Allele annotation in the AP85-441 genome

  A high level of homologous gene retention was detected from sequencing multiple haplotypes in sugarcane,despite extreme autopolyploid redundancy. In autopolyploid genomes, homologous genes at the same locus on homologous chromosomes are defined as alleles. Using two rounds of MAKER followed by manual annotation to separate genes and alleles, annotated 35,525 genes with alleles defined, including 4,289 (12.7%) genes with four alleles, 9,792 (27.6%) with three, 14,797 (41.7%) with two, and 6,647 (18.7%) with one. The total number of alleles was 82,773, with an average 2.3 alleles per gene.

Gene ID: Eg:Sspon.001D0016270
NOTE: AP85-441 is the first homologous polyploid genome with specific allele annotation.On this page, you can query for its alleles by entering a gene id.