Genome sequence and population genomics provide insights into chromosomal evolution and phytochemical innovation of Hippophae rhamnoides

Abstract

Plants of the Elaeagnaceae family are widely used to treat various health disorders owing to their natural phytochemicals. Seabuckthorn (Hippophae rhamnoides L.) is an economically and ecologically important species within the family with richness of biologically and pharmacologically active substances. Here, we present a chromosome-level genome assembly of seabuckthorn (http://hipp.shengxin.ren/), the first genome sequence of Elaeagnaceae, which has a total length of 849.04 Mb with scaffold N50 of 69.52 Mb and 30 864 annotated genes. Two sequential tetraploidizations with one occurring ~36-41 million years ago (Mya) and the last ~24-27 Mya were inferred, resulting in expansion of genes related to ascorbate and aldarate metabolism, lipid biosynthesis, and fatty acid elongation. Comparative genomic analysis reconstructed the evolutionary trajectories of the seabuckthorn genome with the predicted ancestral genome of 14 proto-chromosomes. Comparative transcriptomic and metabonomic analyses identified some key genes contributing to high content of polyunsaturated fatty acids and ascorbic acid (AsA). Additionally, we generated and analysed 55 whole-genome sequences of diverse accessions, and identified 9.80 million genetic variants in the seabuckthorn germplasms. Intriguingly, genes in selective sweep regions identified through population genomic analysis appeared to contribute to the richness of AsA and fatty acid in seabuckthorn fruits, among which GalLDH, GMPase and ACC, TER were the potentially major-effect causative genes controlling AsA and fatty acid content of the fruit, respectively. Our research offers novel insights into the molecular basis underlying phytochemical innovation of seabuckthorn, and provides valuable resources for exploring the evolution of the Elaeagnaceae family and molecular breeding.

How to survive in the world’s third poplar: Insights from the genome of the highest altitude woody plant, Hippophae tibetana (Elaeagnaceae)

“…There were three collinear blocks peaks of H. tibetana were detected, and located at 0.329 ± 0.001, 0.502 ± 0.002 and 2.019 ± 0.021 after data fitting ( Figure 2B ). Combining of our present analyses and the research of H. rhamnoides genome ( Yu et al., 2022 ), indicated that there were two lineage-specific polyploidization events had occurred in the genus Hippophae , and the two rounds of polyploidization occurred within a relatively narrow timeframe ( Figure S9 ) . In addition to the core-eudicot common hexaploidization (whole genome triplication, WGT; γ event, grey arrow, Figure 2A ), two prominent peaks were identified ( Hippophae recent tetraploidization, HRT: 18.7-21.2 Ma, blue arrow; Hippophae ancient tetraploidization, HAT: 28.6-32.4 Ma, red arrow, Figure 2A ) in the K s profiles of the H. tibetana genome, but unlike most other apricot, both HRT and HAT occurred at a K s value less than 1.…”

“…Combining De novo-, transcriptome-and homology-based predictions, 33,367 protein-coding genes were predicted from the genome overall. The number of gene models is comparable to those of other Elaeagnaceae species (Mao et al, 2021;Wu et al, 2022;Yu et al, 2022). Among all the predicted genes, 32,059 genes could be annotated to the functional database, see Table S2.…”

“…This genome assembly size was comparable to the size estimated by a K-mer-based method (1,432.13 Mb) ( Figure S1 ). The assembly genome size is consisting with the DNA content of its related species (2.32-3.88 pg/C) that was previously determined with tissue using flow cytometry ( Zhou et al., 2012 ) and is much larger than other Elaeagnaceae species ( Mao et al., 2021 ; Wu et al., 2022 ; Yu et al., 2022 ). The Contig N50 and N90 of assembly genome reaches 74.31 Mb and 24.93 Mb and the scaffold N50 and N90 reaches 123.42 Mb and 71 Mb respectively ( Table 1 ).…”

“…The morphological characteristics and high altitude habitat of H. tibetana are illustrated in Figures 1A , B . Nowadays, the genome of Hippophae rhamnoides , a relative of H. tibetana , has been published ( Wu et al., 2022 ; Yu et al., 2022 ), H. rhamnoides is a regular or small tree distributed at lower altitude ranged from 490-3,700 meters a.s.l. ( Huang and Yu, 2006 ).…”

Targeted Metabolome and Transcriptome Analyses Reveal the Pigmentation Mechanism of Hippophae (Sea Buckthorn) Fruit

“…The clean reads were aligned to the genome of H. rhamnoides subsp. mongolica using HISAT2–2.0.4 [ 34 , 35 ]. The aligned reads were assembled using StringTie-1.3.4 with default parameters [ 36 ].…”