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.
Highlights
Oryza longistaminata, an AA genome type (2 n = 24), originates from Africa and is closely related to Asian cultivated rice (O. sativa L.)
Sequencing and assembly of 454 pyrosequencing expressed sequence tags (ESTs) In order to obtain transcripts of genes that might be required for growth under nutrient stress, O. longistaminata plants were clonally propagated and were adapted to low-nitrogen conditions in unfertilized soil for several months
In this study, we present a large-scale EST dataset comprising 71,367 unique EST sequences derived from wild rice O. longistaminata by massively parallel pyrosequencing
Summary
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). Available urea fertilizer is the most widely used resource to meet a rice crop’s nitrogen requirement, of which one third is lost through emission of greenhouse gasses and leaching, causing adverse environmental impacts [1,2,3]. To make better use of this potential, more genomic information is required, but there are only few batches of mRNAs or full-length cDNAs (FLcDNAs) of O. longistaminata in public databases, and no genome sequence is available
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