Legume Genomics and Genetics 2024, Vol.15, No.4, 152-162 http://cropscipublisher.com/index.php/lgg 153 2 Understanding Synteny and Chromosomal Evolution 2.1 Concepts of synteny and chromosomal rearrangements Synteny refers to the conservation of blocks of genes on chromosomes across different species. This concept is crucial for understanding the evolutionary relationships between species and the mechanisms driving chromosomal evolution. Chromosomal rearrangements, such as inversions, translocations, fusions, and fissions, play a significant role in the diversification of genomes. For instance, in the legume family, studies have shown that Vigna angularis shares a high degree of macrosynteny with Vigna unguiculata and Phaseolus vulgaris, with conserved syntenic chromosomes and specific chromosomal rearrangements identified (Martins et al., 2021). Similarly, the genus Cercis, an early-diverging clade within legumes, provides insights into the ancestral legume genome, suggesting a progenitor with seven chromosomes (Stai et al., 2019). 2.2 Mechanisms driving chromosomal evolution in plants Chromosomal evolution in plants is driven by various mechanisms, including whole-genome duplications, segmental duplications, and independent gene duplications or losses. These events lead to complex histories of genome rearrangements. For example, the reconstruction of an ancestral genome for papilionoid legumes revealed a common ancestor with nine chromosomes, which likely evolved from an earlier state of 14 chromosomes following a whole-genome duplication (Ren et al., 2019). Additionally, the study of plastome evolution in legumes has highlighted the role of inversions, expansions, contractions, and loss of the inverted repeat in driving plastome variability (Lee et al., 2021). In holocentric plants like Carex, chromosome rearrangements through fission and fusion are more likely to become fixed, contributing to high rates of chromosomal evolution. 2.3 Tools and techniques for studying synteny and chromosome structure Several tools and techniques have been developed to study synteny and chromosome structure in plants. Fluorescence in situ hybridization (FISH) using bacterial artificial chromosome (BAC) and oligonucleotide (oligo) probes is a powerful method for mapping chromosomes and identifying syntenic relationships. For instance, BAC- and oligo-FISH mapping has been used to trace chromosome evolution in Vigna and Phaseolus species, revealing conserved syntenic chromosomes and specific rearrangements (Martins et al., 2021). Chromosome painting probes have also been developed for Citrus species, enabling the identification of individual chromosomes and comparative chromosome painting analysis across different species (He et al., 2020). Additionally, algorithms like syntR and syngraph have been implemented to identify regions of synteny and infer ancestral linkage groups and chromosomal rearrangements from genome data (Ostevik et al., 2020). Understanding synteny and chromosomal evolution in the legume family involves studying the conservation of gene blocks, mechanisms driving chromosomal changes, and utilizing advanced tools and techniques for chromosome mapping and analysis. These studies provide valuable insights into the evolutionary history and genomic diversity of legumes. 3 Syntenic Relationships in Legumes 3.1 Overview of known syntenic blocks within the legume family Synteny, the conservation of blocks of genes across different species, is a crucial aspect of understanding the evolutionary relationships within the legume family. Studies have shown that a significant proportion of genes in legumes are conserved in syntenic blocks. For instance, in the study of receptor-like kinases (RLK) and receptor-like proteins (RLP) across seven legume species, it was found that between 75% and 98% of these genes were present in syntenic blocks, indicating a high degree of conservation (Restrepo-Montoya et al., 2021). Similarly, the genetic map of Bituminaria bituminosa revealed highly conserved synteny with phaseoloid legumes, despite the divergence of these species millions of years ago (Nelson et al., 2020). These findings underscore the importance of syntenic blocks in maintaining genetic integrity and facilitating comparative genomics within the legume family. 3.2 Comparative analysis of synteny between model legume species and crops Comparative synteny analysis between model legume species and crops has provided valuable insights into
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