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. C. reinhardtii also sees intensive study for its ability to produce compounds that could be used as biofuels… and may just save the planet one day. You heard it here first!
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. I am currently employing 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.
Uniparental organelle inheritance in Chlamydomonas reinhardtii
Organelle inheritance is more often than not uniparental in nature - for instance, you, reading this right now, inherited your mitochondria entirely from your mother (sorry, dad). The script is largely similar in plants, with both plastid and mitochondrial genomes usually being inherited from one parent apiece. In C. reinhardtii, a dimorphic mating type locus classifies individuals as being either mt+ or mt-, depending on which of the two mating type alleles they carry; sex then only occurs between mt+ and mt- individuals. Uniparental organelle inheritance also holds in C. reinhardtii: the chloroplast genome is inherited from mt+ parents, and the mitochondrial genome from mt- parents.
However, Ruth Sager’s pioneering work on C. reinhardtii back in the 1950s found evidence of chloroplast markers being biparentally inherited; that is to say, her research showed that the chloroplast genome in a given individual exhibits partial inheritance from the mt- parent as well. More recent work exploiting statistical associations between alleles, or linkage disequilibrium (LD), has shown that the recombination rates in C. reinhardtii’s plastid and nuclear genomes are in fact similar (Ness 2016), which would not occur in the case of uniparental inheritance. LD, however, itself reflects co-inheritance of genomic features - and thus leakage in inheritance can be quantified by reductions in LD between an organelle genome and the corresponding mating type allele it should otherwise be inherited with. I am therefore using estimates of LD to assess both biparental inheritance in the chloroplast and whether there is any leakage in inheritance of the mitochondrial genome. This work aims to paint a clearer picture of these genetic processes in C. reinhardtii, and provide further insight into the evolution of stereotypically non-recombining genomic regions.
phageParser - extracting and organizing CRISPR information from open genetic 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 group on
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