Legume Genomics and Genetics 2024, Vol.15, No.1, 27-36 http://cropscipublisher.com/index.php/lgg 31 In the context of Fabaceae, HTS technologies have been instrumental in resolving phylogenetic relationships and understanding evolutionary processes. For instance, the use of Illumina sequencing has facilitated the generation of extensive nuclear and chloroplast genomic data, enabling the resolution of deep-branching relationships within the family (Koenen et al., 2019). Additionally, PacBio sequencing has been employed to study the transcriptomes of Fabaceae species, providing insights into gene expression and stress response mechanisms (Lyu et al., 2021). These technologies have also supported the identification of whole-genome duplication events and the reconstruction of the evolutionary history of nitrogen-fixing symbiosis in Fabaceae (Figure 2) (Zhao et al., 2021). 3.2 Bioinformatics tools and pipelines The vast amount of data generated by HTS requires robust bioinformatics tools and pipelines for processing and assembly. Tools such as the Fluidigm Access Array System and associated bioinformatics pipelines have been developed to handle large datasets efficiently. These pipelines facilitate the generation of consensus sequences and the recovery of allelic information, which are crucial for phylogenetic analyses (Uribe-Convers et al., 2016). Additionally, specialized pipelines like Purc have been designed to manage the complexities of polyploid data, ensuring accurate sequence inference from raw reads (Rothfels et al., 2017). Phylogenetic tree construction is a critical step in phylogenomics, with methods such as maximum likelihood (ML) and Bayesian inference (BI) being commonly used. These methods provide robust frameworks for inferring evolutionary relationships based on genomic data. For example, ML and BI have been employed to analyze nuclear and chloroplast gene alignments, resolving the deepest divergences in the legume phylogeny (Koenen et al., 2019). Additionally, multispecies coalescent methods have been applied to evaluate support for alternative topologies across gene trees, addressing issues such as incomplete lineage sorting and hybridization (Vargas et al., 2017; Koenen et al., 2019). 3.3 Comparative genomics Comparative genomics allows for the study of gene family evolution, providing insights into the processes of gene duplication and divergence. Phylogenetic approaches are used to assess gene orthology and paralogy, trace evolutionary changes in gene families, and predict structure-function relationships (Thornton and DeSalle, 2000). In Fabaceae, phylogenomic analyses have identified numerous whole-genome duplication events, shedding light on the evolutionary history and diversification of gene families within the family (Zhao et al., 2021). Genome synteny and collinearity analyses are essential for understanding the structural organization and evolutionary history of genomes. These analyses involve comparing the order and orientation of genes across different species to identify conserved genomic regions. In Fabaceae, synteny analyses have revealed patterns of genome evolution and provided evidence for ancient polyploidy events (Zhao et al., 2021). Such studies are crucial for reconstructing the evolutionary trajectories of complex plant genomes and understanding the genetic basis of key traits. By leveraging these methodological advances, researchers can gain a deeper understanding of the evolutionary relationships and genomic architecture of the Fabaceae family, ultimately contributing to the broader field of plant phylogenomics. 4 Major Findings in Fabaceae Phylogenomics 4.1 Phylogenetic relationships Recent advances in phylogenomic studies have significantly enhanced our understanding of the phylogenetic relationships within the Fabaceae family. One of the major findings is the resolution of the deepest divergences among the subfamilies of Fabaceae. By analyzing large-scale genomic sequence data, researchers have been able to generate robust phylogenetic frameworks that clarify the relationships among the six subfamilies. This study utilized alignments of 72 chloroplast genes and 7 621 homologous nuclear-encoded proteins across 157
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