An international team of scientists from the Johns Hopkins University, Pacific Biosciences, and Earlham Institute has produced the first near-complete genomic sequence for the common bread wheat (Triticum aestivum). The research appears in the journal GigaScience.
A field of bread wheat (Triticum aestivum) in Ukraine. Image credit: Oleksii Alieksieiev.
Bread wheat has one of the most complex genomes known to science, with 6 copies of 7 chromosomes, enormous numbers of near-identical sequences scattered throughout, and an overall size of almost 16 billion base pairs of DNA.
By comparison, the human genome is about 5 times smaller, with about 3 billion base pairs and two copies of 23 chromosomes.
“After many years of trying, we’ve finally been able to produce a high-quality assembly of this very challenging genome,” said Professor Steven Salzberg, from the Johns Hopkins University Schools of Engineering and Medicine.
Previously published versions of the bread wheat genome have contained large gaps in its highly repetitive DNA sequence.
“The repetitive nature of this genome makes it difficult to fully sequence. It’s like trying to put together a jigsaw puzzle of a landscape scene with a huge blue sky. There are lots of very similar, small pieces to assemble,” Professor Salzberg said.
The newly assembled bread wheat genome took a year for the team to assemble 1.5 trillion bases of raw data into a final assembly of 15.34 billion base pairs.
To do it, the authors used two types of genome sequencing technology: high throughput short-read sequencing and long-read, single molecule sequencing.
“As its name implies, high throughput sequencing generates massive amounts of DNA base pairs very quickly and cheaply, although the fragments are very short — just 150 base pairs long for this project,” the researchers explained.
“To help assemble the repetitive areas, we used real-time, single molecule sequencing, which reads DNA as it is being synthesized in a tiny, nano-scale well on a chip. The technology enables us to read up to 20,000 base pairs at a time by measuring fluorescent signals that are emitted as each DNA base is copied.”
The newly-assembled bread wheat genome sequence and the recently-published sequence of the bread wheat’s ‘ancestor,’ the Tausch’s goatgrass (Aegilops tauschii), may help biologists not only better understand the evolutionary history of wheat, but also advance the quest for hardier, more pest- and drought-resistant wheat types to help feed the world’s growing population.
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Aleksey V. Zimin et al. 2017. The first near-complete assembly of the hexaploid bread wheat genome, Triticum aestivum. GigaScience 6 (11): 1-7; doi: 10.1093/gigascience/gix097
