Potential functions of microRNAs in starch metabolism and development revealed by miRNA transcriptome profiling of cassava cultivars and their wild progenitor
文献类型： 外文期刊
作者： Chen, Xin 1 ; Xia, Jing 3 ; Xia, Zhiqiang 1 ; Zhang, Hefang 1 ; Zeng, Changying 1 ; Lu, Cheng 1 ; Zhang, Weixiong 3 ; Wan 1 ;
作者机构： 1.CATAS, ITBB, Haikou 571101, Peoples R China
2.Minist Agr, Key Lab Biol & Genet Resources Trop Crops, Haikou 571101, Peoples R China
3.Jianghan Univ, Inst Syst Biol, Wuhan 430056, Peoples R China
4.Washington Univ, Dept Comp Sci & Engn, St Louis, MO 63130 USA
5.Washington Univ, Dept Comp Sci & Engn, St Lou
关键词： MicroRNA;Target Gene;Wild Progenitor;Cassava (Manihot esculenta Crantz)
期刊名称：BMC PLANT BIOLOGY （ 影响因子：4.215； 五年影响因子：4.96 ）
ISSN： 1471-2229
年卷期： 2015 年 15 卷
页码：
收录情况： SCI
摘要： Background: MicroRNAs (miRNAs) are small (approximately 21 nucleotide) non-coding RNAs that are key post-transcriptional gene regulators in eukaryotic organisms. More than 100 cassava miRNAs have been identified in a conservation analysis and a repertoire of cassava miRNAs have also been characterised by next-generation sequencing (NGS) in recent studies. Here, using NGS, we profiled small non-coding RNAs and mRNA genes in two cassava cultivars and their wild progenitor to identify and characterise miRNAs that are potentially involved in plant growth and starch biosynthesis. Results: Six small RNA and six mRNA libraries from leaves and roots of the two cultivars, KU50 and Arg7, and their wild progenitor, W14, were subjected to NGS. Analysis of the sequencing data revealed 29 conserved miRNA families and 33 new miRNA families. Together, these miRNAs potentially targeted a total of 360 putative target genes. Whereas 16 miRNA families were highly expressed in cultivar leaves, another 13 miRNA families were highly expressed in storage roots of cultivars. Co-expression analysis revealed that the expression level of some targets had negative relationship with their corresponding miRNAs in storage roots and leaves; these targets included MYB33, ARF10, GRF1, RD19, APL2, NF-YA3 and SPL2, which are known to be involved in plant development, starch biosynthesis and response to environmental stimuli. Conclusion: The identified miRNAs, target mRNAs and target gene ontology annotation all shed light on the possible functions of miRNAs in Manihot species. The differential expression of miRNAs between cultivars and their wild progenitor, together with our analysis of GO annotation and confirmation of miRNA: target pairs, might provide insight into know the differences between wild progenitor and cultivated cassava.
- 相关文献
作者其他论文 更多>>
-
MePHD1.2 affects the synthesis of cyanogenic glycosides by regulating of MeCYP79D2 in cassava
作者：Li, Mengtao;Li, Yajun;Mai, Weitao;Khan, Luqman;Wang, Wenquan;Liu, Jinping;Chen, Xin;Li, Mengtao;Li, Yajun;Mai, Weitao;Khan, Luqman;Wang, Wenquan;Liu, Jinping;Chen, Xin;Li, Mengtao;Zhao, Xiao;Li, Yajun;Li, Yuanchao;Mai, Weitao;Chen, Xin;Zhao, Xiao;Li, Yuanchao;Zhao, Xiaoye;Liang, Qibing;Yin, Qingchun;Li, Yajun;Chen, Xin
关键词：Cyanogenic glycosides; Cytochrome P450; Manihot esculenta; MePHD1.2
