes’, except that each individual only carries one and that they’re genetically very similar.
Unexpectedly similar, that is. Work has shown that the two MT alleles of C. reinhardtii are hardly differentiated from one another. Meanwhile, its multicellular, anisogamous relative Volvox carteri has shown over 100x more differentiation between its own MT alleles (Ferris 2010). Later work showed evidence for gene conversion, a form of noncrossover recombination, in two C. reinhardtii genes that had copies in both MT alleles, suggesting that genetic exchange was preventing the two alleles from diverging.
For this project, we estimate levels of genetic exchange across the MT locus of C. reinhardtii, and undertake a population genetic analysis to find out whether gene conversion is sufficient to avoid the differentiation and degeneration that is often seen in sex determining loci, asking the questions: 1) What are the spatial patterns of LD across MT? 2) Do patterns of polymorphism or divergence between MT alleles reflect the strength of LD? 3) Do shared and MT-limited regions show evidence for differences in selection efficacy? 4) Do patterns of inter-chromosomal LD between mating type alleles and organelle genomes suggest leaky uniparental inheritance?
Related publication: Hasan AR, Duggal JK, Ness RW. (2019) Consequences of recombination in the mating type locus of Chlamydomonas reinhardtii. bioRxiv. doi:/10.1101/565275. Available online.
Recombination rate variation in Chlamydomonas reinhardtii
The very reason sex evolved in the first place was to shuffle genetic variation via the process of recombination, thus speeding up the rate of adaptation. However, despite the fundamental role recombination plays in genome evolution, the rate of recombination (RR) varies at multiple levels in nature, with variation in recombination frequency observed between species, populations, and even within individual genomes. For this project, I am emplying population genetic methods to estimate the fine-scale landscape of recombination in Chlamydomonas reinhardtii, asking the following questions: 1) Are there recombination hotspots in C. reinhardtii, and if so, to what extent are they active in the genome? 2) What genomic features predict elevations in recombination rate variation? 3) How does recombination rate relate to nucleotide variation, and is there evidence of linked selection in the genome? With this project, I hope to work towards a greater understanding of recombination within protists, as well as the population genetics of this important model alga.
Related publication: Hasan AR, Ness RW. (2018) The genomic landscape of recombination rate variation in Chlamydomonas reinhardtii reveals effects of linked selection. bioRxiv. doi:10.1101/340992. Available online.
phageParser - extracting and organizing CRISPR information from opengenetic data
Unlike us, bacteria do not have the luxury of full-fledged immune systems to
protect them from the harsh world of viruses (or bacteriophages in bacteria
world – often abbreviated to just ‘phage’). Instead, however, bacteria encode
what are known as CRISPR-Cas systems (where CRISPR stands for Clustered
Regularly Interspaced Short Palindromic Repeats) - regions of DNA sequence that
respond to infection by creating both ‘spacer’ sequences from viral DNA as well
as small interfering RNAs. If the same phage invades the bacterium again, these
small interfering RNAs are able to recognize and cut them, effectively granting
the bacterium a form of adaptive immunity. CRISPR-Cas systems are fairly
diverse in nature, and ongoing research continues to characterize new forms.
Outside of my primary projects in C. reinhardtii, I’ve been collaborating
with PhD student Madeleine Bonsma-Fisher and the Goyal
phageParser, a tool currently
still in development that aims to leverage openly available data to compile a
database of CRISPR-related information for downstream analyses. More recently,
I’ve been looking into the repeat arrays across different CRISPR systems; these
are mostly identical sequences interspersed between spacers, and often feature
occasional base substitutions within them, with the number of mismatches
generally ramping up closer to the end of an array (5’ -> 3’). With these data,
I’m looking to answer the following questions: 1) Are certain sites within
repeat regions more liable to experience base substitutions than others? 2)
What is the spectrum of base substitutions in repeat regions? 3) How widespread
is this trend of increased mismatches nearer to the ends of arrays?
Endophytes as biocontrols for the Côte d’Ivoire Lethal Yellowing (CILY) disease
As part of my undergraduate research work, I attempted to identify endophytic microbes that may potentially be used as biocontrols against the Côte d’Ivoire Lethal Yellowing (CILY) disease, which had previously destroyed approximately 350 ha of coconut trees in the West African country. This was done by creating profiles of the microbial communities present within both infected and uninfected trees. A ‘dilution-to-extinction’ method of high-throughput culturing was used in order to cultivate both bacterial and fungal endophytes directly from samples collected from the town of Grand-Lahou, followed by molecular analyses for strain identification. Our results identified Trichoderma, Penicillium, Bacillus, and Pseudomonas as endophytes present within coconut palms. Several of these endophytes have historically been used as part of microbial biocontrol consortia against other plant pathogens such as Fusarium, and show promise as potential biocontrols to be tested for use against CILY in field studies.
Related publication: Morales-Lizcano et al. (2017) Microbial diversity in leaves, trunk and rhizosphere of coconut palms (Cocos nucifera L.) associated with the coconut lethal yellowing phytoplasma in Grand-Lahou, Côte d’Ivoire. Available online.
Bonus: Here’s a fun and largely jargon-free one-minute video summary of the project that I made.
ahmed.hasan [at] mail [dot] utoronto.ca