Abstract

Invasive Lonicera maackii (L. maackii) is one of the highly successful and problematic bush honeysuckles found in the central and eastern of United States of America, which has been reported to pose a threat to native ecosystems by decreasing biodiversity. The mechanism by which L. maackii negatively impact environments is typically through either the direct effect of increased dominance or the indirect effect of territory modification. Numerous studies have documented the negative effects of L. maackii on native biota and the key traits such as seed dispersal, phenology, resistance to herbivory, rapid growth and environmental plasticity that contribute to invasion of L. maackii. In past decades, the studies mainly focused on negative effects and management of L. maackii invasion, and little was done to explore the genetic traits contributing to devastate the native ecosystem. Chloroplast-based genomic and chemical diversity in L. maackii has been reported. However, the whole genomic diversity in L. maackii has not been reported due to the availability of whole genome sequence of L. maackii. The advances in whole genome sequencing technologies and bioinformatic tools allow for studying the genomic diversity of L. maackii at the whole genome level. Genome duplication is a key evolutionary mechanism providing new genetic materials and new gene functions for plants, which play important roles in speciation and adaptation to biotic/abiotic stress. Given the fact that L. maackii is closely related to L. japonica, and whole genome duplication of Lonicera japonica (L. japonica) has been reported (Pu et al., 2020; Yu et al., 2022), we hypothesize that a whole genome duplication is present in L. maackii. In this study, we aim to investigate whether there is a genome duplication in L. maackii with the purpose of exploring the genomic diversity in L. maackii. We also conducted a comparison of genome duplication among the species in Lonicera genus. With the completion of whole genome assembly of L. maackii (Kesel et al., 2022), we conducted the gene prediction using Exonerate and gene duplications analysis using MCScanX in L. maackii. As a result, we predicted 32,642 genes and identified 5,668 genes, 24,911 genes, 703 genes, 902 genes, and 458 genes deriving from Singleton, Dispersed, Proximal, Tandem, and WGD modes, respectively. To our knowledge, this is the first genome duplication analysis that has been reported in L. maackii. Compared to L. japonica, a higher prevalence of Singleton and Dispersed modes of gene duplication was observed in L. maackii. The different genome duplication patterns between L. maackii and L. japonica may result from the difference of whole genome assembly format. The future directions should focus on improving the chromosome-scale genome assembly and whole genome annotation, promoting our understanding on the genome diversity and evolutionary traits in L. maackii and controlling the expansion of L. maackii.

Library of Congress Subject Headings

Honeysuckles--Genome mapping; Invasive plants--United States; Genomics

Publication Date

11-17-2022

Document Type

Thesis

Student Type

Graduate

Degree Name

Bioinformatics (MS)

Department, Program, or Center

Thomas H. Gosnell School of Life Sciences (COS)

Advisor

Michael V. Osier

Advisor/Committee Member

Andre O. Hudson

Advisor/Committee Member

Susan S. Pagano

Campus

RIT – Main Campus

Plan Codes

BIOINFO-MS

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