Computational Molecular Biology 2024, Vol.14, No.5, 202-210 http://bioscipublisher.com/index.php/cmb 204 3.2 Integration into gene regulatory networks The integration of new genes into existing gene regulatory networks (GRNs) is a fundamental aspect of their recruitment during development. GRNs consist of interactions between developmental control genes, cis-regulatory modules, and differentiation genes, which collectively generate refined patterns of gene expression (Fernandez-Valverde et al., 2018). The flexibility of GRNs over time allows for the cooption of individual genes, facilitating the evolution of novel traits. For example, the recruitment of the engrailed gene in the fly Samoaia leonensis to generate a new wing pattern (Figure 1) illustrates how GRN flexibility and the functional time windows of individual genes enable their independent recruitment during evolution (Dufour et al., 2020). Moreover, the integration of omic networks, such as transcriptome, proteome, and phosphoproteome data, enhances the predictive power of GRNs, as seen in the developmental atlas of maize. Figure 1 Cooption of engrailed underlies wing pigmentation pattern in the genus Samoaia (Adopted from Dufour et al., 2020) Image caption: (A) Phylogenetic reconstruction shows that the genus Samoaia is monophyletic and belongs to the Drosophilidae. (B) The black wing species represent the earliest-diverging lineages within the genus Samoaia. (C) The expression domain of the protein En prefigures the localization of the white spots in adult wings in S. leonensis and S. ocellaris. For each wing, two overlapping high-magnification clichés were acquired and manually stitched to cover the whole wing (Adopted from Dufour et al., 2020) 3.3 Patterns across different organisms The recruitment of new genes and their integration into developmental processes can vary significantly across different organisms. Comparative studies across species, such as those involving Drosophila, reveal that despite changes in regulatory DNA sequences, developmental programs can be conserved over millions of years (Wunderlich et al., 2018). This conservation allows for the detection of subtle phenotypic differences and the development of computational models linking regulatory DNA sequences to expression patterns. The study of vertebrate species has shown that changes in cis-regulatory elements can lead to morphological novelties, as exemplified by the regulation of the sonic hedgehog (Shh) gene (Amano, 2020). These findings underscore the importance of understanding the evolutionary origins of novel gene expression patterns and the mechanisms by which new enhancers arise, such as the co-option of latent activities of existing regulatory sequences. 4 Biological Implications of New Gene Recruitment 4.1 Role in functional innovation New gene recruitment plays a crucial role in functional innovation by providing raw material for the evolution of novel traits and functions. The emergence of new genes through various mechanisms, such as gene duplication, de novo gene birth, and co-option of genomic parasites, has been shown to significantly impact the evolution of cellular, physiological, morphological, behavioral, and reproductive traits. For instance, the recruitment of conserved developmental genes has been linked to the formation and diversification of novel traits, such as the eyespots on butterfly wings, which involve the co-option of multiple transcription regulators (Shirai et al., 2012). Additionally, the flexibility of gene regulatory networks (GRNs) allows for the independent recruitment of single
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