The genome of Hippophae salicifolia provides new insights into the sexual differentiation of sea buckthorn

Abstract

Background: Dioecy, a common reproductive strategy in angiosperms, has evolved independently in various plant lineages, and this has resulted in the evolution of diverse sex chromosome systems and sex determination mechanisms. Hippophae is a genus of dioecious plants with an XY sex determination system, but the molecular underpinnings of this process have not yet been clarified. Most previously published sea buckthorn genome data have been derived from females, yet genomic data on males are critically important for clarifying our understanding of sex determination in this genus. Comparative genomic analyses of male and female sea buckthorn plants can shed light on the origins and evolution of sex. These studies can also enhance our understanding of the molecular mechanisms underlying sexual differentiation and provide novel insights and data for future research on sexual reproduction in plants.

Results: We conducted an in-depth analysis of the genomes of 2 sea buckthorn species, including a male Hippophae gyantsensis, a female Hippophae salicifolia, and 2 haplotypes of male H. salicifolia. The genome size of H. gyantsensis was 704.35 Mb, and that of the female H. salicifolia was 788.28 Mb. The sizes of the 2 haplotype genomes were 1,139.99 Mb and 1,097.34 Mb. The sex-determining region (SDR) of H. salicifolia was 29.71 Mb and contained 249 genes. A comparative analysis of the haplotypes of Chr02 of H. salicifolia revealed that the Y chromosome was shorter than the X chromosome. Chromosomal evolution analysis indicated that Hippophae has experienced significant chromosomal rearrangements following 2 whole-genome duplication events, and the fusion of 2 chromosomes has potentially led to the early formation of sex chromosomes in sea buckthorn. Multiple structural variations between Y and X sex-linked regions might have facilitated the rapid evolution of sex chromosomes in H. salicifolia. Comparison of the transcriptome data of male and female flower buds from H. gyantsensis and H. salicifolia revealed 11 genes specifically expressed in males. Three of these were identified as candidate genes involved in the sex determination of sea buckthorn. These findings will aid future studies of the sex determination mechanisms in sea buckthorn.

Conclusion: A comparative genomic analysis was performed to identify the SDR in H. salicifolia. The origins and evolutionary trajectories of sex chromosomes within Hippophae were also determined. Three potential candidate genes associated with sea buckthorn sex determination were identified. Overall, our findings will aid future studies aimed at clarifying the mechanisms of sex determination.

Keywords: Hippophae; chromosomal assembly; sex chromosomes; sex determination.

Figure 1:

Genomic features of male H. salicifolia. (a) Pseudochromosome. (b) Gene density. (c) Repeat sequences density. (d) Ty3 density. (e) Copia density. (f) GC content. (g) Interspecies collinearity. Feature density and GC percentage were calculated with a 5-Mb window size. H. salicifolia is diploid, so the haploid genome was used as the reference genome.

Figure 2:

Comparative genomics analysis. (A) The divergence time tree of 13 species. The number of expanded gene families (red) and the number of contracted gene families (blue) are indicated to the right of each species branch. (B) Synonymous substitution rate per site (Ks) distribution for H. salicifolia, H. gyantsensis, H. rhamnoides, H. tibetana, E. moorcroftii, and Z. jujuba. Two recent WGD events occurred in both Hippophae and Elaeagnus. (C) Macro-synteny plot of H. salicifolia, E. mollis, and Z. jujuba. Syntenic comparison between H. salicifolia and Z. jujuba or between E. mollis and Z. jujuba revealed a 4:1 ratio that suggests 2 lineage-specific WGDs in Elaeagnaceae.

Figure 3:

Identification of the H. salicifolia 2X- and 2Y-SLRs. (A) The resequencing data of male and female H. salicifolia were visualized in the coverage depth of Chr02 of Hap2. The red line represents the depth of female coverage. The blue line represents the depth of male coverage. Y indicates the position of the Y-SLR. (B) Gene distribution in 2Y-SLR. (C) The resequencing data of male and female H. salicifolia were visualized in the coverage depth of Chr02 of Hap1. The red line represents the depth of female coverage. The blue line represents the depth of male coverage. X indicates the position of the X-SLR. (D) Gene distribution in 2X-SLR.

Figure 4:

Sex chromosome evolution of H. salicifolia. (A) The local syntenic blocks identified between the Hap2 Chr02 and the genomes of H. rhamnoides and E. mollis. (B) The order and direction of Y-SLR in homologous blocks in the orthologous region of Hippophae and Elaeagnus. “+” indicates that the internal gene order is consistent, “–” indicates that the internal gene order is opposite, and the absence of a mark suggests that the direction of the internal genes is variable. (C) The distribution of Ks values across different strata, with * indicating the mean value. (D) Phylogenetic structure statistics of single-copy genes within different strata. Structure 1 represents the “ancestral” pattern, structure 2 represents the “recent” pattern, and structure 3 represents the “chaotic” pattern.

Figure 5:

Within the Y-SLR of H. salicifolia, there are male-specific expression genes in both H. salicifolia and H. gyantsensis. “F” represents female, and “M” represents male.