ArticleFrontiers in plant science2016
BAC-Pool Sequencing and Assembly of 19 Mb of the Complex Sugarcane Genome.
Article in Frontiers in plant science, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- DaapNLRSeek, prediction, and evolution of resistance genes in polyploid sugarcane genomes.iScience · 2025Article
- Terpenoid balance inScience advances · 2024Article
- Terpenoid balance inbioRxiv : the preprint server for biology · 2023Article
- Bioinformatic analyses to uncover genes involved in trehalose metabolism in the polyploid sugarcane.Scientific reports · 2022Article
- Recent Advances in Sugarcane Genomics, Physiology, and Phenomics for Superior Agronomic Traits.Frontiers in genetics · 2022Review
- Applying Molecular Phenotyping Tools to Explore Sugarcane Carbon Potential.Frontiers in plant science · 2021Review
- Plant Proteomics and Systems Biology.Advances in experimental medicine and biology · 2021Article
- The Wild Sugarcane and Sorghum Kinomes: Insights Into Expansion, Diversification, and Expression Patterns.Frontiers in plant science · 2021Article
- The control of endopolygalacturonase expression by the sugarcane RAV transcription factor during aerenchyma formation.Journal of experimental botany · 2019Article
- TALEN-mediated targeted mutagenesis of more than 100 COMT copies/alleles in highly polyploid sugarcane improves saccharification efficiency without compromising biomass yield.Plant biotechnology journal · 2018Article
- "Targeted Sequencing by Gene Synteny," a New Strategy for Polyploid Species: Sequencing and Physical Structure of a Complex Sugarcane Region.Frontiers in plant science · 2018Article
- Identification, classification and transcriptional profiles of dirigent domain-containing proteins in sugarcane.Molecular genetics and genomics : MGG · 2017Article
- Initial genome sequencing of the sugarcane CP 96-1252 complex hybrid.F1000Research · 2017Article
- Draft genome sequencing of the sugarcane hybrid SP80-3280.F1000Research · 2017Article
- Article
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4 authors.
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Abstract
Sequencing plant genomes are often challenging because of their complex architecture and high content of repetitive sequences. Sugarcane has one of the most complex genomes. It is highly polyploid, preserves intact homeologous chromosomes from its parental species and contains >55% repetitive sequences. Although bacterial artificial chromosome (BAC) libraries have emerged as an alternative for accessing the sugarcane genome, sequencing individual clones is laborious and expensive. Here, we present a strategy for sequencing and assembly reads produced from the DNA of pooled BAC clones. A set of 178 BAC clones, randomly sampled from the SP80-3280 sugarcane BAC library, was pooled and sequenced using the Illumina HiSeq2000 and PacBio platforms. A hybrid assembly strategy was used to generate 2,451 scaffolds comprising 19.2 MB of assembled genome sequence. Scaffolds of ≥20 Kb corresponded to 80% of the assembled sequences, and the full sequences of forty BACs were recovered in one or two contigs. Alignment of the BAC scaffolds with the chromosome sequences of sorghum showed a high degree of collinearity and gene order. The alignment of the BAC scaffolds to the 10 sorghum chromosomes suggests that the genome of the SP80-3280 sugarcane variety is ∼19% contracted in relation to the sorghum genome. In conclusion, our data show that sequencing pools composed of high numbers of BAC clones may help to construct a reference scaffold map of the sugarcane genome.
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