-
Identification of the cassava NADP-ME gene family and its response and regulation in photosynthesis
作者：Li, Haozheng;Xiao, Jin;Chen, Jiahui;Shen, Xu;Luo, Jia;Guo, Fengguang;Xu, Liangye;Guo, Xin;Wang, Shujuan;Wang, Wenquan;Wang, Shangfei;Wang, Haiyan
关键词：C-3-C-4 intermediate photosynthesis; NADP-ME; cassava; C-4 evolution; coexpression network
-
Water lily pond: a multiomics database for water lilies
作者：Zhao, Chengjun;Zhang, Ji;Chen, Yayu;Yang, Lishuang;Chen, Hongliang;Liang, Yufan;Wang, Wenquan;He, Shuang;Luo, Yunqing;Zhang, Junyu;Zhang, Hongbin;Yang, Shuting;Guo, Guilian;Dai, Wenbai;Yang, Zhijuan;Khan, Wasi Ullah;Chen, Fei;Zhao, Chengjun;Zhang, Ji;Chen, Yayu;Yang, Lishuang;Chen, Hongliang;Liang, Yufan;Wang, Wenquan;He, Shuang;Luo, Yunqing;Zhang, Junyu;Zhang, Hongbin;Yang, Shuting;Guo, Guilian;Dai, Wenbai;Khan, Wasi Ullah;Chen, Fei;Chen, Junhao;Zhou, Yuhan;Zhang, Liangsheng;Liu, Guanhua;Jiang, Yifan;Xu, Yingchun;Xue, Jia-yu;Zhu, Tianlong;Garcia-Caparros, Pedro;van de Peer, Yves;van de Peer, Yves;van de Peer, Yves;van de Peer, Yves;Chen, Chengjie
关键词：
-
Improving gene editing of CRISPR/Cas9 using the callus-specific promoter pYCE1 in cassava (Manihot esculenta Crantz)
作者：Li, Yuanchao;Li, Youzhi;Li, Yuanchao;Bao, Ruxue;Li, Mengtao;Yang, Haojie;Yao, Yuan;Chen, Xin;Bao, Ruxue;Li, Mengtao;Zeng, Changying;Yang, Haojie;Wang, Wenquan;Yao, Yuan;Chen, Xin;Yao, Yuan;Chen, Xin
关键词：cassava; callus; promoter; gene editing; target
-
Beyond nitrate transport: AtNRT2.4 responds to local and systemic nitrogen signaling in Arabidopsis
作者：Zhang, Huaifang;Li, Yanmei;Zhao, Jinling;Mai, Weitao;Khan, Luqman;Wang, Wenquan;Zeng, Changying;Chen, Xin;Zhang, Huaifang;Huang, Jinxia;Li, Yanmei;Zhao, Jinling;Mai, Weitao;Chen, Xin;Zhang, Meng
关键词：Nitrate deficiency; Local N-deficiency signals; Systemic nitrate signals; Root architecture; Anthocyanin accumulation
-
Advancements and strategies of genetic improvement in cassava (Manihot esculenta Crantz): from conventional to genomic approaches
作者：Xiao, Liang;Cheng, Dong;Yan, Huabing;Ou, Wenjun;Li, Kaimian;Chen, Xin;Rabbi, Ismail Yusuf;Wang, Wenquan
关键词：
-
Pan-genome and haplotype map of cassava cultivars and wild ancestors provide insights into its adaptive evolution and domestication
作者：Xia, Zhiqiang;Zhou, Xincheng;Jiang, Sirong;Chen, Fei;Zou, Meiling;Xu, Liangye;Guo, Xin;Wang, Shujuan;Li, Mengtao;Liu, Shisheng;Bao, Yuting;Zhang, Chenji;Xiao, Jianjia;Guo, Fengguang;Shen, Xu;Li, Haozheng;Zhang, Huaifang;He, Shuang;Wan, Yinglang;Chen, Yinhua;Huang, Dongyi;Li, Bin;Peng, Ming;Chen, Xin;Wang, Wenquan;Du, Zhenglin;Chen, Meili;Zhao, Wenming;Xiao, Jingfa;Du, Zhenglin;Chen, Meili;Zhao, Wenming;Xiao, Jingfa;Zhou, Xincheng;Wang, Haiyan;Lu, Cheng;Peng, Ming;Chen, Xin;Zhu, Tingting;Wang, Le;Luo, Ming-Cheng;Qiao, Fei;Li, Kaimian;Carvalho, Luiz;Lopez-Lavalle, Luis Augusto Becerra;Zhang, Xiaofei;Ceballos, Hernan;Wang, Zhenyu;Li, Yuanchao;Zhao, Long;Yan, Huabing;Qin, Xiaochun;Ma, Ling;Zhang, Weixiong;Moller, Birger Lindberg
关键词：genome; pan-genome; structural variations; selective sweeping; evolution and domestication; cassava
