Impact of Chromosomal Fusion and Transposable Elements on the Genomic Evolution and Genetic Diversity of Ilex Species

The genus <i>Ilex</i> belongs to the sole family and is the single genus within the order Aquifoliales, exhibiting significant phenotypic diversity. However, the genetic differences underlying these phenotypic variations have rarely been studied. In this study, collinearity analyses of three <i>Ilex</i> genomes, <i>Ilex latifolia</i> Thunb., <i>Ilex polyneura</i> (Hand.-Mazz.) S. Y. Hu, and <i>Ilex asprella</i> Champ. ex Benth., indicated a recent fusion event contributing to the reduction of chromosomes in <i>I. asprella</i>. Comparative genome analyses showed slight differences in gene annotation among the three species, implying a minimal disruption of genes following chromosomal fusion in <i>I. asprella</i>. Comprehensive annotation of transposable elements (TEs) revealed that TEs constitute a significant portion of the <i>Ilex</i> genomes, with LTR transposons being predominant. TEs exhibited an inverse relationship with gene density, potentially influencing gene regulation and chromosomal architecture. TE insertions were shown to affect the conformation and binding sites of key genes such as 7-deoxyloganetin glucosyltransferase and transmembrane kinase (TMK) genes, highlighting potential functional impacts. The structural variations caused by TE insertions suggest significant roles in the evolutionary dynamics, leading to either loss or gain of gene function. This study underscores the importance of TEs in shaping the genomic landscape and evolutionary trajectories of <i>Ilex</i> species.