Genome-wide identification, characterization and evolutionary analysis of long intergenic noncoding RNAs in cucumber.
Genome-wide identification, characterization and evolutionary analysis of long intergenic noncoding RNAs in cucumber.
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黄瓜长基因间非编码 RNA 的全基因组鉴定、表征和进化分析
DOI：
10.1371/journal.pone.0121800
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发表时间：
2015
期刊：
影响因子：
3.7
通讯作者：
Li G
中科院分区：
文献类型：
--
作者：
Hao Z;Fan C;Cheng T;Su Y;Wei Q;Li G
长基因间非编码RNA(LincRNAs)是一类长度至少为200个核苷酸的基因间转录本，缺乏编码潜能。新出现的证据表明，动物的lincRNAs参与了许多基本的生物学过程。然而，对lincRNAs的系统鉴定只在少数植物中进行过。我们选择黄瓜作为模式植物来分析lincRNAs，是因为它是研究性别分化和果实发育的重要模式植物，并且拥有丰富的基因组和转录组数据。生物信息学管道应用于多种类型的基因表达数据，鉴定和鉴定了3,274个lincRNAs。接下来，还探索了17个miRNAs靶向的10个lincRNAs。基于lincRNAs和mRNAs的共表达分析，共注释了94个lincRNAs，它们可能参与了对刺激的反应、多生物过程、生殖、生殖过程和生长。最后，对lincRNAs进化的研究表明，大多数lincRNAs处于净化选择状态，而16个lincRNAs处于自然选择状态。我们的结果为进一步验证黄瓜lincRNAs及其功能提供了丰富的资源。MiRNAs靶向的lincRNAs的鉴定为研究lincRNAs在基因表达调控中的作用提供了新的线索。最后，对lincRNAs的评价表明，一些lincRNAs处于积极和平衡的选择之下。
Long intergenic noncoding RNAs (lincRNAs) are intergenic transcripts with a length of at least 200 nt that lack coding potential. Emerging evidence suggests that lincRNAs from animals participate in many fundamental biological processes. However, the systemic identification of lincRNAs has been undertaken in only a few plants. We chose to use cucumber (Cucumis sativus) as a model to analyze lincRNAs due to its importance as a model plant for studying sex differentiation and fruit development and the rich genomic and transcriptome data available. The application of a bioinformatics pipeline to multiple types of gene expression data resulted in the identification and characterization of 3,274 lincRNAs. Next, 10 lincRNAs targeted by 17 miRNAs were also explored. Based on co-expression analysis between lincRNAs and mRNAs, 94 lincRNAs were annotated, which may be involved in response to stimuli, multi-organism processes, reproduction, reproductive processes, and growth. Finally, examination of the evolution of lincRNAs showed that most lincRNAs are under purifying selection, while 16 lincRNAs are under natural selection. Our results provide a rich resource for further validation of cucumber lincRNAs and their function. The identification of lincRNAs targeted by miRNAs offers new clues for investigations into the role of lincRNAs in regulating gene expression. Finally, evaluation of the lincRNAs suggested that some lincRNAs are under positive and balancing selection.
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影响因子：
56.9
作者：
Carninci, P;Kasukawa, T;Hayashizaki, Y
通讯作者：
Hayashizaki, Y
影响因子：
64.5
作者：
Huarte M;Guttman M;Feldser D;Garber M;Koziol MJ;Kenzelmann-Broz D;Khalil AM;Zuk O;Amit I;Rabani M;Attardi LD;Regev A;Lander ES;Jacks T;Rinn JL
通讯作者：
Rinn JL
WGCNA：用于加权相关网络分析的 R 包。
影响因子：
3
作者：
Langfelder P;Horvath S
通讯作者：
Horvath S
影响因子：
12.3
作者：
Li L;Eichten SR;Shimizu R;Petsch K;Yeh CT;Wu W;Chettoor AM;Givan SA;Cole RA;Fowler JE;Evans MM;Scanlon MJ;Yu J;Schnable PS;Timmermans MC;Springer NM;Muehlbauer GJ
通讯作者：
Muehlbauer GJ
DOI：
10.1126/science.1240925
发表时间：
2013-08-16
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Carpenter S;Aiello D;Atianand MK;Ricci EP;Gandhi P;Hall LL;Byron M;Monks B;Henry-Bezy M;Lawrence JB;O'Neill LA;Moore MJ;Caffrey DR;Fitzgerald KA
通讯作者：
Fitzgerald KA