Legume Genomics and Genetics 2024, Vol.15, No.4, 152-162 http://cropscipublisher.com/index.php/lgg 156 4.3 Correlation between chromosomal changes and adaptive traits Chromosomal changes in legumes have been closely linked to adaptive traits, particularly in response to biotic and abiotic stresses. The dynamic evolution of RLK and RLP genes, which are involved in stress responses, suggests that chromosomal rearrangements have played a crucial role in enhancing the adaptability and productivity of legumes (Restrepo-Montoya et al., 2021). Additionally, the loss of the inverted repeat (IR) in the plastomes of certain legume species, such as those in the IR-lacking clade (IRLC), has been associated with increased plastome variation and adaptive evolution (Lee et al., 2021). The rapid evolution and pseudogenization of the ycf4 gene in the tribe Fabeae, which plays a role in photosystem I assembly, further exemplify the correlation between chromosomal changes and adaptive traits. The lineage-specific accelerated rate of evolution and gene loss in this tribe indicate that such chromosomal changes have been driven by selective pressures to enhance photosynthetic efficiency and adaptation to diverse environments (Moghaddam and Kazempour-Osaloo, 2020). The chromosomal evolution in legumes has been marked by significant rearrangements and duplications, which have contributed to the diversification and adaptation of this important plant family. These changes have not only shaped the genomic architecture of legumes but also facilitated the development of key adaptive traits, enhancing their ecological and agricultural significance. 5 Genomic Insights from Syntenic Studies 5.1 Insights into gene function and regulation from syntenic alignments Syntenic alignments have proven invaluable in elucidating gene function and regulation across various species. For instance, the study on narrow-leafed lupin (Lupinus angustifolius L.) utilized synteny-based approaches to analyze the glutamine synthetase (GS) and phosphoenolpyruvate carboxylase (PEPC) gene families. This analysis revealed that gene duplications have significantly contributed to the diversity of these gene families, while the function of the duplicates has largely been retained (Czyż et al., 2020). Similarly, synteny-guided phylogenies have been shown to provide more accurate reconstructions of gene trees, which are crucial for understanding the functional impact of whole genome duplications (WGDs) (Parey et al., 2020). These synteny-guided methods help in identifying orthologs and paralogs more reliably, thereby facilitating the exploration of functional consequences ofWGDs. 5.2 Role of whole genome duplications in syntenic conservation Whole genome duplications (WGDs) play a pivotal role in syntenic conservation and the evolution of gene families. The study on the oxytocin and vasotocin receptor gene family highlights how WGDs have shaped the vertebrate genome, suggesting that a single round of WGD is more consistent with the synteny and evolution of chromosomes where these receptors are found. In legumes, WGDs have been instrumental in the diversification of gene families, as evidenced by the evolutionary history of the legume family, where multiple independent WGDs have given rise to the various subfamilies (Stai et al., 2019). Additionally, the study on narrow-leafed lupin corroborates earlier findings that key WGD events have significantly impacted the genistoid lineage, contributing to the extant diversity of gene families (Czyż et al., 2020). 5.3 Contributions of syntenic studies to understanding evolutionary dynamics Syntenic studies have significantly advanced our understanding of evolutionary dynamics by revealing patterns of chromosomal evolution and gene retention. For example, the comparative analysis of Vigna angularis, Vigna unguiculata, and Phaseolus vulgaris demonstrated high degrees of macrosynteny and identified specific chromosomal rearrangements that have occurred since their divergence (Martins et al., 2021). Furthermore, the study on metazoan chromosomes uncovered deeply conserved synteny among bilaterians, cnidarians, and sponges, providing insights into the processes of chromosome evolution from Precambrian progenitors (Simakov et al., 2022). These findings underscore the importance of syntenic studies in reconstructing ancestral chromosomes and understanding the evolutionary history of various taxa.
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