Global characterization of the root transcriptome of a wild species of rice, Oryza longistaminata, by deep sequencing.
Global characterization of the root transcriptome of a wild species of rice, Oryza longistaminata, by deep sequencing.
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DOI：
10.1186/1471-2164-11-705
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发表时间：
2010-12-15
期刊：
影响因子：
4.4
通讯作者：
Reinhold-Hurek B
中科院分区：
文献类型：
--
作者：
Yang H;Hu L;Hurek T;Reinhold-Hurek B
长粒野生稻是一种AA基因组类型(2n=24)，原产于非洲，与亚洲栽培稻有较近的亲缘关系。它包含许多有价值的性状，包括对生物和非生物胁迫的耐受性，具有重要农艺性状的QTL和高效利用氮素的能力(NUE)。然而，目前只有有限的基因组或转录组数据可用。在这项研究中，我们首次提出了利用454焦磷酸测序法对长穗野生稻根转录组进行全面的表征。使用适应低N条件的长穗野生稻归一化cDNA文库进行的一次测序产生了337,830个读数，这些读数组装成41,189个重叠群和30,178个单态。通过与蛋白质数据库的相似性搜索，推测的功能被分配给超过34,510个单位。与栽培稻的EST进行比较，发现在不同的植物中都有表达，但有16.7%的长秆野生稻EST没有在栽培稻中表达。此外，15.7%的序列与已知序列没有显著的相似性。RT-PCR和Southern印迹分析证实，筛选出的新转录本在长穗野生稻中得到了表达。我们的结果表明，使用来自454生命科学/罗氏的基因组测序仪FLX进行一次运行，就可以产生足够的基因组信息，以便对野生稻物种(O.long gistainata)中的大量转录本进行充分的从头组装。所生成的序列数据是公开可用的，并将有助于在长秆野生稻和水稻功能基因组研究中发现基因。大量丰富的新EST表明，与普通野生稻相比，长穗野生稻具有不同的代谢活性。
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. 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. 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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影响因子：
5.1
作者：
Lian, XM;Wang, SP;Zhang, QF
通讯作者：
Zhang, QF
DOI：
10.1093/dnares/dsn018
发表时间：
2008-10
期刊：
DNA research : an international journal for rapid publication of reports on genes and genomes
影响因子：
--
作者：
Lu T;Yu S;Fan D;Mu J;Shangguan Y;Wang Z;Minobe Y;Lin Z;Han B
通讯作者：
Han B
影响因子：
64.8
作者：
Matsumoto, T;Wu, JZ;Sugiura, M
通讯作者：
Sugiura, M
影响因子：
56.9
作者：
Tanksley, SD;McCouch, SR
通讯作者：
McCouch, SR
影响因子：
2.3
作者：
Sacks, EJ;Roxas, JP;Cruz, MTS
通讯作者：
Cruz, MTS