Amazing stuff!
"... Some of this success stems from grasses’ turbocharged growth: The plants can produce both energy-rich starch and structurally supportive lignin through two different metabolic pathways apiece, allowing them to grow faster and taller than their competitors. But researchers never knew how and when these innovations sprouted.
In a new Science study, botanists analyzed the genomes of the grass family’s closest relatives to reveal the evolutionary history of grasses’ key innovations. They found that the doubled starch production pathway was truly unique to grasses, having resulted from a previously documented whole-genome duplication event that also instilled the plants with some of their other world-conquering traits. This duplication “ likely gave a competitive advantage to grasses to grow in open habitat, where a lot of plants would love to grow because of all the sun,” ...
By contrast, their sister groups had only one strategy to produce starch, restricting them to slow growth in the shade of their fast-rising relatives.
In addition, both grasses and related plants can also make lignin from two different precursor molecules, indicating that a separate gene duplication gave rise to the dual pathway before grasses split into their own lineage 100 million years ago. The researchers were able to track the specific genetic causes of the doubled route, potentially allowing them to introduce the mutation into other plants to help produce crops and feedstocks for bioenergy."
"One hundred million years ago, long before human intervention, ancestors of grasses, like wheat, rice and maize generated “bypasses” of chemical pathways that are used to create two critical compounds: lignin and starch. These more efficient pathways could explain why grass plants are so successful in nature and agriculture, according to a new paper recently published ...
Just as scientists use the chimpanzee’s genome as a comparison tool to study how humans evolved, Maeda’s group and their collaborators ... turned to one of the closest relatives of grasses, Joinvillea ascendens.
This long-leafed plant is found in wet forests of the South Pacific islands and grows much more slowly than many grasses. ..."
"... The researchers then mapped the genome of Joinvillea and three related species. Comparing the thousands of genes in these genomes revealed that, unlike grasses, Joinvillea has only one pathway to create starch.
“We knew that a common ancestor of all grasses doubled its gene content through a whole genome duplication,” ... “Some of the duplicated genes then enabled the evolution of an additional starch synthesis pathway, or a bypass route, which emerged in an early common ancestor of all grasses.”
As a result ... grasses are able to produce twice the amount of starch relative to Joinvillea and all other non-grass plants. ..."
From the editor's summary and abstract:
"Editor’s summary
Grasses include many economically important food crops and function as primary producers in diverse ecosystems. They also exhibit distinctive metabolic traits, such as the ability to synthesize starch in both plastids and cytosol and the synthesis of lignin from both phenylalanine and tyrosine.
However, the evolutionary origin of these traits has been unclear.
Takeda-Kimura et al. sequenced the genomes from grass sister clades and found that although some cytosolic starch synthesis genes emerged within grasses, a key plastid membrane transporter predates their evolution.
An earlier tandem duplication event predating a grass-specific whole-genome duplication gave rise to the bifunctional phenylalanine/tyrosine ammonia lyase, enabling dual lignin biosynthesis in grasses. ...
Structured Abstract
INTRODUCTION
The grass family (Poaceae) includes foundational primary producers in global ecosystems and economically important crops. Rice, wheat, and maize account for more than 40% of caloric intake for humans, and sugarcane, sorghum, and bamboo make abundant sugars and lignocellulosic biomass for renewable bioenergy and biomaterial production. Their genome assemblies have advanced our understanding of critical traits in agriculturally and ecologically important grass species. However, we still lack chromosomal assemblies for their closest relatives, which diverged from grass progenitors more than 100 million years ago, before the rho whole-genome duplication (ρWGD) in the ancestor of all grasses. This gap limits our understanding of how gene and genome duplications contributed to evolutionary innovations that define the grass lineage.
RATIONALE
This study generated reference-quality genomes for Joinvillea ascendens and Ecdeiocolea monostachya, which represent the sister lineage to all grasses, along with Pharus latifolius and Typha latifolia, which represent sister lineages to core grasses and all other members of the order Poales, respectively. Using these new genomic resources, we traced the evolutionary history of two distinctive metabolic traits of grasses: dual starch and lignin biosynthetic pathways. These grass-specific metabolic innovations contribute to the starch-rich endosperm of cereals and substantial lignin deposition in the vasculatures and fibers of grasses.
RESULTS
In this study, the new high-quality genome assemblies and annotations enabled comparative genomic analyses to place the timing of the ρWGD event just after the divergence of ancestral lineages leading to the grasses and their sister clade, including Joinvilleaceae and Ecdeiocoleaceae. Phylogenetic and molecular evolutionary analyses of more than 20 gene families involved in starch biosynthesis across many Poaceae and Poales species revealed that ρWGD contributed to the duplication of several of these genes, which now support cytosolic starch biosynthesis in grass endosperms. By contrast, genome comparisons and biochemical analyses of the lignin biosynthesis pathway revealed that an earlier tandem duplication of phenylalanine ammonia lyase (PAL) gave rise to phenylalanine/tyrosine ammonia lyase (PTAL) before the ρWGD and the origin of grasses, enabling grasses to synthesize lignin and other phenylpropanoid compounds from two aromatic amino acid precursors, phenylalanine and tyrosine. Precise determination of the timing of the plant PTAL evolution, combined with site-directed mutagenesis and x-ray crystal structural analyses, further identified two key residues, Ile112 and His140, that are responsible for the neofunctionalization of plant PAL into PTAL, providing a promising gene-editing strategy to enhance diverse phenylpropanoid production in plants.
CONCLUSION
Our integrated genomic, biochemical, and structural analyses, supported by robust phylogenetic resolution of grasses and their relatives, have unveiled the evolutionary history and molecular basis of key metabolic innovations predating the emergence of grasses. Our findings highlight critical roles for both WGDs and tandem gene duplications as drivers of evolutionary innovation. The nonmodel, noncrop Poales reference genomes generated for this study now offer valuable resources for dissecting the diverse and complex traits that contribute to the ecological and economic importance of grasses. The evolutionary basis of grass-specific traits will inform efforts to conserve grass-dominated ecosystems and accelerate breeding and engineering of cereals and other grass crops for sustainable production of food, feed, bioenergy, and biomaterials."
Molecular “bypasses” improve grass plants’s synthesis of lignin and starch, laying the early groundwork for evolutionary success (original news release)
Grass plant ancestors evolved metabolic pathway to ecological success (original news release)
Genomes of Poaceae sisters reveal key metabolic innovations preceding the evolution of grasses (preprint, open access, published already in December 2024 and never updated recently)
Metabolic innovations that predate the origin of grasses.
Fig. 1: Sequencing genomes of Poaceae sisters to trace the evolutionary history of grass metabolic innovations.
Fig. 2. Alteration of starch and fatty acid biosynthesis during the grass evolution.
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