Chromosome-level genome assembly of Hippophae neurocarpa

Hippophae neurocarpa (H. neurocarpa) is a deciduous shrub from the Elaeagnaceae family, widely distributed in the Qinghai-Tibet Plateau. It possesses significant ecological and economic value, while also being rich in nutrients and offering various health benefits. In this study, we successfully assembled the chromosome-level genome of H. neurocarpa utilizing Illumina sequencing, Nanopore sequencing, and chromosome conformation capture techniques. The total genome size is 682.80 Mb, with an N50 length of 62.17 Mb. We successfully anchored 669.20 Mb to 12 chromosomes, achieving a mapping rate of 98.0%. Furthermore, using RepeatMasker, we annotated repetitive sequences, revealing that 56.27% of the genome consists of repetitive elements, with long terminal repeats (LTRs) accounting for 36.26% of the total genome. We also annotated gene structures using de novo, homology, and transcriptome assembly strategies, predicting 36844 protein-coding genes, of which 32952 genes had successful functional annotations. Lastly, we employed various strategies for quality evaluation, with a Benchmarking Universal Single-Copy Orthologs (BUSCO) completeness score reaching 97.6% and a Long Terminal Repeat (LTR) Retrotransposon Assembly Index (LAI) of 11.61, the mapping rate further indicating high assembly quality. This study provides valuable genomic data for future research on H. neurocarpa and the broader sea buckthorn genus.