Many paths to separate sexes: the genomics of sex-determination in the Hawaiian Wikstroemia

Project Information

separatingSexes

Grant agreement ID: 101117517

DOI

10.3030/101117517

EC signature date 12 September 2023

Start date 1 January 2024

End date 31 December 2028

Funded under

• European Research Council (ERC)

Total cost

€ 1 447 995,00

EU contribution

€ 1 447 995,00

Coordinated by

LUNDS UNIVERSITET
Sweden

Periodic Reporting for period 1 - separatingSexes (Many paths to separate sexes: the genomics of sex-determination in the Hawaiian Wikstroemia)

Reporting period: 2024-01-01 to 2026-06-30

Summary of the context and overall objectives of the project

Life on earth has undergone several major evolutionary transitions, but perhaps none so striking or relevant to our daily lives as the origin of separate sexes. Yet, despite intense study for over 100 years, understanding how and why genes determining sex evolve -- and the consequences for the chromosomes harboring them -- remains an open problem in evolutionary biology. One reason answering this question is so challenging is that many of the most well-studied organisms have ancient sex chromosome systems (like our own mammalian XY chromosomes), where recombination suppression and genetic degeneration has obliterated any signs or signals of how genetic sex-determination evolved in the first place. Flowering plants (Angiosperms), on the other hand, exhibit a staggering diversity of reproductive forms, and have transitioned from combined (hermaphroditism) to separate sexes (dioecy) many times in their evolutionary history, making them ideal for studying recent evolutionary origins of new sex-determining genes and sex chromsomes.

This ERC project aims to understand the genomic changes giving rise to multiple new sex chromosome systems within an endemic Hawaiian radiation of the flowering plant genus Wikstroemia (Thymelaeaceae; ~12 spp.). We are using a combination of genomics, bioinformatics, gene expression, and greenhouse experiments to achieve three main research goals: (1) locate and fully annotate sex-linked regions of the genome associated with each form of dioecy; (2) clarify species relationships within this radiation, study the biogeography of sex-linked genes, as well as how recombination suppression has evolved for each form; and (3) determine what genes/developmental pathways are involved in sex-determination in these closely related lineages. This fascinating radiation offers a unique snapshot of repeated evolution of genetic sex-determination from a common genetic starting point, shedding new light on how and why evolutionary transitions to separate sexes occur.

Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far

Recruitment -- In the first year of funding (2024) I successfully recruited 1 postdoc (providing bioinformatics support), and two very talented Ph.D students whose thesis research projects correspond roughly to work packages 1 & 2 in the project proposal.

Genomic data -- (WP1 & 2) In the first year of the project, my team generated draft genomes based on long-read DNA sequence data for one male and female of each of four species for which we had greenhouse specimens, along with short-read sequence data for all greenhouse individuals. In 2025, one Ph.D. student conducted field work in Hawai'i, and collected short read genomic data for over 30 populations of 5 different species across the islands of O'ahu and Hawai'i. The draft genomes were given preliminary annotations based on lift-over from closely related Stellera chamaejasme and gene prediction with BRAKER using several plant protein dbs, until we can supplement/replace with our own gene expression data (expected 2026).

(WP1) Using the preliminary genomic data described above, the bioinformatics postdoc and one PhD student focused on identifying sex-linked genome regions and candidate sex-determining genes. Using a combination of kmer based mapping, GWAS, and synteny analyses, we successfully identified two unique sex-linked genomic regions, each associated with one of the two forms of dioecy located on different chromosomes, and each associated with a chromosomal inversion present only on the male haplotype. This major achievement confirms the putative origin of two different sex determining systems in the Hawaiian Wikstroemia, and lays the foundation for the remaining goals in this WP, including identification of sex-determining genes, and study of the expansion of the non-recombining region associated with one of the dioecy forms.

Greenhouse crosses aimed at generating F1 individuals for gene expression and segregation analyses have been ongoing through 2025, and we are currently waiting for the offspring to mature to flowering.

(WP2) For the goals of WP2, we sampled Wikstroemia specimens extensively from herbaria across Europe and Hawaii. We successfully sampled more than half of the species covering the entire geographic range of the genus (from continental Asia, through Australasia, the pacific islands, to Hawaii), and generated short-read DNA sequence data for over 200 specimens with which to construct a genus-level phylogeny. Preliminary phylogenomic analyses based on the herbarium specimens combined with greenhouse and field collected samples indicate a genus origin in mainland China, and colonization route to Hawaii through Australasia and the south Pacific, and confirm that the Hawaiian clade is monophyletic (originated from a single colonization event). Species relationship within the Hawaiian radiation appear to follow a linear 'stepping-stone' colonization pattern that corresponds to the relative ages of the high Hawaiian islands. The genomic dataset we have compiled represents a second major achievement that far exceeded the original goals for WP2, and provides the macroevolutionary context needed for the broader project as well as a variety of new insights into the systematics of the genus.

Progress beyond the state of the art and expected potential impact (including the socio-economic impact and the wider societal implications of the project so far)

Although all of our results to date are still preliminary, the outlook for the project is extremely optimistic because each of the major questions and scientific contributions for the first two WPs appear to supported by the genomic data and analyses. We have already generated a high-impact genomic resource that will only increase in value as our genome assemblies are finalized and annotations supplemented with gene expression data. Our main findings from WP1 already constitute a major result beyond the state of the art by confirming the unique origin of different sex determining regions in closely related lineages and identifying the role of chromosomal inversions in both. The results from WP2 far exceed our original goals, and will not only contribute the needed context for understanding the colonization and diversification of sexual systems in the Hawaiian clade, but will contribute high-impact new knowledge about the broader systematics and biogeography of the genus, and also raise new research questions related to the adaptive radiation of Hawaiian Wikstroemia.

To ensure further uptake and success, by far the most important need is continued bioinformatics support through an in-house bioinformatician. Generating our genomic data set has raised new questions and applications, and specifically the opportunity to adopt cutting edge methods to construct a pangenome with which to study the adaptive radiation of the Hawaiian Wikstroemia. As our results become finalized and the resulting publications come out, a second major need to ensure impact and update will be dissemination. Here again, we see great opportunities to partner with the various herbaria, botanical gardens, and partner institutions that have helped provide access to specimens, to perform outreach, exhibits, and dissemination of our results with both local and international impact.