ArticleGigaScience2019
Assembly of the 373k gene space of the polyploid sugarcane genome reveals reservoirs of functional diversity in the world's leading biomass crop.
Article in GigaScience, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 55 papers, 1 of them a synthesis that pooled it.
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Who cites it
55 citing papers in PubMed, 1 synthesis or guideline pooled it, 159 citations in OpenAlex.
- Antisense Transcription in Plants: A Systematic Review and an Update on cis-NATs of Sugarcane.International journal of molecular sciences · 2022Pooled it
- 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
- A sorghum-anchored pan-grass syntenic gene set in grasses.NAR genomics and bioinformatics · 2026Article
- Nitrogen starvation induces arbuscular mycorrhizal fungi to optimize resource allocation in sugarcane roots via suppression of basal metabolism.NPJ biofilms and microbiomes · 2026Article
- Sugarcane Breeding in the Genomic Era: Integrative Strategies and Emerging Technologies.Plants (Basel, Switzerland) · 2026Review
- Integrated multi-omics analysis reveals hormonal and nutrient networks regulating sugarcane tillering.Frontiers in plant science · 2026Article
- Turbo-charging crop improvement: harnessing multiplex editing for polygenic trait engineering and beyond.The Plant journal : for cell and molecular biology · 2025Review
- Unveiling the Genome of the Diploid Wild Sugarcane RelativeInternational journal of molecular sciences · 2025Article
- RNAi and genome editing of sugarcane: Progress and prospects.The Plant journal : for cell and molecular biology · 2025Review
- Insights of cellular and molecular changes in sugarcane response to oxidative signaling.BMC plant biology · 2025Article
- Cell wall modulation by drought and elevated COFrontiers in plant science · 2025Article
- Identification and Characterization of Key Genes for Nitrogen Utilization fromInternational journal of molecular sciences · 2024Article
- CRISPR/Cas technology: fueling the future of Biofuel production with sugarcane.Functional & integrative genomics · 2024Review
- Bioinformatic insights into sugar signaling pathways in sugarcane growth.Scientific reports · 2024Article
- The extent of multiallelic, co-editing of LIGULELESS1 in highly polyploid sugarcane tunes leaf inclination angle and enables selection of the ideotype for biomass yield.Plant biotechnology journal · 2024Article
- Genetic Engineering for Enhancing Sugarcane Tolerance to Biotic and Abiotic Stresses.Plants (Basel, Switzerland) · 2024Review
- A chromosomal-scale genome assembly of modern cultivated hybrid sugarcane provides insights into origination and evolution.Nature communications · 2024Article
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Authors and funding
29 authors at 7 institutions in 5 countries.
Funding
Abstract
backgroundSugarcane cultivars are polyploid interspecific hybrids of giant genomes, typically with 10-13 sets of chromosomes from 2 Saccharum species. The ploidy, hybridity, and size of the genome, estimated to have >10 Gb, pose a challenge for sequencing.
resultsHere we present a gene space assembly of SP80-3280, including 373,869 putative genes and their potential regulatory regions. The alignment of single-copy genes in diploid grasses to the putative genes indicates that we could resolve 2-6 (up to 15) putative homo(eo)logs that are 99.1% identical within their coding sequences. Dissimilarities increase in their regulatory regions, and gene promoter analysis shows differences in regulatory elements within gene families that are expressed in a species-specific manner. We exemplify these differences for sucrose synthase (SuSy) and phenylalanine ammonia-lyase (PAL), 2 gene families central to carbon partitioning. SP80-3280 has particular regulatory elements involved in sucrose synthesis not found in the ancestor Saccharum spontaneum. PAL regulatory elements are found in co-expressed genes related to fiber synthesis within gene networks defined during plant growth and maturation. Comparison with sorghum reveals predominantly bi-allelic variations in sugarcane, consistent with the formation of 2 "subgenomes" after their divergence ∼3.8-4.6 million years ago and reveals single-nucleotide variants that may underlie their differences.
conclusionsThis assembly represents a large step towards a whole-genome assembly of a commercial sugarcane cultivar. It includes a rich diversity of genes and homo(eo)logous resolution for a representative fraction of the gene space, relevant to improve biomass and food production.
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Registered trials
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