NEW YORK (GenomeWeb News) – In a paper appearing online today in Nature, an international research team reported that they have sequenced the complete 730 million-base genome of Sorghum bicolor, an African grass grown for human and animal food that also holds promise as a biofuel crop.
Sorghum is commonly grown as a food crop in parts of Africa where its drought tolerance is particularly advantageous. It is also grown in the southern US, mainly for animal feed or biofuel. Ethanol produced from the sorghum grain requires about a third of the water used to produce corn ethanol. And because it can grow eight to 15 feet tall in one growing season, sorghum is a candidate for cellulosic biofuel production, which relies on the non-edible parts of plants.
"Sorghum is an excellent candidate for biofuels production, with its ability to withstand drought and prosper on more marginal land," Anna Palmisano, associate director of biological and environmental research at DOE, who was not directly involved in the study, said in a statement. "The fully sequenced genome will be an indispensable tool for researchers seeking to develop plant variants that maximize these benefits."
The international research team that sequenced the genome was led by researchers at the US Department of Energy's Joint Genome Institute and Stanford University's Human Genome Center. They used Sanger sequencing to do paired-end shotgun sequencing of plasmid, fosmid, and BAC libraries of the 730 megabase genome — including the repeat sequences that make up about 61 percent of the genome.
Repetitive DNA is often considered "a horror" for whole-genome shotgun sequencing, lead author Andrew Paterson, director of the University of Georgia's Plant Genome Mapping Laboratory, told GenomeWeb Daily News. But he said the method worked well for sequencing sorghum because very good genetic maps were available for the plant and because researchers could refer to sequences from the rice genome.
"We could locate the things that were different [between sorghum and rice] and scrutinize them further," Paterson said.
Conversely, the sorghum genome is helping researchers better understand the rice genome, Paterson noted. "With each [genome], we develop greater confidence in what the common ancestor looked like," he said. "We're much more confident if we get the same answer in sorghum and rice."
For example, the comparison uncovered more than 10,000 proposed rice genes that actually seem to be gene fragments. As for the sorghum genome, the researchers detected some 27,640 protein-coding genes, more than 5,000 gene models, and 727 pseudogenes. They also found 67 known and 82 new sorghum microRNAs.
"One thing that was particularly striking was that there was a high degree of similarity between sorghum and rice," Paterson said. "That suggests their genomes will be predictive, to a large degree, for the remainder of the cereals."
Although the plants diverged roughly 50 million years ago, the results suggest sorghum's genome actually has more in common with the rice genome than with the genome of maize, its closer relative. While this may be somewhat surprising in light of the plants' evolutionary history, Paterson explained, it makes sense in terms of the whole-genome duplication event in maize.
Though the sorghum genome is roughly 75 percent larger than the rice genome, the genomes have similar gene counts and gene structure. In addition, the two plants seem to contain comparable numbers of gene families and gene families of similar sizes. Based on their assessment of the sorghum and rice genomes, the researchers suggested that there are nearly 20,000 conserved grass gene families.
Even so, the similarities between the sorghum and rice genomes were not uniformly distributed. While the euchromatic, gene-coding regions of the genomes were very similar, the sorghum genome contained much more heterochromatin than rice.
Paterson said it will also be interesting to compare the S. bicolor genome with that of Brachypodium distachyon, or purple false brome grass, since its sequence is closely related to wheat and barley but hasn't been through whole-genome duplication.
Researchers hope that by having the S. bicolor genome sequence in hand they will be able to develop tools and markers for increasing sorghum yield and disease resistance. The genome may also offer an opportunity to tweak the biofuel potential of sorghum and gain a better understanding of biofuel crops with more complex, polyploid genomes, Paterson said.
In addition, getting a handle on sorghum's drought tolerance could not only aid sorghum development but also lead to other crop improvements as well, Paterson explained. He said several sorghum re-sequencing projects using various high-throughput sequencing methods are underway at the University of Georgia and elsewhere.