Nanopore Data-Driven Near-T2T Genome Assembly of <em>Hippophae rhamnoides</em> ssp. <em>mongolica</em> Rousi

Sea buckthorn (Hippophae rhamnoides L.) is a valuable woody oil plant which is rich in biologically active compounds. High-quality genome assemblies are necessary for genetic studies and breeding of the plant. We sequenced the genome of variety Triumf of H. rhamnoides ssp. mongolica using Oxford Nanopore Technology (ONT) platform and obtained 155 Gb of raw reads with an N50 of 31.4 kb. Using the Hifiasm algorithm optimized for ONT data, we assembled the 1.17 Gb genome into 13 contigs: eleven complete chromosomes and one chromosome (Chr3) consisting of two contigs, which were scaffolded. Eleven of twelve chromosomes had pronounced telomeric repeats at both ends and were assembled as telomere-to-telomere (T2T), and one chromosome (Chr12) had telomeres only at one end. Hi-C interaction map confirmed the accuracy of the obtained genome assembly. We predicted 24,761 genes and 27,949 transcript models. Repetitive elements comprised 66.9% of the genome size. Thus, we obtained a near-T2T genome assembly of H. rhamnoides ssp. mongolica variety Triumf using only ONT sequencing data. The obtained genome is an essential tool for various basic and applied studies, as well as for genome editing of H. rhamnoides.