| Description |
Sugarcane is a vital crop with significant economic and industrial value, contributing to the global production of sugar and bioenergy. Understanding the sugarcane genome is crucial for improving yield, stress tolerance, and disease resistance. However, the cultivated sugarcane's ultra-complex genome still needs to be resolved due to its extremely high ploidy and extensive recombination between the two subgenomes, S. officinarum (ZZSO) and S. officinarum (ZZSS). In this study, we generated a chromosomal-scale, haplotype-resolved genome assembly for a hybrid cultivated sugarcane ZZ1, facilitated by multiple sequencing technologies and a series of bioinformatics approaches we developed. This assembly contains 10.4 Gb genomic sequences and 68,509 well-annotated genes with defined alleles in two sub-genomes distributed in 99 original and 15 recombined chromosomes. Analysis of RNA-seq data from various developmental stages of ZZ1 revealed that most of the chromosomes showed similar average expression levels between the SO and SS subgenomes, but the asymmetric expression patterns were detected within a few homoeologous chromosome groups. In addition, we found that sugar accumulation-associated gene families were expanded mostly from ZZSO subgenome, but genes responding to Pokkah boeng were derived dominantly from ZZSS subgenome. Our findings provide valuable insights into the complex genome of modern hybrid sugarcane cultivars, paving the way for future functional genomics and molecular breeding studies in sugarcane. |
