Doctor of Philosophy
Smith, David R.
DNA sequencing technologies have undergone tremendous advancements in recent years, but assembling, annotating, and analyzing a nuclear genome is still a huge undertaking, especially for small laboratory groups, partly because many eukaryotic genomes are repeat-rich and contain thousands of genes and introns. The Antarctic harbors a variety of algae that can withstand extreme cold but do not grow at warmer temperatures (psychrophiles), including the unicellular green alga Chlamydomonas sp. UWO241 (a.k.a. UWO241). Little is known, however, about how psychrophilic algae evolved from their respective mesophilic ancestors by adapting to particular cold environments. To present insights into this issue,I critically determined the draft nuclear genome (~212 Mb, 16,325 protein-coding genes) sequence of UWO241 and performed comparative genomic analyses. Firstly, an assembly pipeline was developed for processing high throughput sequencing (DNA-Seq) reads into genomic contigs. These contigs, alongside transcriptome sequencing (RNA-Seq) reads, were fed into an annotation pipeline, containing the commonly used bioinformatics gene-profiling software. Computational analyses were carried out on a powerful in-house computer. Finally, comparative genomic analyses were performed between UWO241 and its close green algal relatives in the Chlamydomonadales revealing: (1) UWO241 harbors hundreds of highly similar duplicate genes involved in diverse cellular processes, some of which I argue are aiding its survival in the Antarctic via gene dosage; (2) UWO241 encodes a large number (³37) of ice-binding proteins (IBPs), putatively originating from horizontal gene transfer; and (3) UWO241 appears to have an expanded set of orthologous gene families for reverse transcriptase, IBPs and antenna proteins. These investigations deepen our understanding of evolution between psychrophilic and mesophilic algae and help unravel the existence of common mechanisms in the adaptation to cold environments.
Summary for Lay Audience
Most of the Earth exists at or below the freezing point of water. Such extreme environments can harbour a variety of organisms, including psychrophiles, which can withstand intense cold and cannot survive at more moderate temperatures. Lake Bonney is a permanently ice-covered lake in the McMurdo Dry Valleys of Antarctica. It is home to many cold-adapted microbes including the unicellular green alga Chlamydomonas sp. UWO241 (a.k.a. UWO241). Several important aspects of its biology, including physiology, molecular biology of photosynthesis and comparative genomics, have been studied in detail over the past 25 years. Here, the draft genome of UWO241 was determined, including a highly contiguous genome assembly and well-annotated coding regions. Furthermore, a comparative genomic framework between UWO241 and its close green algal relatives as well as other cold-adapted algae was built. Remarkably, UWO241 is unique in many ways. For example, the genome has large size of noncoding regions. On the other hand, many genes are duplicated and some gene families encoding important functions even contain more genes in the UWO241 genome than other green algal relatives, such as antenna protein genes, ribosome genes, and ice-binding protein genes. These features deepen our understanding of evolution between psychrophilic and mesophilic algae and help unravel the existence of common mechanisms in the adaptation to cold environments.
Zhang, Xi, "Sequencing and Assembling the Nuclear Genome of the Antarctic Psychrophilic Green Alga Chlamydomonas sp. UWO241: Unravelling the Evolution of Cold Adaptation" (2021). Electronic Thesis and Dissertation Repository. 7609.
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Available for download on Thursday, July 01, 2021