Accession PRJCA001890
Title Allele-defined genome of the autopolyploid sugarcane Saccharum spontaneum L.
Relevance Agricultural
Data types Whole genome sequencing
Organisms Saccharum spontaneum
Description Modern sugarcanes are polyploid interspecific hybrids, combining high sugar content from Saccharum officinarum with hardiness, disease resistance and ratooning of Saccharum spontaneum. Sequencing of a haploid S. spontaneum, AP85-441, facilitated the assembly of 32 pseudo-chromosomes comprising 8 homologous groups of 4 members each, bearing 35,525 genes with alleles defined. The reduction of basic chromosome number from 10 to 8 in S. spontaneum was caused by fissions of 2 ancestral chromosomes followed by translocations to 4 chromosomes. Surprisingly, 80% of nucleotide binding site-encoding genes associated with disease resistance are located in 4 rearranged chromosomes and 51% of those in rearranged regions. Resequencing of 64 S. spontaneum genomes identified balancing selection in rearranged regions, maintaining their diversity. Introgressed S. spontaneum chromosomes in modern sugarcanes are randomly distributed in AP85-441 genome, indicating random recombination among homologs in different S. spontaneum accessions. The allele-defined Saccharum genome offers new knowledge and resources to accelerate sugarcane improvement.
Sample scope Monoisolate
Release date 2019-11-14
PubMed ID Article title Journal name DOI Year
Agency program Grant ID Grant title
the US Department of Energy DESC0010686
the US National Science Foundation Plant Genome Research Program IOS1025976
the International Consortium for Sugarcane Biotechnology N/A
the European Bioinformatics Institute BP2012OO2J17
the 863 program 2013AA102604
National Natural Science Foundation of China (NSFC) 31201260
the Program for New Century Excellent Talents in Fujian Province N/A
the DOE Center for Advanced Bioenergy and Bioproducts Innovation DESC18420
the Sao Paulo Research Foundation 2008/521460
the Sao Paulo Research Foundation 2012/510623
the Sao Paulo Research Foundation 2014/509218
the Sao Paulo Research Foundation 2008/520748
Submitter Jing    Lin  (
Organization Fujian Agriculture and Forestry University
Submission date 2019-11-07

Project Data

Resource name Description
BioSample (64)  show -
GSA (1) -
CRA002097 Allele-defined genome of the autopolyploid sugarcane Saccharum spontaneum L.