Genome-Wide Analysis Identified a Set of Conserved lncRNAs Associated with Domestication-Related Traits in Rice.
Genome-Wide Analysis Identified a Set of Conserved lncRNAs Associated with Domestication-Related Traits in Rice.
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全基因组分析鉴定了一组与水稻驯化相关性状相关的保守 lncRNA
DOI：
10.3390/ijms22094742
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发表时间：
2021-04-29
影响因子：
5.6
通讯作者：
Yu Y
中科院分区：
文献类型：
--
作者：
He H;Zhou YF;Yang YW;Zhang Z;Lei MQ;Feng YZ;Zhang YC;Chen YQ;Lian JP;Yu Y
作物驯化产生了许多理想的农艺性状，是植物进化的典型模式系统。大量基因组证据表明，在作物驯化过程中，诸如微小RNA（miRNA）和phasiRNA等非编码RNA以及蛋白质编码基因都受到了选择。然而，仅有有限的数据显示植物长链非编码RNA（lncRNA）也参与了这一生物学过程。在本研究中，我们对栽培稻粳稻（Oryza sativa ssp. japonica）、籼稻（O. sativa ssp. indica）及其野生祖先普通野生稻（O. rufipogon）进行了链特异性RNA测序。我们共鉴定出8528个lncRNA，其中普通野生稻中有4072个lncRNA，粳稻中有2091个lncRNA，籼稻中有2365个lncRNA。研究发现，与栽培稻的lncRNA相比，野生稻中表达的lncRNA长度更短，外显子数量更少。我们还在野生稻和栽培稻中鉴定出一些保守的lncRNA。功能研究表明，其中一些保守的lncRNA与水稻驯化相关性状有关。我们的研究结果揭示了水稻驯化过程中lncRNA的特征和保守性，将进一步推动水稻lncRNA的功能研究。
Crop domestication, which gives rise to a number of desirable agronomic traits, represents a typical model system of plant evolution. Numerous genomic evidence has proven that noncoding RNAs such as microRNAs and phasiRNAs, as well as protein-coding genes, are selected during crop domestication. However, limited data shows plant long noncoding RNAs (lncRNAs) are also involved in this biological process. In this study, we performed strand-specific RNA sequencing of cultivated rice Oryza sativa ssp. japonica and O. sativa ssp. indica, and their wild progenitor O. rufipogon. We identified a total of 8528 lncRNAs, including 4072 lncRNAs in O. rufipogon, 2091 lncRNAs in japonica rice, and 2365 lncRNAs in indica rice. The lncRNAs expressed in wild rice were revealed to be shorter in length and had fewer exon numbers when compared with lncRNAs from cultivated rice. We also identified a number of conserved lncRNAs in the wild and cultivated rice. The functional study demonstrated that several of these conserved lncRNAs are associated with domestication-related traits in rice. Our findings revealed the feature and conservation of lncRNAs during rice domestication and will further promote functional studies of lncRNAs in rice.
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影响因子：
3.7
作者：
Chen Z;Li F;Yang S;Dong Y;Yuan Q;Wang F;Li W;Jiang Y;Jia S;Pei X
通讯作者：
Pei X
影响因子：
10.7
作者：
Choi JY;Platts AE;Fuller DQ;Hsing YI;Wing RA;Purugganan MD
通讯作者：
Purugganan MD
影响因子：
4.2
作者：
Sweeney M;McCouch S
通讯作者：
McCouch S
影响因子：
11.4
作者：
Gauley A;Boden SA
通讯作者：
Boden SA
影响因子：
7.2
作者：
Jeong, DH;An, S;An, G
通讯作者：
An, G