Global characterization of the root transcriptome of a wild species of rice, Oryza longistaminata, by deep sequencing
Open accessAbstract
Background: Oryza 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. Results: In 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. Conclusion: Our 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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KNOXI genes have been previously shown to be involved in development of sweetpotato storage roots, regulating cytokinin levels in that organ.
“KNOXI genes have been previously shown to be involved in the development of sweetpotato SRs [17,36], regulating cytokinin levels in that organ.”
From Transcriptional profiling of sweetpotato (Ipomoea batatas) roots indicates down-regulation of lignin biosynthesis and up-regulation of starch biosynthesis at an early stage of storage root formation (2013) · cites this paper as [17]
The Methods (Plant materials; page not provided) describe Oryza longistaminata, and the Results and Discussion (Sequencing and assembly of 454 pyrosequencing ESTs; page not provided) describe its root transcript sequencing. Searches for KNOXI, sweetpotato storage roots, and cytokinin found no passage in our copy addressing the attributed claim. (LLM, conf=0.76)
Experimental — accuracy not yet measuredExpressions of ibkn1, ibkn2 and ibkn3 were faint or undetectable in fibrous, non-storage roots.
“Expressions of ibkn1, ibkn2 and ibkn3 were faint or undetectable in fibrous, non-storage roots [17].”
From Transcriptional profiling of sweetpotato (Ipomoea batatas) roots indicates down-regulation of lignin biosynthesis and up-regulation of starch biosynthesis at an early stage of storage root formation (2013) · cites this paper as [17]
The Results and Discussion section reports expression of selected transcripts in O. longistaminata roots, but does not identify ibkn1, ibkn2 or ibkn3 or compare storage and non-storage roots. Searches for those gene names and for fibrous-root expression found no passage addressing the claim; the available passages have no page numbers. (LLM, conf=0.76)
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- Authors
- Yang, H., Hu, L., Hurek, T., & Reinhold-Hurek, B.
- Affiliations
- University of Bremen (DE)
- Venue
- BMC Genomics
- Published
- 2010-12
- Volume
- 11
- Issue
- 1
- Pages
- 705-705
- ISSN
- 1471-2164 (ISSN-L)
- PMC
- PMC3016420
- OpenAlex
- W1984078008
- Cited by
- 42
- References
- 37
- Citations by year
- 2026: 1 · 2021: 9 · 2020: 1 · 2019: 2 · 2018: 2 · 2017: 1 · 2016: 3 · 2015: 4 · 2014: 4 · 2013: 4 · 2012: 9
- FWCI
- 1.95
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- BMC Genomics (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
- Funders
- Bundesministerium für Bildung und Forschung
- Ministry of Environment
- Ministry of Environment and Tourism Namibia
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Mapping and Diversity in Plants and Animals
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
- Keywords
- Oryza longistaminata, wild rice, root transcriptome, expressed sequence tags, de novo transcriptome assembly, nitrogen use efficiency, novel transcripts, gene discovery, functional genomics
- MeSH terms
- Chromosome Mapping, Molecular Sequence Data, Oryza, Species Specificity, Reproducibility of Results, Sequence Analysis, DNA, Gene Expression Regulation, Plant, Plant Roots, Genome, Plant, Expressed Sequence Tags, Gene Expression Profiling, High-Throughput Nucleotide Sequencing
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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