Nanopore Data-Driven Near-T2T Genome Assembly of Hippophae rhamnoides ssp. mongolica Rousi and Its Complex Annotation

Sea buckthorn (Hippophae rhamnoides L.) is a valuable plant whose fruits are rich in biologically active compounds. We sequenced the genome of variety Triumf of H. rhamnoides ssp. mongolica Rousi on the Oxford Nanopore Technologies (ONT) platform. With the Hifiasm algorithm optimized for ONT data, we assembled the 1.17-Gb genome into eleven complete chromosomes and one chromosome consisting of two contigs, which were scaffolded (Chr3). Eleven of twelve chromosomes had pronounced telomeric repeats at both ends and were assembled as telomere-to-telomere (T2T), and one chromosome (Chr12) had telomeric repeats only at one end. We also sequenced transcriptomes of thirteen Triumf organs/tissues and performed genome annotation using these and previously obtained RNA-Seq data for this variety. As a result, we predicted 25,915 genes and 30,527 transcripts. Repetitive elements comprised 66.9% of the genome size. The obtained near-T2T annotated genome assembly of H. rhamnoides ssp. mongolica variety Triumf enabled the identification of correct composition and sequences of important gene families in sea buckthorn. We demonstrated this with the FAT, SAD, and FAD gene families involved in fatty acid synthesis. Expression analysis revealed which FAT, SAD, and FAD genes are essential for specific organs/tissues. Thus, the Triumf genome assembly is a crucial tool for basic and applied studies of H. rhamnoides.