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Publication Date

2023-5

First Advisor

Laura A. Katz

Document Type

Honors Project

Degree Name

Bachelor of Arts

Department

Biological Sciences

Keywords

Eukaryotic microbes, bioinformatics, Arcellinida, protists, evolution and genetics, transcriptomics

Abstract

The evolution of lineage-specific genes, genes found in one lineage with no homologs in others, remains poorly understood in uncultivable microbial eukaryotes. Here, we study lineage-specific genes in Arcellinida, an uncultivable clade of shelled amoebae whose fossil record dates back ~800 million years. As this lineage lacks reference genomes, we used single-cell transcriptomic data to explore lineage-specific gene families (LSGFs) in this diverse clade. Here, we characterize Arcellinida-specific and Hyalosphenia species-specific gene families through analyses of 131 Arcellinida transcriptomes representing most major lineages. We deployed bioinformatic tools such as a machine-learning algorithm (TIdeS) to identify open-reading frames (ORFs) from transcripts and analyze the results. Using scripts written for this project, we identified 82 ancient Arcellinida-specific gene family candidates as well as 123 gene families and 86 gene families specific to Hyalosphenia papilio and Hyalosphenia elegans, respectively. Hyalosphenia papilio and Hyalosphenia elegans are two ubiquitous Arcellinida species found in bog habitats that are suspected to have cryptic species. Our results show that it is possible to study the evolution of new genes in uncultivable microorganisms using transcriptomic data and bioinformatic tools. Future work includes looking for positive selection signatures in these genes, and finding LSGF evolutionary patterns by mapping the appearance of LSGFs onto the Arcellinida phylogenetic tree. These new genes can give us insight into the population genomics and the evolution patterns of new genes in these understudied taxa.

Rights

©2023 Angela Kaijia Jiang. Access limited to the Smith College community and other researchers while on campus. Smith College community members also may access from off-campus using a Smith College log-in. Other off-campus researchers may request a copy through Interlibrary Loan for personal use.

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