Transcriptome phase distribution analysis reveals diurnal regulated biological processes and key pathways in rice flag leaves and seedling leaves.
Transcriptome phase distribution analysis reveals diurnal regulated biological processes and key pathways in rice flag leaves and seedling leaves.
复制标题
转录组相位分布分析揭示了水稻旗叶和幼苗叶的昼夜调节生物过程和关键途径
DOI：
10.1371/journal.pone.0017613
复制
发表时间：
2011-03-02
期刊：
影响因子：
3.7
通讯作者：
Xue Y
中科院分区：
文献类型：
--
作者：
Xu W;Yang R;Li M;Xing Z;Yang W;Chen G;Guo H;Gong X;Du Z;Zhang Z;Hu X;Wang D;Qian Q;Wang T;Su Z;Xue Y
植物昼夜振荡是基于 24 小时周期的变化。不同物种的微阵列分析广泛揭示了昼夜基因与生物途径之间的相关性。大米（Oryza sativa）是世界上约一半人口的主要主食。水稻剑叶对于为籽粒灌浆提供光合产物至关重要。然而，目前对于水稻叶片的昼夜转录组还没有全面的认识。在本研究中，我们应用水稻芯片来监测水稻幼苗和旗叶中节律表达的基因。我们开发了一种新的计算分析方法，并在幼苗叶片中识别出 6,266 个（10.96%）昼夜探针组，在旗叶中识别出 13,773 个（24.08%）昼夜探针组。大约 65% 的转录因子被确定为旗叶首选。在幼苗叶中，相位分布的峰值是从上午2:00到凌晨4:00，而在旗叶中，相位分布的峰值是在晚上8:00到凌晨2:00。基因本体（GO）和顺式元素富集的昼相分布分析表明，一些重要的过程被光唤醒，如光合作用和非生物刺激，而一些与核和核糖体相关过程相关的基因主要在光到暗的转换时间内活跃。淀粉和蔗糖代谢途径基因也表现出昼相。我们在整个昼夜周期中对拟南芥和水稻叶片转录组进行了比较分析。总之，我们的分析方法对于相对公正地识别昼间转录本是可行的，可以有效地检测一些具有非正弦周期模式的特殊周期模式。与水稻旗叶相比，幼苗叶的基因转录水平相对局限于昼夜节律。我们对水稻幼苗和旗叶进行全面的微阵列分析，提供了水稻昼夜转录组的概述，并指出了水稻的一些昼夜调节生物过程和关键功能途径。
Plant diurnal oscillation is a 24-hour period based variation. The correlation between diurnal genes and biological pathways was widely revealed by microarray analysis in different species. Rice (Oryza sativa) is the major food staple for about half of the world's population. The rice flag leaf is essential in providing photosynthates to the grain filling. However, there is still no comprehensive view about the diurnal transcriptome for rice leaves. In this study, we applied rice microarray to monitor the rhythmically expressed genes in rice seedling and flag leaves. We developed a new computational analysis approach and identified 6,266 (10.96%) diurnal probe sets in seedling leaves, 13,773 (24.08%) diurnal probe sets in flag leaves. About 65% of overall transcription factors were identified as flag leaf preferred. In seedling leaves, the peak of phase distribution was from 2:00am to 4:00am, whereas in flag leaves, the peak was from 8:00pm to 2:00am. The diurnal phase distribution analysis of gene ontology (GO) and cis-element enrichment indicated that, some important processes were waken by the light, such as photosynthesis and abiotic stimulus, while some genes related to the nuclear and ribosome involved processes were active mostly during the switch time of light to dark. The starch and sucrose metabolism pathway genes also showed diurnal phase. We conducted comparison analysis between Arabidopsis and rice leaf transcriptome throughout the diurnal cycle. In summary, our analysis approach is feasible for relatively unbiased identification of diurnal transcripts, efficiently detecting some special periodic patterns with non-sinusoidal periodic patterns. Compared to the rice flag leaves, the gene transcription levels of seedling leaves were relatively limited to the diurnal rhythm. Our comprehensive microarray analysis of seedling and flag leaves of rice provided an overview of the rice diurnal transcriptome and indicated some diurnal regulated biological processes and key functional pathways in rice.
登录
查看更多内容
影响因子：
9.8
作者：
Michael, Todd P.;Breton, Ghislain;Hazen, Samuel P.;Priest, Henry;Mockler, Todd C.;Kay, Steve A.;Chory, Joanne
通讯作者：
Chory, Joanne
影响因子：
56.9
作者：
Harmer, SL;Hogenesch, LB;Kay, SA
通讯作者：
Kay, SA
影响因子：
11.6
作者：
Gibon, Y;Blaesing, OE;Stitt, M
通讯作者：
Stitt, M
影响因子：
4.3
作者：
Matt, P;Schurr, U;Stitt, M
通讯作者：
Stitt, M
影响因子：
7.2
作者：
Geigenberger, P;Stitt, M
通讯作者：
Stitt, M