International Journal of Molecular Zoology 2024, Vol.14, No.4, 222-232 http://animalscipublisher.com/index.php/ijmz 222 Research Insight Open Access Comparative Genomics of Fish: Insights into Evolutionary Processes ManmanLi Hainan Institute of Biotechnology, Haikou, 570206, Hainan, China Corresponding email: manman.li@hibio.org International Journal of Molecular Zoology, 2024, Vol.14, No.4 doi: 10.5376/ijmz.2024.14.0020 Received: 26 May, 2024 Accepted: 08 Jul., 2024 Published: 29 Jul., 2024 Copyright © 2024 Li, This is an open access article published under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Preferred citation for this article: Li M.M., 2024, Comparative genomics of fish: insights into evolutionary processes, International Journal of Molecular Zoology, 14(4): 222-232 (doi: 10.5376/ijmz.2024.14.0020) Abstract Comparative genomics provides a powerful tool for understanding evolutionary processes, particularly in the diverse and ecologically significant group of fish. This study explores the evolutionary significance of fish genomics, highlighting the diversity of fish genomes and their key evolutionary milestones through comparative analyses with other vertebrates. Utilizing advanced genome sequencing techniques, bioinformatics tools, and comprehensive genomic databases, this study identifies gene family expansions, adaptive evolution, and evolutionary innovations within fish genomes. A case study on the evolution of antifreeze proteins in Antarctic fish illustrates the broader implications of these findings for understanding adaptation. This study also reveals critical evolutionary processes such as speciation, convergent evolution, and horizontal gene transfer. Looking forward, the integration of emerging technologies and interdisciplinary approaches in fish comparative genomics holds significant potential for advancing our understanding of evolutionary biology and informing conservation efforts. Keywords Comparative genomics; Fish evolution; Gene family expansion; Antifreeze proteins; Speciation 1 Introduction Comparative genomics is a field of biological research in which the genomic features of different organisms are compared. This approach allows scientists to identify similarities and differences in the DNA sequences of various species, providing insights into their evolutionary relationships and the functional elements of their genomes. By comparing the genomes of different species, researchers can uncover conserved sequences that have been maintained throughout evolution, as well as lineage-specific adaptations that have arisen in response to unique environmental pressures (Fertin and Rusu, 2011; Sarropoulou and Fernandes, 2011). Fish represent a highly diverse group of vertebrates, making them an ideal subject for evolutionary studies. Teleost fish, in particular, are the second most well-characterized group of vertebrates in terms of genomic data, with high-quality draft genome sequences available for several model species such as Danio rerio (zebrafish), Gasterosteus aculeatus (stickleback), Oryzias latipes (medaka), Takifugu rubripes (fugu), and Tetraodon nigroviridis (tetraodon) (Negrisolo et al., 2010). The diversity within and among fish species, such as the salmonid fishes, provides a rich context for studying genetic polymorphisms important in adaptation and speciation (Elmer, 2016). Additionally, the availability of recently sequenced genomes for various fish species, including those native to New Zealand, further enhances the potential for comparative genomic studies to reveal evolutionary patterns and processes (Papa et al., 2022). This study utilizes comparative genomics to gain a deeper understanding of the evolutionary processes that have shaped the genomes of fish. By analyzing the genomic data from both model and non-model fish species, this study identifies conserved genomic regions and lineage-specific adaptations; addresses unresolved taxonomic issues among teleost fish and to explore the influence of various factors on phylogenetic tree topology. Ultimately, this study aims to provide new insights into the genetic mechanisms underlying the diversity and adaptation of fish species, contributing to a broader understanding of vertebrate evolution. 2 Evolutionary Significance of Fish Genomics 2.1 Diversity of fish genomes Fish genomes exhibit remarkable diversity, both in terms of size and composition. This diversity is largely driven by the presence and variation of transposable elements (TEs), which can constitute a significant portion of the
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