Gene turnover and contingency facilitated the repeated evolution of C4 photosynthesis in grasses
Data files
Oct 08, 2025 version files 1.27 GB
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Aristida_nuclear-softMasked.fna
451.51 MB
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Aristida_nuclear-softMasked.gff3
57.22 MB
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Core-set-OF.zip
484.51 KB
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ML_trees.zip
57.49 KB
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Re-annotations-Helixer.zip
54.93 MB
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README.md
1.65 KB
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Stipagrostis_4n_nuclear-softMasked.fna
613.38 MB
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Stipagrostis_4n_nuclear-softMasked.gff3
94.81 MB
Abstract
In grasses, almost all species belong to two evenly sized clades (BOP and PACMAD), yet the >20 independent origins of C4 photosynthesis in this family only occur in the PACMAD lineage. Here, we identify potential genetic precursors for C4 photosynthesis that were present at the base of the PACMAD clade, representing the last common ancestor of all C4 grasses. We generated the first reference genomes for Aristidoideae species (Aristida adscensionis and Stipagrostis hirtigluma), the sister lineage of all other PACMAD grasses. In combination with 34 other Poales genomes, we identify gene gains at the base of the PACMAD clade, and genes lost in the sister BOP lineage. Candidate C4 precursors include β-carbonic anhydrase, as well as genes involved in amino acid and nitrate transport, carbon metabolism, oxidative stress management and transcription regulation. Gene turnover created the necessary genetic contingency, facilitating the independent recruitment and refinement of C4 genes in multiple independent origins. Our results support the idea that the repeated evolution of C4 photosynthesis in PACMAD grasses was not driven by a single genetic event but was instead underwritten by chance genetic changes that originated long before there was selection for the trait itself.
Dataset DOI: 10.5061/dryad.xgxd254t2
Description of the data and file structure
We generated HiFi reads of two Aristidoideae species, Aristida adscensionis and Stipagrostis hirtigluma (grasses from the PACMAD clade), assembled a draft genome, and performed gene annotation for each of them.
Files and variables
File: Stipagrostis_4n_nuclear-softMasked.gff3
Description: Gene annotation for Stipagrostis hirtigluma using Helixer.
File: Stipagrostis_4n_nuclear-softMasked.fna
Description: Fasta file containing all the contig sequences assembled for Stipagrostis hirtigluma.
File: Aristida_nuclear-softMasked.gff3
Description: Gene annotation for Aristida adscensionis using Helixer.
File: Aristida_nuclear-softMasked.fna
Description: Fasta file containing all the contig sequences assembled for Aristida adscensionis.
File: Re-annotations-Helixer.zip
Description: GFF3 files for the 7 re-annotated grass genomes detailed in Table S1.
File: Core-set-OF.zip
Description: Trees and multiple sequence alignments generated by OrthoFinder for the core set of candidate genes.
File: ML_trees.zip
Description: Maximum likelihood trees constructed with PhyML.
Code/software
The used software is detailed in the associated preprint article.
Access information
Other publicly accessible location of the data: NCBI bioproject PRJNA1254624
