Uncovering the Genetic Basis of Sex Determination in Amborella trichopoda

Although a complicated process, plant reproduction is essential to ecological balance and the food chain. Some plants are hermaphrodites, some are male or female, and some change sex during their lives. These diverse reproductive strategies are both intriguing and vital, as modern agriculture relies on a deep understanding of the mechanisms that control plant sexuality.

A ground-breaking study published in the journal Nature Plants clarifies the intricate reproductive strategies of flowering plants. The study examined the genetics of Amborella trichopoda, a type of flowering plant that provides a unique window into the early history of flowering plants.

It was headed by researchers from the University of Georgia and the HudsonAlpha Institute for Biotechnology. Thanks to their significantly better assembly of the Amborella genome and sex chromosomes, the researchers have learned much about the development of flowering plants and their reproductive strategies.

The Evolution of the Amborella Genome

Amborella trichopoda is the only extant member of a lineage that split off from all other flowering plants early in their evolutionary history. Its genome offers priceless information about the genetic foundations of plant variety.

The first genome was finished 11 years ago by a multinational team of scientists led by Jim Leebens-Mack, PhD, a Professor of Plant Biology at the University of Georgia. Over the past eleven years, the groundbreaking study, the findings of which were published in the journal Science in 2013, has received over 575 citations.

The evolutionary lineage leading to Amborella diverged from all other flowering plant lineages approximately 150 million years ago, so our draft genome published in 2013 has been a foundation for comparative analyses of genes tracing back to the origin of flowering plants and earlier.”

Jim Leebens-Mack, Professor, University of Georgia

Alex Harkess, PhD, a HudsonAlpha Faculty Investigator who worked on the Amborella genome as a PhD student in Leebens-Mack's lab, is particularly excited by the new insights gleaned from the improved genome assembly.

Harkess, who is now in charge of his lab at HudsonAlpha, collaborated with Leebens-Mack and HudsonAlpha Faculty Investigators Jeremy Schmutz and Jane Grimwood, PhD, on the latest Amborella genome analysis alongside one of his mentees, HudsonAlpha Senior Scientist Sarah Carey, PhD.

Working on the original Amborella genome in Jim’s [Leeben-Mack] lab was transformative because it allowed me as a first-year PhD student to be on the very edge of newly developing technologies and software that was coming out to help handle all of this massive genomic data we were creating, This genome reveals so much about the evolution of flowers, but also about the evolution of my research career and the way I, and now my entire laboratory, view reproduction through the lens of diversity.”

Alex Harkess, Faculty Investigator, HudsonAlpha Institute for Biotechnology

When the new Amborella genome assembly was finished, Carey was working as a postdoctoral fellow in the Harkess lab. She oversaw a large portion of the genome analysis, including the sex chromosomal analysis for Amborella.

Advancing Technology Enabled a More Complete Amborella Genome

Carey and colleagues of the HudsonAlpha Genome Sequencing Center assembled a significantly enhanced Amborella genome using cutting-edge sequencing and assembly technologies and new computational techniques.

Carey found it easier to look for the Amborella sex chromosomes, which are Z and W rather than the well-known human X and Y, thanks to the new, highly-contiguous genome reference.

“The first Amborella genome was a mixture of short segments of DNA from different sequencing types and technologies. Advancements in long-read sequencing and access to other pieces of information, like Hi-C data, allowed us to assemble larger pieces that made it easier to search for the ZW chromosomes than if it were in lots of smaller pieces,” said Carey when asked how the improved genome came to be.

Carey attributes this to remaining on the cutting edge of new and developing computational techniques, as well as enhanced sequencing and assembly technologies. To make it easier and less expensive to identify and characterize sex chromosomes in plants, the lab created a pipeline dubbed cytogenetics-by-sequencing. It has been successfully applied to about 30 dioecious plant and animal species.

By analyzing the sex chromosomes, the team learned some fascinating facts about Amborella's sex-determination machinery. For example, the Z and W chromosomes are relatively recent, having emerged about 100 million years after Amborella split off from all other flowering plant lineages.

In many sex-determination systems (think the tiny human Y chromosome), the sex chromosomes stop swapping genetic material with their chromosome pair partner, a phenomenon known as recombination.

The halting of recombination allows for the divergence of the two sex chromosomes through the accumulation of different rearrangements, deletions, and insertions.

Although the team found evidence of suppressed recombination in Amborella, the Z and W chromosomes look very similar, making assembling each sex chromosome more difficult. 

The Cytogenetics-by-Sequencing pipeline helped us to identify a difficult border on the Amborella sex chromosomes: where they no longer recombine. This is an important task because within this region of non-recombination are expected to be the carpel and stamen sterility genes associated with the evolution of separate female and male plants.”

Sarah Carey, Senior Scientist, HudsonAlpha Institute for Biotechnology

Carey and the crew discovered two genes that are thought to be in charge of Amborella's sex determination by closely examining the sex chromosomes.

Harkess said, “The big picture takeaway from this study is that we are learning another exception for how you can maintain separate sexes in plants. That gives us another tool in our toolkit for engineering new ways to do plant breeding, creating separate sexes, preventing plants from self-pollinating, and enforcing outcrossing in a way that is controllable and predictable.”

The Open Green Genomes Initiative, a Department of Energy Joint Genome Institute Community Science Program, includes the new Amborella genome project.

 “The Open Green Genomes initiative is filling phylogenetic gaps in the availability of reference-quality genomes for land plants. Our haplotype-resolved chromosomal assembly of the Amborella genome has enabled us to better understand aspects of the ancestral angiosperm genome and the derived characteristics of Amborella’s sex chromosomes,” said Leebens-Mack, lead PI for the OGG initiative.