Supporting data for "The telomere-to-telomere (T2T) genome provides insights into the evolution of specialized centromere sequences in sandalwood"

Sandalwood, a prized hemiparasitic plant, is highly sought in the commercial market because of its aromatic core materia. The structure and stability of the genome are instrumental in the rapid adaptation of parasitic plants to their surroundings. However, there is a conspicuous lack of research on the genomic-level adaptive evolution of sandalwood. <br>In this study, we assembled a gap-free telomere-to-telomere (T2T) reference genome for <i>Santalum album</i> using PacBio HiFi, Hi-C, and ultra-long ONT data. The T2T reference genome (Sal_t2t) encompassed annotations of 24,171 genes and 25.34% repetitive sequences, in addition to all 10 centromeres and 20 telomeres across the 10 chromosomes. The results revealed that the three distinct parasitic species of Santalales had diverse centromeric compositions. The <i>Copia</i>-type LTR transposon emerged as the most significant in the <i>S. album</i> genome, constituting the primary sequence of the centromere and influencing gene expression. Third, in sandalwood, the presence of <i>Copia</i> affected the size of the centromeres, and consequently, the genome size. Identification of the sandalwood T2T genome in this study also enabled the identification of more precise organelle transfer fragments. <br>Our research provides a sandalwood T2T genome, laying the groundwork for future investigations on the evolution of energy organs in parasitic plants. Moreover, it offers novel insights into the function and evolution of centromeres, as well as the mechanisms of adaptation and parasitism.