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
Publication
PubMed ID Article title Journal name DOI Year
30425353
Grants
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
the Natural Science Foundation of China 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  (lolyemily@163.com)
Organization Fujian Agriculture and Forestry University
Submission date 2019-11-07

Project Data

Resource name Description
BioSample (64) -
SAMC113949 DNA of Saccharum spontaneum L.:leaf
SAMC113948 DNA of Saccharum spontaneum L.:leaf
SAMC113947 DNA of Saccharum spontaneum L.:leaf
SAMC113946 DNA of Saccharum spontaneum L.:leaf
SAMC113945 DNA of Saccharum spontaneum L.:leaf
SAMC113944 DNA of Saccharum spontaneum L.:leaf
SAMC113943 DNA of Saccharum spontaneum L.:leaf
SAMC113942 DNA of Saccharum spontaneum L.:leaf
SAMC113941 DNA of Saccharum spontaneum L.:leaf
SAMC113940 DNA of Saccharum spontaneum L.:leaf
SAMC113939 DNA of Saccharum spontaneum L.:leaf
SAMC113938 DNA of Saccharum spontaneum L.:leaf
SAMC113937 DNA of Saccharum spontaneum L.:leaf
SAMC113936 DNA of Saccharum spontaneum L.:leaf
SAMC113935 DNA of Saccharum spontaneum L.:leaf
SAMC113934 DNA of Saccharum spontaneum L.:leaf
SAMC113933 DNA of Saccharum spontaneum L.:leaf
SAMC113932 DNA of Saccharum spontaneum L.:leaf
SAMC113931 DNA of Saccharum spontaneum L.:leaf
SAMC113930 DNA of Saccharum spontaneum L.:leaf
SAMC113929 DNA of Saccharum spontaneum L.:leaf
SAMC113928 DNA of Saccharum spontaneum L.:leaf
SAMC113927 DNA of Saccharum spontaneum L.:leaf
SAMC113926 DNA of Saccharum spontaneum L.:leaf
SAMC113925 DNA of Saccharum spontaneum L.:leaf
SAMC113924 DNA of Saccharum spontaneum L.:leaf
SAMC113923 DNA of Saccharum spontaneum L.:leaf
SAMC113922 DNA of Saccharum spontaneum L.:leaf
SAMC113921 DNA of Saccharum spontaneum L.:leaf
SAMC113920 DNA of Saccharum spontaneum L.:leaf
SAMC113919 DNA of Saccharum spontaneum L.:leaf
SAMC113918 DNA of Saccharum spontaneum L.:leaf
SAMC113917 DNA of Saccharum spontaneum L.:leaf
SAMC113916 DNA of Saccharum spontaneum L.:leaf
SAMC113915 DNA of Saccharum spontaneum L.:leaf
SAMC113914 DNA of Saccharum spontaneum L.:leaf
SAMC113913 DNA of Saccharum spontaneum L.:leaf
SAMC113912 DNA of Saccharum spontaneum L.:leaf
SAMC113911 DNA of Saccharum spontaneum L.:leaf
SAMC113910 DNA of Saccharum spontaneum L.:leaf
SAMC113909 DNA of Saccharum spontaneum L.:leaf
SAMC113908 DNA of Saccharum spontaneum L.:leaf
SAMC113907 DNA of Saccharum spontaneum L.:leaf
SAMC113906 DNA of Saccharum spontaneum L.:leaf
SAMC113905 DNA of Saccharum spontaneum L.:leaf
SAMC113904 DNA of Saccharum spontaneum L.:leaf
SAMC113903 DNA of Saccharum spontaneum L.:leaf
SAMC113902 DNA of Saccharum spontaneum L.:leaf
SAMC113901 DNA of Saccharum spontaneum L.:leaf
SAMC113900 DNA of Saccharum spontaneum L.:leaf
SAMC113899 DNA of Saccharum spontaneum L.:leaf
SAMC113898 DNA of Saccharum spontaneum L.:leaf
SAMC113897 DNA of Saccharum spontaneum L.:leaf
SAMC113896 DNA of Saccharum spontaneum L.:leaf
SAMC113895 DNA of Saccharum spontaneum L.:leaf
SAMC113894 DNA of Saccharum spontaneum L.:leaf
SAMC113893 DNA of Saccharum spontaneum L.:leaf
SAMC113892 DNA of Saccharum spontaneum L.:leaf
SAMC113891 DNA of Saccharum spontaneum L.:leaf
SAMC113890 DNA of Saccharum spontaneum L.:leaf
SAMC113889 DNA of Saccharum spontaneum L.:leaf
SAMC113888 DNA of Saccharum spontaneum L.:leaf
SAMC113887 DNA of Saccharum spontaneum L.:leaf
SAMC113886 DNA of Saccharum spontaneum L.:leaf
GSA (1) -
CRA002097 Allele-defined genome of the autopolyploid sugarcane Saccharum spontaneum L.