First genomes decoded for close relatives of rice, wheat and corn, shedding light on origins of starch and lignin

The genomes of plants that are close relatives of major grains, including rice, wheat and corn, have been decoded for the first time. Using the genomes, researchers traced the evolutionary origins of the abundant starch accumulation in grain seeds and lignin buildup in stems.

An international research team, including researchers from Japan, announced on the 27th in the journal Science that it had decoded reference-quality genomes for Joinvillea ascendens and Ecdeiocolea monostachya, sister lineages to the grass family (Poaceae), as well as Pharus latifolius and Typha latifolia.

Rice, wheat and corn provide more than 40% of the calories consumed by humans. Sugarcane, sorghum and bamboo are also sources of bioenergy and biomaterials. However, scientists had lacked chromosome-level genomes for the closest relatives that diverged before the common ancestor of grasses underwent rho whole-genome duplication (ρWGD) 100 million years ago. This limited their ability to explain how gene duplication gave rise to key traits of grasses.

Using the new genomes, the researchers confirmed that ρWGD occurred after the ancestral lineage leading to grasses and their sister lineages, Joinvilleaceae and Ecdeiocoleaceae, had diverged.

An analysis of more than 20 gene families involved in starch biosynthesis found that ρWGD duplicated some of these genes. The duplicated genes now support cytosolic starch synthesis in the endosperm of grasses.

By contrast, the lignin biosynthesis pathway appears to have formed before ρWGD. Before grasses emerged, a tandem duplication of phenylalanine ammonia-lyase (PAL) gave rise to phenylalanine/tyrosine ammonia-lyase (PTAL), enabling grasses to synthesize phenylpropanoids, including lignin, from two aromatic amino acid precursors: phenylalanine and tyrosine.

Through point mutations and X-ray crystallographic analysis, the researchers also identified isoleucine 112 (Ile112) and histidine 140 (His140) as key residues involved in the functional shift of plant PAL to PTAL. The researchers said the findings could inform gene-editing strategies to increase the production of diverse phenylpropanoid compounds in plants.

The researchers said the findings "show that whole-genome duplication and tandem gene duplication are key drivers of evolutionary innovation." They added that the newly generated reference genomes for nonmodel, noncrop members of the order Poales will be a useful resource for studying the diverse traits underlying the ecological and economic importance of grasses.