Date of Award

2025

Document Type

Thesis

Degree Name

MS in Biology

Department

Biological Sciences

First Advisor

Dianella G Howarth

Second Advisor

Richard Stalter

Third Advisor

Florin Catrina

Abstract

The genus Lonicera (Caprifoliaceae) exhibits great diversity in floral symmetry, petal fusion, and organ arrangement, making it an ideal system for exploring the genetic basis of morphological evolution. We focus here on the roles of CYC and CUC gene families, (CYC2A, CYC2B, CYC3A, CYC3B, CUC2A, and CUC2B) and their potential contributions in shaping floral symmetry and organ fusion. The data set included nucleotide sequences from over 90 Lonicera species, extracted from samples collected from natural habitats or herbaria and then sequenced. A custom bioinformatics pipeline was developed in R using Bioconductor packages to automate BLAST searches, filter results, scan for motifs, reverse complementation, and multiple sequence alignment. Sequence verification was performed using NCBI BLASTn, with orientation correction guided by conserved motifs identified from MEME. PlantPAN 4.0 was used to identify transcription factor binding sites (TFBSs) across multiple regions for each gene. Sequences were aligned using DECIPHER and further curated based on conserved motifs and start/stop codon presence. Compared to traditional alignment software, the specificities of each gene were able to be accounted for through this flexible and semi-automated approach allowed for improved biological accuracy from gene specific alignment adjustments, producing more viable alignments compared to conventional software such as Clustal Omega or MUSCLE. The resulting alignments will be used to generate phylogenetic trees and examine transcription factor binding sites presence comparatively between various species, and overall shedding light onto evolution through gene regulation contributing to morphological development. This provides new insights into how conserved gene expression patterns and regulatory region evolution has contributed to the vast diversification of floral morphology in Lonicera. Ultimately, the utility of integrating custom bioinformatics pipelines with motif-based alignment strategies to study gene family evolution was performed and shown as viable in providing broader implications for understanding the genetic regulation of plant morphology in angiosperms and be used as a tool for comparative genomics and developmental biology as a whole.

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