ArticleBMC genomics2010
Global characterization of the root transcriptome of a wild species of rice, Oryza longistaminata, by deep sequencing.
Article in BMC genomics, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- Microbiome eco-evolution of cultivated and wild rice species across the genus Oryza and its importance in supporting rice growth.Microbiome · 2026Article
- Strategies and Structure Feature of the Aboveground and Belowground Microbial Community Respond to Drought in Wild Rice (Oryza longistaminata).Rice (New York, N.Y.) · 2021Article
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- Four resistance alleles derived fromBreeding science · 2019Article
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- Identification of QTLs for yield-related traits in RILs derived from the cross between pLIA-1 carryingBreeding science · 2016Article
- Genomics of crop wild relatives: expanding the gene pool for crop improvement.Plant biotechnology journal · 2016Review
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- De Novo Transcriptome Sequencing of Oryza officinalis Wall ex Watt to Identify Disease-Resistance Genes.International journal of molecular sciences · 2015Article
- Transcriptomic Analysis and the Expression of Disease-Resistant Genes in Oryza meyeriana under Native Condition.PloS one · 2015Article
- Transcriptome and proteome profiling of adventitious root development in hybrid larch (Larix kaempferi × Larix olgensis).BMC plant biology · 2014Article
- A systems-wide comparison of red rice (Oryza longistaminata) tissues identifies rhizome specific genes and proteins that are targets for cultivated rice improvement.BMC plant biology · 2014Article
- Transcriptional profiling of nitrogen fixation and the role of NifA in the diazotrophic endophyte Azoarcus sp. strain BH72.PloS one · 2014Article
- Conservation and utilization of African Oryza genetic resources.Rice (New York, N.Y.) · 2013Article
- Article
- Analysis of the leaf transcriptome of Musa acuminata during interaction with Mycosphaerella musicola: gene assembly, annotation and marker development.BMC genomics · 2013Article
- Article
- Evaluating characteristics of de novo assembly software on 454 transcriptome data: a simulation approach.PloS one · 2012Article
- Global transcriptome profiling of the pine shoot beetle, Tomicus yunnanensis (Coleoptera: Scolytinae).PloS one · 2012Article
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4 authors.
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No grant is acknowledged in the PubMed record.
Abstract
backgroundOryza longistaminata, an AA genome type (2 n = 24), originates from Africa and is closely related to Asian cultivated rice (O. sativa L.). It contains various valuable traits with respect to tolerance to biotic and abiotic stress, QTLs with agronomically important traits and high ability to use nitrogen efficiently (NUE). However, only limited genomic or transcriptomic data of O. longistaminata are currently available.
resultsIn this study we present the first comprehensive characterization of the O. longistaminata root transcriptome using 454 pyrosequencing. One sequencing run using a normalized cDNA library from O. longistaminata roots adapted to low N conditions generated 337,830 reads, which assembled into 41,189 contigs and 30,178 singletons. By similarity search against protein databases, putative functions were assigned to over 34,510 uni-ESTs. Comparison with ESTs derived from cultivated rice collections revealed expressed genes across different plant species, however 16.7% of the O. longistaminata ESTs had not been detected as expressed in O. sativa. Additionally, 15.7% had no significant similarity to known sequences. RT-PCR and Southern blot analyses confirmed the expression of selected novel transcripts in O. longistaminata.
conclusionOur results show that one run using a Genome Sequencer FLX from 454 Life Science/Roche generates sufficient genomic information for adequate de novo assembly of a large number of transcripts in a wild rice species, O. longistaminata. The generated sequence data are publicly available and will facilitate gene discovery in O. longistaminata and rice functional genomic studies. The large number of abundant of novel ESTs suggests different metabolic activity in O. longistaminata roots in comparison to O. sativa roots.
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