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MicroSugar: A database of comprehensive miRNA target prediction framework for sugarcane (Saccharum officinarum L.)

文献类型： 外文期刊

作者： Qiu, Lihang 1 ; Luo, Hanmin 1 ; Zhou, Huiwen 1 ; Yan, Haifeng 1 ; Fan, Yegeng 1 ; Zhou, Zhongfeng 1 ; Chen, Rongfa 1 ; Liu, Junxian 1 ; Luo, Ting 1 ; Deng, Yuchi 1 ; Xiong, Faqian 1 ; Wu, Jianming 1 ;

作者机构： 1.Guangxi Acad Agr Sci, Sugarcane Res Inst, East Daxue Rd 172, Nanning 530007, Guangxi, Peoples R China

2.Guangxi Key Lab Sugarcane Genet Improvement, East Daxue Rd 172, Nanning 530007, Guangxi, Peoples R China

3.Minist Agr, Key Lab Sugarcane Biotechnol & Genet Improvement G, East Daxue Rd 172, Nanning 530007, Guangxi, Peoples R China

关键词： Database; Expression; microRNAs; Sequences; Sugarcane

期刊名称：GENOMICS （ 影响因子：4.31； 五年影响因子：4.38 ）

ISSN： 0888-7543

年卷期： 2022 年 114 卷 4 期

页码：

收录情况： SCI

摘要： microRNA (miRNA) is a group of small non-coding RNA that plays important role in post-transcription of gene expression. With the studies about miRNA increase in sugarcane, the researchers lack an exhaustive resource to achieve the data. To fill this gap, we developed MicroSugar, a database that supported mRNA and miRNA annotation for sugarcane (http://suc.gene-db.com). MicroSugar is an integrated resource developed for 194,528 genes including 80,746 unigenes from long reads of Pacbio platform and 468 miRNAs from 72 samples. Inter -node elongation (jointing) is the key biological characteristic for the growth of sugarcane tillers into sugarcane stems. The present study combined the sequencing data from the different stages in internode elongation of stem and tiller. In total, the 14,300 3 ' untranslated region (UTR) sequences were extracted from the gene sequences and 3019 mRNAs as target of 327 miRNA were identified by miRanda algorithm and Spearman's Rho of expression levels. To determine the gene functions regulated by these miRNAs, the gene ontology enrichment analysis was performed and it confirmed that the over-represented Gene Ontology (GO) terms were associated with organism formation indicating the growth controlling function by miRNAs in sugarcane. Moreover, MicroSugar is a comprehensive and integrated database with a user-friendly responsive template. By browsing, searching and downloading of the nucleotide sequences, expression and miRNA targets, the user can retrieve information promptly. The database provides a valuable resource to facilitate the understanding of miRNA in sugarcane development and growth which will contribute to the study of sugarcane and other plants.

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