International Journal of Molecular Zoology 2024, Vol.14, No.4, 222-232 http://animalscipublisher.com/index.php/ijmz 224 3.3 Comparative genomics databases Comparative genomics databases are essential for storing, organizing, and accessing genomic data from multiple fish species. These databases enable researchers to perform comparative analyses and identify orthologous genes and genomic regions across different species. For instance, a comprehensive phylogenomic database of ray-finned fishes has been compiled, providing genome-scale support for phylogenetic relationships and resolving contentious nodes in fish phylogeny. The Fish-T1K project has generated a large database of fish transcriptomes, integrating them with published fish genomes for potential applications in functional verification, molecular breeding, and drug development (Bian et al., 2019). Additionally, databases such as Ensembl and COSMIC have been utilized to match sequenced fish genomes with cancer gene information, facilitating comparative studies of cancer-related gene copy number variation in fish (Baines et al., 2022). By leveraging these methodologies, researchers can gain deeper insights into the evolutionary processes that shape fish genomes, enhancing our understanding of their biology and informing practical applications in areas such as conservation, aquaculture, and medicine. 4 Key Findings in Fish Comparative Genomics 4.1 Gene family expansions and contractions Gene family expansions and contractions play a significant role in the adaptive evolution of fish. For instance, the study on vertebrate gene family size revealed that gene families in Danio rerio (zebrafish) had undergone substantial expansions, likely due to genome-wide duplication events in their ancestors, followed by contractions due to gene fractionation (Meng and Yang, 2019). Additionally, the whale shark genome study highlighted a major increase in gene families at the origin of jawed vertebrates, independent of genome duplication, suggesting that gene family expansions are crucial for vertebrate evolution (Tan et al., 2021). Furthermore, the 14-3-3 gene family in various fish species showed dynamic evolution characteristics, with recombination events accelerating their evolution (Cao and Tan, 2018). 4.2 Adaptive evolution in fish Adaptive evolution in fish is driven by various genomic mechanisms. The study on whitefish (Coregonus ssp.) demonstrated that relaxed purifying selection is driving the high nonsynonymous evolutionary rate of the NADH2 gene, which may be associated with adaptive divergence and speciation (Jacobsen et al., 2016). Similarly, the analysis of cancer-related gene duplications in fish revealed that higher numbers of tumor suppressor genes are correlated with longer lifespans, suggesting that these genes play a role in adaptive evolution by providing genetic defenses against oncogenic processes (Baines et al., 2022). Additionally, orphan genes in bony fish have been implicated in adaptive evolution, contributing to traits such as fin and tail development and kidney physiology. 4.3 Evolutionary innovations in fish genomes Fish genomes exhibit several evolutionary innovations that contribute to their adaptability and diversity. The study on salmonid fishes, particularly charr (Salvelinus), highlighted the use of genomic tools to identify genetic polymorphisms important in adaptation and speciation, revealing the genetic mechanisms behind the diversity of salmonid fishes (Elmer, 2016). The whale shark genome study also discovered a new toll-like receptor (TLR29) and multiple copies of NOD1, indicating novel immune system adaptations in chondrichthyan fish. Moreover, the comparative cytogenetic analysis of Pyrrhulina species revealed the presence of a multiple X1X2Y sex chromosome system and the dynamics of repetitive DNA, contributing to karyotype divergence and evolutionary innovations in these small-sized fish (Moraes et al., 2019). 4.4 Comparative genomics and phylogenomic approaches Comparative genomics and phylogenomic approaches are essential for understanding the evolutionary relationships among fish species. The study on model fish species used robust phylogenetic frameworks to reconstruct genome-level evolution, revealing common features conserved across genomes and identifying lineage-specific characteristics (Negrisolo et al., 2010). This approach is crucial for resolving taxonomic issues and understanding the evolutionary history of teleost fish. Additionally, the comparative analysis of gene family size across vertebrates provided insights into the evolutionary patterns of gene family size changes, highlighting the importance of comparative genomics in studying vertebrate evolution.
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