ArticleFrontiers in plant science2015
Sequencing, de novo assembly and comparative analysis of Raphanus sativus transcriptome.
Article in Frontiers in plant science, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed, 29 citations in OpenAlex.
- Transcriptomic analysis reveals candidate genes associated with salinity stress tolerance during the early vegetative stage in fababean genotype, Hassawi-2.Scientific reports · 2023Article
- De novo transcriptome assembly of Dalbergia sissoo Roxb. (Fabaceae) under Botryodiplodia theobromae-induced dieback disease.Scientific reports · 2023Article
- Global gene expression perturbations in rapeseed due to the introduction of alien radish chromosomes.Journal of genetics · 2021Article
- Phenotypic and Transcriptomic Analysis of Two Pinellia ternata Varieties T2 line and T2Plus line.Scientific reports · 2020Article
- Article
- Comprehensive Stress-Based De Novo Transcriptome Assembly and Annotation of Guar (International journal of genomics · 2019Article
- Identification of critical genes associated with lignin biosynthesis in radish (Raphanus sativus L.) by de novo transcriptome sequencing.Molecular genetics and genomics : MGG · 2017Article
- Comparative transcriptomics uncovers alternative splicing and molecular marker development in radish (Raphanus sativus L.).BMC genomics · 2017Article
- Integration of omics approaches to understand oil/protein content during seed development in oilseed crops.Plant cell reports · 2017Review
- A 2-Oxoglutarate-Dependent Dioxygenase Mediates the Biosynthesis of Glucoraphasatin in Radish.Plant physiology · 2017Article
- RNA-Seq of Guar (Frontiers in plant science · 2017Article
- De Novo RNA Sequencing and Transcriptome Analysis of Monascus purpureus and Analysis of Key Genes Involved in Monacolin K Biosynthesis.PloS one · 2017Article
- Exploring drought stress-regulated genes in senna (Cassia angustifolia Vahl.): a transcriptomic approach.Functional & integrative genomics · 2017Article
- Review
- Identification of Flowering-Related Genes Responsible for Differences in Bolting Time between Two Radish Inbred Lines.Frontiers in plant science · 2016Article
- Transcriptome Analysis of Stem and Globally Comparison with Other Tissues inFrontiers in plant science · 2016Article
- De novo Taproot Transcriptome Sequencing and Analysis of Major Genes Involved in Sucrose Metabolism in Radish (Raphanus sativus L.).Frontiers in plant science · 2016Article
- Commentary: Comparative Transcriptome Analysis of Raphanus sativus Tissues.Frontiers in plant science · 2015Article
Corrections and comments
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Authors and funding
7 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Raphanus sativus is an important Brassicaceae plant and also an edible vegetable with great economic value. However, currently there is not enough transcriptome information of R. sativus tissues, which impedes further functional genomics research on R. sativus. In this study, RNA-seq technology was employed to characterize the transcriptome of leaf tissues. Approximately 70 million clean pair-end reads were obtained and used for de novo assembly by Trinity program, which generated 68,086 unigenes with an average length of 576 bp. All the unigenes were annotated against GO and KEGG databases. In the meanwhile, we merged leaf sequencing data with existing root sequencing data and obtained better de novo assembly of R. sativus using Oases program. Accordingly, potential simple sequence repeats (SSRs), transcription factors (TFs) and enzyme codes were identified in R. sativus. Additionally, we detected a total of 3563 significantly differentially expressed genes (DEGs, P = 0.05) and tissue-specific biological processes between leaf and root tissues. Furthermore, a TFs-based regulation network was constructed using Cytoscape software. Taken together, these results not only provide a comprehensive genomic resource of R. sativus but also shed light on functional genomic and proteomic research on R. sativus in the future.
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