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On-line Access: 2021-05-07

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 ORCID:

Jianhong XU

https://orcid.org/0000-0002-5620-0410

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Journal of Zhejiang University SCIENCE B 2021 Vol.22 No.5 P.366-382

http://doi.org/10.1631/jzus.B2000519


Genome-wide analysis of microRNA156 and its targets, the genes encoding SQUAMOSA promoter-binding protein-like (SPL) transcription factors, in the grass family Poaceae


Author(s):  Erkui YUE, Hua TAO, Jianhong XU

Affiliation(s):  Institute of Crop Science, Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou 310058, China; more

Corresponding email(s):   jhxu@zju.edu.cn

Key Words:  MicroRNA156 (miR156), SQUAMOSA promoter-binding protein-like (SPL) gene, DNA methylation, Gene expression, Grass genome


Erkui YUE, Hua TAO, Jianhong XU. Genome-wide analysis of microRNA156 and its targets, the genes encoding SQUAMOSA promoter-binding protein-like (SPL) transcription factors, in the grass family Poaceae[J]. Journal of Zhejiang University Science B, 2021, 22(5): 366-382.

@article{title="Genome-wide analysis of microRNA156 and its targets, the genes encoding SQUAMOSA promoter-binding protein-like (SPL) transcription factors, in the grass family Poaceae",
author="Erkui YUE, Hua TAO, Jianhong XU",
journal="Journal of Zhejiang University Science B",
volume="22",
number="5",
pages="366-382",
year="2021",
publisher="Zhejiang University Press & Springer",
doi="10.1631/jzus.B2000519"
}

%0 Journal Article
%T Genome-wide analysis of microRNA156 and its targets, the genes encoding SQUAMOSA promoter-binding protein-like (SPL) transcription factors, in the grass family Poaceae
%A Erkui YUE
%A Hua TAO
%A Jianhong XU
%J Journal of Zhejiang University SCIENCE B
%V 22
%N 5
%P 366-382
%@ 1673-1581
%D 2021
%I Zhejiang University Press & Springer
%DOI 10.1631/jzus.B2000519

TY - JOUR
T1 - Genome-wide analysis of microRNA156 and its targets, the genes encoding SQUAMOSA promoter-binding protein-like (SPL) transcription factors, in the grass family Poaceae
A1 - Erkui YUE
A1 - Hua TAO
A1 - Jianhong XU
J0 - Journal of Zhejiang University Science B
VL - 22
IS - 5
SP - 366
EP - 382
%@ 1673-1581
Y1 - 2021
PB - Zhejiang University Press & Springer
ER -
DOI - 10.1631/jzus.B2000519


Abstract: 
MicroRNAs (miRNAs) are endogenous small non-coding RNAs that play an important role in post-transcriptional gene regulation in plants and animals by targeting messenger RNAs (mRNAs) for cleavage or repressing translation of specific mRNAs. The first miRNA identified in plants, miRNA156 (miR156), targets the SQUAMOSA promoter-binding protein-like (SPL) transcription factors, which play critical roles in plant phase transition, flower and plant architecture, and fruit development. We identified multiple copies of MIR156 and SPL in the rice, Brachypodium, sorghum, maize, and foxtail millet genomes. Sequence and chromosomal synteny analysis showed that both MIR156s and SPLs are conserved across species in the grass family. Analysis of expression data of the SPLs in eleven juvenile and adult rice tissues revealed that four non-miR156-targeted genes were highly expressed and three miR156-targeted genes were only slightly expressed in all tissues/developmental stages. The remaining SPLs were highly expressed in the juvenile stage, but their expression was lower in the adult stage. It has been proposed that under strong selective pressure, non-miR156-targeted mRNA may be able to re-structure to form a miRNA-responsive element. In our analysis, some non-miR156-targeted SPLs (SPL5/8/10) had gene structure and gene expression patterns similar to those of miR156-targeted genes, suggesting that they could diversify into miR156-targeted genes. DNA methylation profiles of SPLs and MIR156s in different rice tissues showed diverse methylation patterns, and hypomethylation of non-CG sites was observed in rice endosperm. Our findings suggested that MIR156s and SPLs had different origination and evolutionary mechanisms: the SPLs appear to have resulted from vertical evolution, whereas MIR156s appear to have resulted from strong evolutionary selection on mature sequences.

禾本科microRNA156及其靶基因SPL转录因子的全基因组分析

目的:为了探究microRNA156(miR156)及其靶基因SPL两者在禾本科基因组中拷贝数以及它们在植物基因组中的进化选择关系。
创新点:在5个已完成全基因组测序的禾本科作物中鉴定miR156及其靶基因SPL的拷贝数,利用比较基因组学和分子进化方法并结合DNA甲基化组数据阐明miR156及其靶基因SPL的起源和进化机制。
方法:基于全基因测序序列鉴定SPL基因和MIR156基因及其成熟序列在基因组中的拷贝数,利用MEGA X软件构建起进化树;下载水稻不同组织中SPLMIR156基因的转录组和DNA甲基化组数据,并根据软件与程序检测其表达量与DNA甲基化水平。
结论:MIR156SPL具有不同的起源和进化机制,SPL似乎是由垂直进化产生的,而MIR156似乎是对成熟序列的强烈进化选择产生的。

关键词:MicroRNA156;SPL基因;DNA甲基化;基因表达;禾本科基因组

Darkslateblue:Affiliate; Royal Blue:Author; Turquoise:Article

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