title: Potential functions of microRNAs in starch metabolism and development revealed by miRNA transcriptome profiling of cassava cultivars and their wild progenitor.
abstract: 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.
  
  
  CONCLUSIONS
  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.
authors: The Institute of Tropical Bioscience and Biotechnology (ITBB), Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou, 571101, PR China. chenxin@itbb.org.cn.|Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Haikou, 571101, PR China. chenxin@itbb.org.cn.
authors: Xin
authors: X
authors: Chen
authors: Institute for Systems Biology, Jianghan University, Wuhan, 430056, China. jxia@wustl.edu.|Department of Computer Science and Engineering, Washington University in St. Louis, St. Louis, Missouri, MO, 63130, USA. jxia@wustl.edu.
authors: Jing
authors: J
authors: Xia
authors: The Institute of Tropical Bioscience and Biotechnology (ITBB), Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou, 571101, PR China. xiazhiqiang@itbb.org.cn.|Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Haikou, 571101, PR China. xiazhiqiang@itbb.org.cn.
authors: Zhiqiang
authors: Z
authors: Xia
authors: The Institute of Tropical Bioscience and Biotechnology (ITBB), Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou, 571101, PR China. yuyehua001@126.com.|Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Haikou, 571101, PR China. yuyehua001@126.com.
authors: Hefang
authors: H
authors: Zhang
authors: The Institute of Tropical Bioscience and Biotechnology (ITBB), Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou, 571101, PR China. zengchangying@itbb.org.cn.|Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Haikou, 571101, PR China. zengchangying@itbb.org.cn.
authors: Changying
authors: C
authors: Zeng
authors: The Institute of Tropical Bioscience and Biotechnology (ITBB), Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou, 571101, PR China. lucheng@itbb.org.cn.|Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Haikou, 571101, PR China. lucheng@itbb.org.cn.
authors: Cheng
authors: C
authors: Lu
authors: Institute for Systems Biology, Jianghan University, Wuhan, 430056, China. weixiong.zhang@wustl.edu.|Department of Computer Science and Engineering, Washington University in St. Louis, St. Louis, Missouri, MO, 63130, USA. weixiong.zhang@wustl.edu.
authors: Weixiong
authors: W
authors: Zhang
authors: The Institute of Tropical Bioscience and Biotechnology (ITBB), Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou, 571101, PR China. wangwenquan@itbb.org.cn.|Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Haikou, 571101, PR China. wangwenquan@itbb.org.cn.
authors: Wenquan
authors: W
authors: Wang
mesh_terms: D020869:Gene Expression Profiling; D017343:Genes, Plant; D002365:Manihot / Q000235:genetics*; D035683:MicroRNAs / Q000235:genetics* / Q000378:metabolism / Q000502:physiology*; D018515:Plant Leaves / Q000378:metabolism; D018517:Plant Roots / Q000378:metabolism; D013213:Starch / Q000378:metabolism*; D059467:Transcriptome
chemical_list: D035683:MicroRNAs; D013213:Starch
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