ArticlePloS one2015
De novo Transcriptome Assembly of Common Wild Rice (Oryza rufipogon Griff.) and Discovery of Drought-Response Genes in Root Tissue Based on Transcriptomic Data.
Article in PloS one, 2015. 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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17 citing papers in PubMed, 30 citations in OpenAlex.
- Comparative Cytological and Gene Expression Analysis Reveals That a Common Wild Rice Inbred Line Showed Stronger Drought Tolerance Compared with the Cultivar Rice.International journal of molecular sciences · 2024Article
- Systems biology for crop improvement.The plant genome · 2021Review
- Physiological and Multi-Omics Approaches for Explaining Drought Stress Tolerance and Supporting Sustainable Production of Rice.Frontiers in plant science · 2021Review
- Transcriptomic analysis of Eruca vesicaria subs. sativa lines with contrasting tolerance to polyethylene glycol-simulated drought stress.BMC plant biology · 2019Article
- RNA-Seq analysis of soft rush (Juncus effusus): transcriptome sequencing, de novo assembly, annotation, and polymorphism identification.BMC genomics · 2019Article
- Development of introgression lines of AA genomeBreeding science · 2019Article
- Leaf Transcriptome Assembly ofGenes · 2019Article
- Enriched networks 'nucleoside/nucleotide and ribonucleoside/ribonucleotide metabolic processes' and 'response to stimulus' potentially conferred to drought adaptation of the epiphytic orchidPhysiology and molecular biology of plants : an international journal of functional plant biology · 2019Article
- Isolation and Characterization of a Green-Tissue Promoter from Common Wild Rice (International journal of molecular sciences · 2018Article
- Article
- Effects of drought stress on global gene expression profile in leaf and root samples of Dongxiang wild rice (Bioscience reports · 2017Article
- Selection and Validation of Appropriate Reference Genes for qRT-PCR Analysis inFrontiers in plant science · 2017Article
- De novo assembly, functional annotation, and analysis of the giant reed (Biotechnology for biofuels · 2017Article
- A walk on the wild side: Oryza species as source for rice abiotic stress tolerance.Genetics and molecular biology · 2017Article
- Identification of microRNAs in Response to Drought in Common Wild Rice (Oryza rufipogon Griff.) Shoots and Roots.PloS one · 2017Article
- Article
- Genetic determination of the enhanced drought resistance of rice maintainer HuHan2B by pedigree breeding.Scientific reports · 2016Article
Corrections and comments
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Authors and funding
9 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe perennial O. rufipogon (common wild rice), which is considered to be the ancestor of Asian cultivated rice species, contains many useful genetic resources, including drought resistance genes. However, few studies have identified the drought resistance and tissue-specific genes in common wild rice.
resultsIn this study, transcriptome sequencing libraries were constructed, including drought-treated roots (DR) and control leaves (CL) and roots (CR). Using Illumina sequencing technology, we generated 16.75 million bases of high-quality sequence data for common wild rice and conducted de novo assembly and annotation of genes without prior genome information. These reads were assembled into 119,332 unigenes with an average length of 715 bp. A total of 88,813 distinct sequences (74.42% of unigenes) significantly matched known genes in the NCBI NT database. Differentially expressed gene (DEG) analysis showed that 3617 genes were up-regulated and 4171 genes were down-regulated in the CR library compared with the CL library. Among the DEGs, 535 genes were expressed in roots but not in shoots. A similar comparison between the DR and CR libraries showed that 1393 genes were up-regulated and 315 genes were down-regulated in the DR library compared with the CR library. Finally, 37 genes that were specifically expressed in roots were screened after comparing the DEGs identified in the above-described analyses.
conclusionThis study provides a transcriptome sequence resource for common wild rice plants and establishes a digital gene expression profile of wild rice plants under drought conditions using the assembled transcriptome data as a reference. Several tissue-specific and drought-stress-related candidate genes were identified, representing a fully characterized transcriptome and providing a valuable resource for genetic and genomic studies in plants.
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