NEW YORK (GenomeWeb) – An international team of researchers has sequenced the sunflower genome, giving insight into its evolution.
Sunflower, Helianthus annuus, reliably produces oil in a range of environmental conditions — including drought — suggesting that it could also be a model crop for climate change studies.
As it reported in Nature today, a University of Toulouse-led team of researchers generated a 3.6-gigabase H. annuus genome, which it reported largely consisted of long terminal repeats. By comparing the sunflower genome to those of other plants, the team found that it has a complex evolutionary history, including a number of whole-genome duplication events. The researchers also uncovered a number of genes influencing flowering time and oil production.
"The sunflower now has the potential to become a model crop for climate change adaptation, which can be achieved by exploiting genome-enabled systems biology and multi-disciplinary analyses of interactions between abiotic stressors, pathogen attacks, and agronomic practices," Toulouse's Nicolas Langlade and his colleagues wrote in their paper.
As the sunflower genome was known to consist of long and very similar repeats that made it tricky to sequence and assemble, Langlade and his colleagues turned to a long-read sequencing approach. They sequenced an inbred line, called XRQ, using Pacific Biosciences' RS II platform to give them 102x sequencing coverage. They assembled those reads into 17 pseudo-chromosomes that anchored 97 percent of the gene content and encompassed 3 gigabases.
More than 75 percent of the flower's genome was made up of long terminal repeat retrotransposons, 59 percent of which belong to the Gypsy evolutionary lineage. However, the researchers also noted that the sunflower LTR-RT lineages were mostly young and showed little sequence divergence due to expansion during the last million years. The LTR-RTs were further distributed non-randomly in the sunflower genomes and were most intact.
In addition, more than 6,000 transposons, especially Helitron transposons, acquired gene fragments.
By further comparing the sunflower genome to other members of the Asterid family like lettuce, artichoke, and coffee, the researchers began to peel back the paleohistory of Asterid.
They reported that sunflower has a complex evolutionary history. In addition to a genome duplication event common to all eudicots that occurred 122 million to 164 million years ago, the sunflower, as well as lettuce and artichoke, underwent a whole-genome triplication event — possibly independent genome duplication events that occurred close together in time — between 38 million and 50 million years ago and a lineage-specific duplication event some 29 million years ago.
At the same time, a number of chromosomal fissions and fusions led to its current 17-chromosome karyotype.
Using gene network and transcriptomic data generated from sunflower tissues, the researchers searched for candidate genes that might influence either flowering time or seed oil content or quality in the plants — both major breeding traits.
By relying on that as well as a database of Arabidopsis flowering time gene networks and a genome-wide association study of flowering time variation in sunflower, the researchers homed in on new candidate genes for flowering time, including AGL24, an in-paralog that co-localized with SNPs linked to flowering time.
Langlade and his colleagues noted that sunflower's most recent genome duplication event influenced the genomic architecture of flowering time, indicating that paralogs can stay in the same regulatory networks for millions of years.
Similarly, they also examined oil metabolic networks in sunflower and examined different genotypes between oil-producing and non-oil-producing lines. In particular, they reported that the gene FAD2-1 appeared to be under selection after domestication occurred.
"This genome represents a cornerstone for future research programs aiming to exploit genetic diversity to improve biotic and abiotic stress resistance and oil production, while also considering agricultural constraints and human nutritional needs," the researchers wrote.