A new window into the early evolution of flowering plants

Plant reproduction is fundamental to our food systems and ecological balance, yet it remains a complex and diverse process. 

Some plants are male or female, others are hermaphroditic, and some even change sex over their lifetime. 

Understanding the mechanisms that determine plant sex is crucial for advancing modern agriculture.

Reproductive strategies of flowering plants

A study published in the journal Nature Plants has unveiled new perspectives on the intricate reproductive strategies of flowering plants. 

Led by researchers at the HudsonAlpha Institute for Biotechnology and the University of Georgia, the study was focused on the genetics of Amborella trichopoda. This unique species offers a rare glimpse into the early evolution of flowering plants. 

By producing a much-improved assembly of the Amborella genome and its sex chromosomes, the researchers have gained valuable insights into plant evolution and reproduction.

Evolution of the Amborella genome

Amborella trichopoda is the sole surviving member of a lineage that branched off early from all other flowering plants. Its genome provides essential information about the genetic foundations of plant diversity.

Eleven years ago, an international team of researchers co-led by Jim Leebens-Mack, a professor of plant biology at the University of Georgia, completed the first Amborella genome. The results, published in Science in 2013, have been cited over 575 times.

“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,” Leebens-Mack said.

New insights into the evolution of flowers

The new insights from the improved genome assembly are particularly exciting for HudsonAlpha Faculty Investigator Alex Harkess, who was a PhD student in Leebens-Mack’s lab during the original Amborella genome project. 

Now leading his own lab at HudsonAlpha, Harkess and his mentee, senior scientist Sarah Carey, collaborated with Leebens-Mack and HudsonAlphafFaculty investigators Jeremy Schmutz and Jane Grimwood, on the new genome analyses.

“Working on the original Amborella genome in Jim’s 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,” Harkess reflected. 

“This genome reveals so much about the evolution of flowers, but also about the evolution of my own research career and the way I, and now my entire laboratory, view reproduction through the lens of diversity.”

Carey, who was a postdoctoral fellow in the Harkess lab when the new genome assembly was completed, led much of the genome analysis, including the study of the Amborella sex chromosomes.

Advanced technology and plant reproduction

Thanks to advanced sequencing and assembly technology, as well as emerging computational tools, Carey and the team at the HudsonAlpha Genome Sequencing Center were able to assemble a significantly improved Amborella genome. 

The new, highly contiguous genome reference made it easier to search for the Amborella sex chromosomes, which are Z and W chromosomes, unlike the familiar human X and Y chromosomes.

“The first Amborella genome was a mixture of short segments of DNA from different sequencing types and technologies,” Carey explained. 

“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.”

In addition to the improved sequencing tools, the team stayed at the forefront of new computational methods. 

They developed a pipeline called cytogenetics-by-sequencing to more easily and cost-effectively identify and characterize sex chromosomes in plants, successfully applying it to nearly 30 dioecious plant and animal species.

The mechanisms of sex determination

Through their analysis of the Amborella sex chromosomes, the researchers discovered intriguing aspects of the plant’s sex-determination system. 

Notably, the Z and W chromosomes are relatively young, having emerged more than 100 million years after Amborella diverged from other flowering plant lineages.

In many sex-determination systems, such as the human Y chromosome, the sex chromosomes stop exchanging genetic material with their partner chromosome – a phenomenon known as recombination suppression. 

This allows the two sex chromosomes to diverge over time due to different rearrangements, deletions, and insertions.

Genes associated with flower evolution

While the team found evidence of suppressed recombination in Amborella, the Z and W chromosomes appear very similar, making their assembly more challenging.

“The cytogenetics-by-sequencing pipeline helped us to identify a difficult border on the Amborella sex chromosomes: where they no longer recombine,” Carey noted. 

“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.”

By carefully analyzing the sex chromosomes, Carey and the team identified two genes hypothesized to be responsible for sex determination in Amborella.

Implications for agriculture and plant breeding

“The big picture takeaway from this study is that we’re learning another exception for how you can maintain separate sexes in plants,” Harkess said. 

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

“The Open Green Genomes initiative is filling phylogenetic gaps in the availability of reference-quality genomes for land plants,” said Leebens-Mack, lead principal investigator for the initiative. 

“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.”

This research not only advances our understanding of plant reproduction but also offers practical applications for agriculture and plant breeding. 

By unraveling the genetic mechanisms behind sex determination in plants, scientists can develop new strategies to improve crop yields, enhance biodiversity, and ensure food security.

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