ArticlePloS one2014
De novo assembly and transcriptome analysis of contrasting sugarcane varieties.
Article in PloS one, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 68 papers.
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Who cites it
68 citing papers in PubMed.
- Adaptive Responses of Tropical Crops: A Multi-Scale Omics Integrated Perspective.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Review
- Review
- Identifying candidate genes for sugar accumulation in sugarcane: an integrative approach.BMC genomics · 2024Article
- Transcriptomic and Proteomic Landscape of Sugarcane Response to Biotic and Abiotic Stressors.International journal of molecular sciences · 2023Review
- Development of unigene-derived SSR markers from RNA-seq data of Uraria lagopodioides (Fabaceae) and their application in the genus Uraria Desv. (Fabaceae).BMC plant biology · 2023Article
- Long read transcriptome sequencing of a sugarcane hybrid and its progenitors,Frontiers in plant science · 2023Article
- Species-specific transcriptomic changes upon respiratory syncytial virus infection in cotton rats.Scientific reports · 2022Article
- Review
- Taxonomically Restricted Genes Are Associated With Responses to Biotic and Abiotic Stresses in Sugarcane (Frontiers in plant science · 2022Article
- Comparative de novo transcriptome analysis identifies salinity stress responsive genes and metabolic pathways in sugarcane and its wild relative Erianthus arundinaceus [Retzius] Jeswiet.Scientific reports · 2021Article
- Genome-wide approaches for the identification of markers and genes associated with sugarcane yellow leaf virus resistance.Scientific reports · 2021Article
- Metatranscriptomic Analysis of Bacterial Communities on Laundered Textiles: A Pilot Case Study.Microorganisms · 2021Article
- Overexpression of a Sugarcane BAHD Acyltransferase Alters Hydroxycinnamate Content in Maize Cell Wall.Frontiers in plant science · 2021Article
- Applying Molecular Phenotyping Tools to Explore Sugarcane Carbon Potential.Frontiers in plant science · 2021Review
- Article
- Transcriptomic Analysis of Changes in Gene Expression During Flowering Induction in Sugarcane Under Controlled Photoperiodic Conditions.Frontiers in plant science · 2021Article
- Leaping into the Unknown World ofJournal of fungi (Basel, Switzerland) · 2020Article
- Amino Acid and Carbohydrate Metabolism Are Coordinated to Maintain Energetic Balance during Drought in Sugarcane.International journal of molecular sciences · 2020Article
- Machine learning approaches reveal genomic regions associated with sugarcane brown rust resistance.Scientific reports · 2020Article
- Current breeding and genomic approaches to enhance the cane and sugar productivity under abiotic stress conditions.3 Biotech · 2020Review
8 more citing papers are in PubMed but not listed here.
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Authors and funding
10 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Sugarcane is an important crop and a major source of sugar and alcohol. In this study, we performed de novo assembly and transcriptome annotation for six sugarcane genotypes involved in bi-parental crosses. The de novo assembly of the sugarcane transcriptome was performed using short reads generated using the Illumina RNA-Seq platform. We produced more than 400 million reads, which were assembled into 72,269 unigenes. Based on a similarity search, the unigenes showed significant similarity to more than 28,788 sorghum proteins, including a set of 5,272 unigenes that are not present in the public sugarcane EST databases; many of these unigenes are likely putative undescribed sugarcane genes. From this collection of unigenes, a large number of molecular markers were identified, including 5,106 simple sequence repeats (SSRs) and 708,125 single-nucleotide polymorphisms (SNPs). This new dataset will be a useful resource for future genetic and genomic studies in this species.
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