Date of Award

2023

Document Type

Dissertation

Degree Name

Philosophy (Ph.D)

Department

Biological Sciences

First Advisor

Juan C Santos

Second Advisor

Dianella G Howarth

Third Advisor

Javier F Juárez

Abstract

The onset of high-throughput RNA-sequencing (RNA-seq) technology allowed research into transcriptomics to accelerate exponentially aided by the rapid advancement of bioinformatic pipelines. The Pincho workflow, my first research endeavor, is a transcriptomic workflow developed to create an avenue of high-quality reconstructions from RNA-seq data. High-quality reconstruction standards entail longer transcripts, more complete transcripts, and more raw data utilization. We have discovered an ideal trio of assemblers between transABySS, rnaSPAdes and TransLiG that would best reconstruct next-generation sequencing data according to these standards. We utilized Pincho to drive two distinct experiments: (1) exploring the genetic basis for the successful invasion of Eleutherodactylus coqui (E. coqui) from Puerto Rico (PR) to mainland US and (2) exploring the genetic variation across anuran oxygen delivery and consumption systems. E. coqui is one of the top four invasive anurans in the US; described as a pest that has destabilized ecosystems and cost the taxpayers millions of dollars. Few researchers delve into the genetic explanations as to how and why E. coqui are so successful in colonizing locations outside PR. We discovered several differentially expressed defense response transcripts that differ between the two populations; with a focus on a novel cathelicidin sequence that is only expressed in native E. coqui. The absence of cathelicidin expression in invasive E. coqui leads us to attribute their successful invasion to entering a cleaner environment and subsequently having more energy to utilize on reproduction and expansion. As we further studied E. coqui cathelicidin we questioned how variability in transcript structure might be more widespread in anurans, especially within oxygen delivery and conservation systems. Anurans are described as hypoxia/anoxia resilient in literature, thus we hypothesized these systems would be highly conserved. Our results revealed that hemoglobin was instead under significant episodic diversifying selection. Sites neighboring crucial heme and oxygen binding sites were also found to be under positive selection leading us to believe that these changes could alter overall oxygen affinity and lead to hematological consequences. We speculate that even if anurans are hypoxia/anoxia resilient, resilience levels can differ between species as shown in the sequence divergence in anuran protein alignments.

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