Legume Genomics and Genetics 2024, Vol.15, No.1, 27-36 http://cropscipublisher.com/index.php/lgg 28 of polyploidization events, and the reconstruction of the evolutionary history of nitrogen-fixing symbiosis. We will also review the methodologies used in these studies, including nuclear and chloroplast gene alignments, maximum likelihood, Bayesian inference, and multispecies coalescent summary methods. Additionally, this study will identify gaps in the current knowledge of Fabaceae phylogenomics and propose directions for future research. Despite significant advancements, challenges persist in resolving specific phylogenetic relationships and understanding the evolutionary mechanisms driving trait diversity in this family. Future research should aim to generate more comprehensive genomic datasets, improve phylogenetic resolution, and investigate the functional implications of evolutionary events such as polyploidization and hybridization. By addressing these objectives, this study will enhance the understanding of the evolutionary history and diversity of the Fabaceae family, providing a foundation for future research and applications in plant breeding and conservation. 2 Historical Context of Fabaceae Phylogeny 2.1 Early studies Early studies on the phylogeny of the Fabaceae family primarily relied on morphological and anatomical characteristics to classify and understand the evolutionary relationships among different species. These traditional methods, while foundational, often faced limitations due to convergent evolution and phenotypic plasticity, which could obscure true phylogenetic relationships. The advent of molecular techniques, particularly DNA barcoding, marked a significant advancement in the study of Fabaceae phylogeny. DNA barcoding, which involves the use of specific gene regions to identify species, provided a more objective and accurate method for species identification compared to morphological approaches. For instance, the MatK gene of the chloroplast has been utilized effectively for barcoding in various legume species, demonstrating high accuracy and simplicity in species identification (Abdelsalam et al., 2021). These early molecular studies laid the groundwork for more comprehensive phylogenetic analyses by providing initial insights into the genetic relationships within the family. 2.2 Development of phylogenomics The introduction of high-throughput sequencing technologies revolutionized phylogenetic studies by enabling the analysis of large-scale genomic data. This technological advancement allowed researchers to move beyond single-gene analyses to more comprehensive whole-genome approaches. High-throughput sequencing facilitated the acquisition of complete plastome sequences and mitochondrial protein-coding gene sequences, which provided deeper insights into the evolutionary history and relationships within plant families (McManus et al., 2018). The transition from single-gene to whole-genome analyses marked a significant leap in resolving complex phylogenetic relationships. In the case of the Fabaceae family, large-scale genomic sequence data have been instrumental in resolving deep divergences and understanding the evolutionary origins of its subfamilies. For example, a study utilizing alignments of 72 chloroplast genes and 7 621 homologous nuclear-encoded proteins successfully resolved the deepest divergences in the legume phylogeny, highlighting the near-simultaneous evolutionary origin of all six subfamilies (Figure 1) (Koenen et al., 2019). This comprehensive approach provided a robust phylogenetic framework, overcoming the limitations of earlier methods that relied on fewer genetic markers. Overall, the development of phylogenomics has significantly advanced our understanding of the Fabaceae family’s evolutionary history, enabling researchers to resolve complex relationships that were previously unattainable with traditional and early molecular methods. 3 Methodological Advances in Phylogenomics 3.1 High-throughput sequencing technologies High-throughput sequencing (HTS) technologies have revolutionized phylogenomic studies by enabling the rapid and cost-effective generation of large-scale sequence data. Platforms such as Illumina and PacBio are at the forefront of these advancements. Illumina sequencing, known for its high accuracy and throughput, is widely used for generating short-read data, which is essential for various genomic applications, including phylogenetic analyses (Mandel et al., 2015; Uribe-Convers et al., 2016). On the other hand, PacBio's
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