Researchers broke through the mysteries of the sugarcane genome / ScienceDaily

Producing the complete sequence required a concerted effort by more than 100 scientists from 16 institutions; the work took five years and resulted in a publication in Nature Genetics. But the motivation to attack the project had come long before.

"Personally, I have waited 20 years for this genome to be sequenced," said Ray Ming, a professor of plant biology at the University of Illinois, who initiated and led the research team. sequencing effort. "I dreamed of having a reference genome for sugarcane when I was working on mapping the genome of sugar cane in the late 1990s." Ming is a member of the Carl R. Woese Institute for Genomic Biology, one of the groups of researchers interested in the development of sugarcane and related crops to stimulate food production and biofuels.

The complete sequence of the genome was well worth the wait and effort because of its potential to aid in the improvement of sugarcane. Cane sugar grown by most farmers is a hybrid of two species: Saccharum officinarum, which grows large plants with high sugar content, and Saccharum spontaneum, whose size and softness are offset by increased resistance to disease and tolerance to environmental stress. In the absence of a complete genome sequence, breeders have created robust, high-yielding strains after several generations of crosses and selections, but this is an arduous process. which requires time and luck.

"Sugarcane is the fifth most valuable crop, and the lack of a reference genome hinders genomics research and molecular breeding for the improvement of sugarcane," he said. Ming said. . Sequencing technology was not ready to handle large autopolyploid genomes before 2015, when the throughput, read length, and cost of third-generation sequencing technology [e.g. that developed by biotechnology company Pacific Biosciences] has become quite competitive. "

Why is the sequencing of the sugarcane genome so difficult? A natural phenomenon common to plants created an important technical barrier. During the evolutionary history of sugar cane, his genome had been duplicated twice, giving rise to four slightly different versions of each pair of chromosomes, all sunk into the same nucleus.

These events not only quadrupled the size of the genome (and thus the considerable volume of the DNA sequence), but they also made the very similar sequences of genome duplication to be assembled into distinct chromosomes much more difficult. The genomic DNA is usually sequenced or read in small superimposed fragments, and the sequence data of these fragments become superimposed elements of a huge linear puzzle. While the size of the sugarcane genome doubled, then doubled again, this puzzle not only got bigger; he took repeated but not exactly identical elements in which it was difficult to insert these many tiny pieces correctly.

To meet this challenge, the sequencing team used a technique called high-throughput chromatin or Hi-C conformational capture. This method allows researchers to discover what parts of the entangled long strands of chromosomal DNA are in contact with each other within the cell. When they were analyzed with the help of a custom algorithm called ALLHIC developed by the team, the resulting data was used to define the image on the lid. a puzzle box, providing an approximate map of the sequence sections most likely to belong to which chromosome.

"The biggest surprise was that by combining long sequence readings and the Hi-C physical map, we assembled an autotetraploid system. [quadrupled] genome into 32 chromosomes and achieved our goal of specific annotation of the allele among homologous chromosomes, "said Ming.In other words, the researchers now knew what gene sequences belonged to each of the four variations of the original genome, that of pre-duplication – a level of detail much higher than what they expected.

With this information, researchers could formulate better hypotheses about the mysteries of evolution of the genome evolution of sugarcane.

By comparing the genomes of related species, researchers realized that at one point, the number of unique chromosomes increased from 10 to eight. To the surprise of the team, the new sequence data revealed that two different chromosomes had separated and the four halves had then merged with different existing chromosomes, a more complex set of events than the one they had presumed.

How does understanding these physical changes help? These large physical rearrangements in the genome accompany gene modifications in the affected regions. For example, Ming and his colleagues found that large chunks of chromosomes moved to new locations contained many more genes that help plants resist disease than those found elsewhere.

"This helped to understand why S. spontaneum is such a superior source of genes for disease resistance and stress tolerance," Ming said. "Chromosomal rearrangements are probably the cause, not the consequence of this enrichment, although the underlying mechanism of this enrichment remains to be investigated, then the implementation of molecular selection. [of sugarcane]. "

The high quality of the genome sequence also allowed researchers to identify the possible origins of the incredible sweetness of modern sugar cane: even in the less spontaneous S. spontaneum, mutations that produced multiple copies of protein genes carrying sugar have accumulated. They also found that, in hybridization between S. officinarum and S. spontaneum, the DNA sequence derived from S. spontaneum is randomly dispersed throughout the hybrid genome.

"The ALLHIC method has already proven effective for building the autopolyploid genome of sugarcane," Ming said. He predicts that techniques successfully used for the sugarcane genome will also help researchers to sequence other complex genomes.