Plant scientists plan massive effort to sequence 10,000 genomes

[China] Hopes of sequencing the DNA of every living thing on Earth are taking a step forward with the announcement of plans to sequence at least 10,000 genomes representing every major clade of plants and eukaryotic microbes.

Chinese sequencing giant BGI and the China National GeneBank (CNGB) held a workshop yesterday on the sidelines of the International Botanical Congress, being held this week in BGI’s hometown of Shenzhen, to discuss what they are calling the 10KP plan. About 250 plant scientists participated in the discussions and “are raring to go,” says Gane Ka-Shu Wong, a genomicist and bioinformaticist at University of Alberta in Edmonton, Canada.

The 10KP plan will be a key part of the Earth BioGenome Project (EBP), an ambitious and still evolving scheme to get at least rough sequence data on the 1.5 million eukaryotic species, starting with detailed sequences of one member of each of the 9000 eukaryotic families. The effort to sequence plants is moving ahead a bit faster than other aspects of EBP “because plant scientists are more collaborative,” Wong says jokingly.

The 10KP plan is also building on a previous 1000 plant (1KP) transcriptome project. That effort, launched in 2012 and now nearing completion, was also led by BGI, where Wong is an associate director.

“One thing we focused on (for 1KP) was sampling phylogenetic diversity, not just crops and model organisms,” Wong says. That strategy will continue with 10KP. The transcriptome project has resulted in more than 50 papers, with the overall summary publication still to come. A lot of the analysis has focused on plant evolution. One surprise was that important transcription factors previously thought to have evolved as land plants colonized terrestrial habitats can actually be traced back to green algae, says Michael Melkonian, a botanist at the University of Cologne in Germany. Screening green algae also turned up new light-sensitive proteins that neuroscientists now use to study how different neurons interact and better understand neurological functioning.

Whereas the 1KP project only tackled the transcriptome, or all the messenger RNA expressed by an organism, 10KP will produce completely new sequences of the entire genome. And scientists expect an even larger bonanza of fundamental insights and economic spin-offs.

The 10KP project “is 1KP on steroids,” says Douglas Soltis, a plant biologist at the Florida Museum of Natural History at the University of Florida in Gainesville. He adds that one  “wonderful thing” about the project is that it will provide reference genomes for “the numerous plant researchers studying nonmodel systems,” he says. The project will also present “an unprecedented opportunity to address fundamental questions about plant evolution,” says Stephen Smith, an evolutionary biologist at the University of Michigan in Ann Arbor. Study targets are expected to include the role of genome duplication, the correlation between genomic and morphological changes, and how rates of evolution changed over time.

 

Photo: Freshwater alga in the genus Zygnema would be one target of sequencing project. Norbert Hülsmann/Flickr (CC BY-NC-SA 2.0)

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