ArticleScientific reports2022
A draft chromosome-scale genome assembly of a commercial sugarcane.
Article in Scientific reports, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- From family trials to genomic mate allocation: statistical and genomic strategies to accelerate sugarcane genetic improvement.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Review
- Decoding the Mystery of Sugarcane Genome-Based Breeding: Current Advancements, Strategies, and Future Challenges.Plant, cell & environment · 2026Review
- Revisiting the Molecular Roadmap for Sugar Crops: Genome Reading, Trait Writing and Variety Redesigning.Plant biotechnology journal · 2026Review
- Review
- Sugarcane Breeding in the Genomic Era: Integrative Strategies and Emerging Technologies.Plants (Basel, Switzerland) · 2026Review
- Unveiling the Genome of the Diploid Wild Sugarcane RelativeInternational journal of molecular sciences · 2025Article
- Article
- Recent Advances in Sugarcane Leaf Scald Disease: Pathogenic Insights and Sustainable Management Approaches.Plants (Basel, Switzerland) · 2025Review
- Identification and Characterization of Key Genes for Nitrogen Utilization fromInternational journal of molecular sciences · 2024Article
- Genome-Wide Analysis of the Auxin/Indoleacetic Acid (International journal of molecular sciences · 2024Article
- A chromosomal-scale genome assembly of modern cultivated hybrid sugarcane provides insights into origination and evolution.Nature communications · 2024Article
- Article
- Two long read-based genome assembly and annotation of polyploidy woody plants, Hibiscus syriacus L. using PacBio and Nanopore platforms.Scientific data · 2023Article
- A Large-Scale Candidate-Gene Association Mapping for Drought Tolerance and Agronomic Traits in Sugarcane.International journal of molecular sciences · 2023Article
- A complete gap-free diploid genome in Saccharum complex and the genomic footprints of evolution in the highly polyploid Saccharum genus.Nature plants · 2023Article
- A SNP variation in the Sucrose synthase (PeerJ · 2023Article
- Developing new sugarcane varieties suitable for mechanized production in China: principles, strategies and prospects.Frontiers in plant science · 2023Article
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Authors and funding
20 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Sugarcane accounts for a large portion of the worlds sugar production. Modern commercial cultivars are complex hybrids of S. officinarum, S. spontaneum, and several other Saccharum species, resulting in an auto-allopolyploid with 8-12 copies of each chromosome. The current genome assembly gold standard is to generate a long read assembly followed by chromatin conformation capture sequencing to scaffold. We used the PacBio RSII and chromatin conformation capture sequencing to sequence and assemble the genome of a South East Asian commercial sugarcane cultivar, known as Khon Kaen 3. The Khon Kaen 3 genome assembled into 104,477 contigs totalling 7 Gb, which scaffolded into 56 pseudochromosomes containing 5.2 Gb of sequence. Genome annotation produced 242,406 genes from 30,927 orthogroups. Aligning the Khon Kaen 3 genome sequence to S. officinarum and S. spontaneum revealed a high level of apparent recombination, indicating a chimeric assembly. This assembly error is explained by high nucleotide identity between S. officinarum and S. spontaneum, where 91.8% of S. spontaneum aligns to S. officinarum at 94% identity. Thus, the subgenomes of commercial sugarcane are so similar that using short reads to correct long PacBio reads produced chimeric long reads. Future attempts to sequence sugarcane must take this information into account.
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