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.
- 相关文献
作者其他论文 更多>>
-
Cloning and functional analysis of 1-deoxy-D-xylulose-5-phosphate synthase (DXS) in Santalum album L
作者:Chen, Xiaohong;Zhang, Yueya;Niu, Meiyun;Xiong, Yuping;Zhang, Xinhua;Li, Yuan;Ma, Guohua;Chen, Xiaohong;Zhang, Yueya;Niu, Meiyun;Yan, Haifeng;da Silva, Jaime A. Teixeira
关键词:Chlorophylls and carotenoids; Ethylene; Jasmonate; MEP pathway; SaDXS1A; 1B; Sandalwood; Sesquiterpenes
-
Construction of EMS-Induced Peanut Mutant Libraries and Identification of Pod-Related Traits Mutant Lines
作者:Chen, Hao;Xu, Rilong;Chen, Xiangyu;Zhong, Haifeng;Zhang, Yumei;Lan, Xinlong;Zhang, Hong;Chen, Yuhua;Hu, Runfang;Lin, Guoqiang;Tang, Zhaoxiu;Xiong, Faqian
关键词:Peanut; EMS-induced; mutant line; pod-related traits; re-sequencing; pod constriction
-
Genome-wide identification of papain-like cysteine protease family genes in cultivated peanut (Arachis hypogaea L.) and functional characterization of AhRD21B in response to chilling stress
作者:Zhang, Chong;Chen, Yuting;Wang, Lihui;Liu, Lu;Zhong, Xin;Chu, Panpan;Gao, Meijia;Chen, Hua;Cai, Tiecheng;Raza, Ali;Zhuang, Weijian;Zhang, Chong;Chen, Yuting;Wang, Lihui;Liu, Lu;Zhong, Xin;Chu, Panpan;Gao, Meijia;Chen, Hua;Cai, Tiecheng;Raza, Ali;Zhuang, Weijian;Xiong, Faqian;Zhang, Chong;Zhang, Xiurong;Liu, Fengzhen;Pan, Rong-long;Varshney, Rajeev K.
关键词:Arachis hypogaea; PLCPs; Gene expression; AhRD21B; Cold stress
-
Genome-wide characterization and expression analysis of alpha-amylase and beta-amylase genes underlying drought tolerance in cassava
作者:Yang, Taiyi;Li, Liangwu;Huang, Yuanhang;Wei, Maogui;Li, Hengrui;Wei, Wanling;Xiong, Faqian;Wei, Maogui;Wei, Maogui
关键词:Cassava; Amylase; Abiotic stress; Bio-informatics; Gene expression
-
Genome, transcriptome, and metabolome analyses provide new insights into the resource development in an edible fungus Dictyophora indusiata
作者:Duan, Mingzheng;Li, Yijie;Li, Xiang;Li, Changning;Wu, Jianming;Wang, Zeping;Duan, Mingzheng;Wang, Lingqiang;Zhao, Falin;Long, Shengfeng;Wu, Xiaojian;Zhao, Chenggang;Yan, Yong;Chen, Zhendong;Feng, Bin;Qin, Sunqian
关键词:widely-targeted metabolome; food chemistry; edible fungi; tryptophan; UPLC-ESI-MS; MS
-
Genome-Wide Association Study Unravels Quantitative Trait Loci and Genes Associated with Yield-Related Traits in Sugarcane
作者:Zhang, Baoqing;Huang, Yuxin;Zhou, Zhongfeng;Zhou, Shan;Duan, Weixing;Yang, Cuifang;Gao, Yijing;Li, Yangrui;Zhang, Gemin;Huang, Dongliang;Zhang, Lijun;Li, Sicheng;Chen, Meiyan;Yang, Xiping
关键词:sugarcane; quantitativetrait loci (QTL); genome-wideassociation study (GWAS); candidate genes; yield
-
Genome-Wide Identification of the PP2C Gene Family and Analyses with Their Expression Profiling in Response to Cold Stress in Wild Sugarcane
作者:Huang, Xing;Zhang, Ronghua;Zhang, Baoqing;Song, Xiupeng;Liu, Junxian;Lu, Manman;Qin, Zhenqiang;Li, Dewei;Li, Song;Li, Yangrui;Liang, Yongsheng
关键词:wild sugarcane; type 2C protein phosphatase (PP2C); phylogenetic analysis; gene expression profiling; cold stress