Amborella trichopoda sheds light on ZW sex chromosome evolution in angiosperm plants

By Dr. Chinta SidharthanReviewed by Laura ThomsonDec 4 2024

The evolution of sex chromosomes is a fascinating process that has occurred independently across various species, including flowering plants. These chromosomes play a critical role in determining the reproductive systems of organisms. A recent study in Nature Plants focused on understanding the genetic structure and evolution of sex chromosomes in Amborella trichopoda. This plant species is considered a living representative of ancient angiosperms and exhibits the ZW sex-determination system.

The researchers constructed a highly detailed haplotype-resolved genome assembly using advanced genome sequencing. They identified features such as a sex-determination region (SDR) which contains candidate genes related to fertility. The findings shed light on the early stages of sex chromosome evolution in plants.

Sex-determination in plants

Dioecy, or the evolution of separate sexes, is rare in flowering plants and occurs in only a small fraction of species. Despite this, dioecy has arisen independently multiple times, making flowering plants valuable models for studying sex chromosome evolution.

Unlike the widely studied XY systems in many species, the ZW systems remain less explored, yet they hold unique insights into recombination suppression and genetic differentiation.

Amborella trichopoda, which diverged from other angiosperms approximately 140 million years ago, is an essential model for understanding ancestral genome structures. The species possesses ZW sex chromosomes that likely evolved from a hermaphroditic ancestor, making it ideal for examining early mechanisms underlying sex chromosome formation. Furthermore, while significant progress has been made in identifying the genes involved in dioecy in other angiosperms, the molecular basis in Amborella remains less understood.

The current study

Plant biologists and biotechnologists from the United States utilized advanced sequencing technologies to construct a haplotype-resolved genome assembly for Amborella trichopoda.

They employed PacBio HiFi sequencing and Phase Genomics Hi-C technologies to achieve high coverage and continuity, which separated Z and W chromosomes into distinct haplotypes. The assembly was refined using complementary methods, including Illumina short-read sequencing for error correction and ribonucleic acid (RNA) sequencing for transcriptome analysis. 

To identify the SDR, k-mer analysis was applied to distinguish female-specific sequences (W-mers) from shared genomic regions. K-mers are fixed-length substrings of nucleotides or amino acids derived from a biological sequence and are widely used in bioinformatics, especially in computational genomics and sequence analysis.

These W-mers were mapped to chromosome 9, which narrowed the SDR to a 2.94 Mb region enriched with repetitive elements and containing a 292 kb inversion. The researchers further examined gene content and expression patterns within the SDR to identify sex-biased genes through comparative transcriptomic analyses of male and female flowers.

Synonymous substitution rates were calculated to understand the evolutionary dynamics of the SDR. This revealed two evolutionary strata within the SDR corresponding to distinct phases of recombination suppression.

Major findings

The study found that Amborella trichopoda’s ZW sex chromosomes exhibit unique characteristics that reflect their recent evolution. The SDR spans approximately 2.94 Mb and contains two distinct evolutionary strata. These strata represent stages of recombination suppression, with the older stratum containing a 292 kb inversion enriched in repetitive sequences. 

The gene expression analyses revealed differential patterns between males and females, with several SDR-associated genes showing sex-biased transcription. Notably, the METHYLTHIOADENOSINE NUCLEOSIDASE (MTN1-2) homolog, located within the inversion, exhibited the highest divergence between Z and W copies and is hypothesized to contribute to male sterility.

Other candidate genes, such as WUSCHEL and LONELY GUY, are believed to regulate floral development and may play roles in female or male fertility suppression. 

Amborella’s W chromosome indicated minimal signs of degeneration. The region lacked extensive repeat accumulation or significant gene loss, and its repeat density was comparable to the autosomes. These findings suggested a slower evolutionary degeneration rate than other plant species with older sex chromosomes. 

The study also highlighted the conserved synteny or co-localization of genetic loci between the Z and W chromosomes, indicating that structural differences are limited mainly to the SDR. This synteny, combined with the absence of large-scale inversions or proximity to centromeric regions, suggested a non-canonical mechanism for recombination suppression. 

The calculated evolutionary ages of the strata further supported the recent evolution of this SDR, with the estimated age being 4.97 million years for the older stratum and 2.41 million years for the younger one.

The researchers found that this timing also aligned with the hypothesis that Amborella’s ZW system evolved well after it diverged from other angiosperms. These findings provide critical insights into the early stages of sex chromosome differentiation and offer a model for understanding similar processes in other species. 

Conclusions

To conclude, the findings provided a detailed characterization of the ZW sex chromosomes in Amborella trichopoda, highlighting minimal degeneration and unique evolutionary features in the species. The identification of candidate genes within the SDR also offered insights into mechanisms of sex determination and recombination suppression. These findings indicated the value of Amborella as a model for studying early sex chromosome evolution and contributed to a broader understanding of genetic and evolutionary dynamics in flowering plants.