International Journal of Molecular Zoology, 2025, Vol.15, No.1, 38-47 http://animalscipublisher.com/index.php/ijmz 41 Figure 1 Gene family comparisons. (a) Dynamic evolution of gene families among eight teleost species. Green and red numbers represent the expanded or contracted gene families in each lineage, respectively. MRCA: most recent common ancestor. (b) Specific and expanded gene families in the NOD-like signalling pathway in the giant grouper. The giant grouper-specific gene family is indicated in blue. The expanded gene families are indicated in blue. Gene copy numbers are shown in front of the corresponding genes. (c) Comparison of the expanded gene families in the NOD-like signalling pathway. The areas of circles are proportional to the size of the gene family (Adopted from Zhou et al., 2019) 4 Transcriptomic and Functional Genomic Insights in Groupers 4.1 RNA-seq analysis of fast-growing vs slow-growing groupers When studying the growth differences of groupers, RNA-seq technology provides direct evidence. For example, in hybrid groupers, transcriptome sequencing of brain, liver and muscle tissues revealed a large number of differentially expressed genes (DEGs), 27 of which were closely related to growth traits. It is worth noting that genes involved in the regulation of the actin skeleton and genes related to the GH/IGF system are generally upregulated in fast-growing individuals (Cao et al., 2024). These expression changes suggest that these pathways may be the key to the growth advantage of hybrid individuals. In the study of giant grouper (E. lanceolatus), Wu et al. (2023) constructed a high-density genetic map containing 2,988 SNP loci and found 6 growth-related QTLs, which can explain 4.65% to 12.56% of the phenotypic differences. Further RNA-seq analysis identified a total of 484 differentially expressed genes (DEGs), which were enriched in pathways such as RNA transport, carbon metabolism, and PPAR signaling. Among them, 27 DEGs overlapped with the QTL interval and involved key processes such as cell growth, sugar metabolism, and bone development. Kalrn, ccnd2, and mybpc2 were significantly upregulated in the fast-growing group. Similar patterns also appear in other grouper species. Transcriptome data revealed that metabolic pathways such as glycolysis and gluconeogenesis, as well as structural genes, were more highly expressed in fast-growing
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