Telomere-to-Telomere Assembly of LH244 genome and Comparative Analysis with B73 and Mo17 (PRJCA033451)
LH244 is one of the few maize inbred lines capable of genetic transformation, while also possessing superior agronomic traits. The lack of a high-quality genome assembly for LH244 has hindered its application as a model for functional research. In this study, we generated a high-quality telomere-to-telomere (T2T) assembly of the LH244 genome by integrating ultra-long Oxford Nanopore Technology (ONT) and PacBio HiFi reads. The assembly achieved a base accuracy of 99.998% and exceptional continuity, with a genome size of 2.29 Gb. Comparative analysis with the B73 reference genome revealed that approximately 84% of the sequences are syntenic, and about 90% of the genes are structurally conserved, further confirming the potential of LH244 as an alternative model for maize genetics. Structural variation analysis of the two T2T genomes compared with Mo17 revealed unique genomic configurations in LH244, particularly in the knob regions. For the first time, we identified two distinct structures in the maize knob regions: a nested configuration of TR-1 and knob180, and island structures with low repeat density. These structures provide us with new insights into the evolutionary process of knob sequences and enhance our mechanistic understanding of gene expression in heterochromatic regions. Our findings position LH244 as a valuable resource for functional genomics, offering new insights into the structural and evolutionary dynamics of the maize genome.