Olivier Garsmeur1, Adam Healey2, Robert Henry3,4, Karen S Aitken3, Jeremy Schmutz2,5 and Angélique D’Hont1
1CIRAD, UMR AGAP Institut, F-34398 Montpellier, France and UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
2Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
3Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, Queensland, Australia
4ARC Centre of Excellence for Plant Success in Nature and Agriculture, University of Queensland, Brisbane, Queensland, Australia
5DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
In 2024, we produced a polyploid genome assembly of the modern cultivar R570. This assembly was obtained using a combination of approaches and sequencing technologies and resulted in 67 assembled chromosomes. We found that many chromosome segments, representing ~50% of the genome, were nearly identical and thus collapsed in the assembly. This genomic redundancy is due to a partially inbred genome resulting from the 2n transmission of S. officinarum chromosomes in the early steps of modern breeding and from POJ2878 being twice the grandparent of cultivar R570.This explains why the assembly contains 67 chromosomes compared to the 114 chromosomes present in the R570 genome. The 67 assembled chromosomes thus correspond to the unique haplotypes on each of the ~ 12 chromosome copies of the 10 basic chromosomes. In addition, we sequenced the whole genomes of 305 accessions representing the Saccharum genus and related genera. We developed an approach based on the distribution of short repeated sequences (k-mers) as a proxy for transposable elements. Sets of repeated k-mers representative of species or subgroups were identified among the 305 sequenced accessions. By analyzing their distribution in the R570 genome, we were able to assign an origin to the chromosome segments of the R570 assembly. Our results showed that 77% of the R570 assembly originated from S. officinarum and 22% from S. spontaneum. The assembly also contained several interspecific recombinant chromosomes.