Language like behavior in protein secondary structure and analysis of mitochondrial genomes and transposable elements in Antarctic notothenioid fishes

Minhas, Bushra Fazal

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https://hdl.handle.net/2142/132733 Copy

Description

Title

Language like behavior in protein secondary structure and analysis of mitochondrial genomes and transposable elements in Antarctic notothenioid fishes

Author(s)

Minhas, Bushra Fazal

Issue Date

2025-09-02

Director of Research (if dissertation) or Advisor (if thesis)

Catchen, Julian M

Doctoral Committee Chair(s)

Catchen, Julian M

Committee Member(s)

• Bell, Alison M
• Roca, Alfred L
• Beck, Emily A

Department of Study

Illinois Informatics Institute

Discipline

Informatics

Degree Granting Institution

University of Illinois Urbana-Champaign

Degree Name

Ph.D.

Degree Level

Dissertation

Keyword(s)

bioinformatics, genomics,

Abstract

The organization and evolution of genomes can be shaped by underlying evolutionary principles, particularly adaptive forces that contribute to the structural and functional changes in genome architecture. This thesis explores the evolution of genome architecture in two distinct perspectives. In the first, I explore the evolution and organization of hierarchical biological systems using the Menzerath Altman Law (MA law) to examine the secondary structure of transcribed proteins. This law, derived within the field of linguistics, states that “the longer the system, the smaller its parts,” presenting an energy-balance principle in which system-level growth is compensated for by the reduction in size of the individual components thereby maintaining the system’s overall functional and metabolic costs. I checked the dependence of length of secondary structure elements against the number of secondary structures in a protein domain in 60 proteomes and observed a negative correlation between the number of secondary structures and their average lengths in all proteomes, showing that protein secondary structures follow the MA law. In the second perspective, I explored the potential role of components of the genomes of Antarctic notothenioids: mitochondrial genomes and transposable elements (TEs) in their adaptation to extreme cold temperatures of Southern Ocean. For mitochondrial genomes, I assembled and annotated five Antarctic notothenioid genomes, including four icefishes (Champsocephalus gunnari, C. esox, Chaenocephalus aceratus, and Pseudochaenichthys georgianus) and the cold specialized Trematomus borchgrevinki. Using long-read sequencing and k-mer analysis I was able to identify extensive tandem duplications of the mitochondrial genome including the ND6 gene, two tRNAs, and the associated control regions in all icefishes, and I also detected heteroplasmy in C. aceratus and C. esox. Given the role of mitochondrial genomes in energy production and other significant biological processes, these extensive genomic changes may provide an insight into their potential contribution in cold adaptation. Given the abundance of TEs in most eukaryotic genomes, I wanted to explore their potential role in the adaptation of Antarctic notothenioids to extreme temperatures. I selected twelve notothenioids, including two non-Antarctic species and 10 cryonotothenioids, which included two secondarily temperate species, to perform a comparative analysis of their respective TE repertoires. I annotated these genomes for TEs and observed a correlation between genome sizes and TE expansion. I also explored the distribution of TEs in genomic regions to understand where in the genome most TE expansion is taking place. I also analyzed the distribution of intact vs fragmented TEs and observed that only a small percentage of annotated TEs are actually intact and the annotation reports form annotation software could be an overestimation of actual TE activity. Altogether this thesis offers an insight in the organization of hierarchical systems using the MA law and sheds light on how non-genic elements can provide raw material or be involved in adaptation to changing environments.

Graduation Semester

2025-12

Type of Resource

Thesis

Handle URL

https://hdl.handle.net/2142/132733

Copyright and License Information

Copyright 2025 Bushra Fazal Minhas

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