title: Novel and Recently Evolved MicroRNA Clusters Regulate Expansive F-BOX Gene Networks through Phased Small Interfering RNAs in Wild Diploid Strawberry.
abstract: The wild strawberry (Fragaria vesca) has recently emerged as an excellent model for cultivated strawberry (Fragaria × ananassa) as well as other Rosaceae fruit crops due to its short seed-to-fruit cycle, diploidy, and sequenced genome. Deep sequencing and parallel analysis of RNA ends were used to identify F. vesca microRNAs (miRNAs) and their target genes, respectively. Thirty-eight novel and 31 known miRNAs were identified. Many known miRNAs targeted not only conserved mRNA targets but also developed new target genes in F. vesca. Significantly, two new clusters of miRNAs were found to collectively target 94 F-BOX (FBX) genes. One of the miRNAs in the new cluster is 22 nucleotides and triggers phased small interfering RNA production from six FBX genes, which amplifies the silencing to additional FBX genes. Comparative genomics revealed that the main novel miRNA cluster evolved from duplications of FBX genes. Finally, conserved trans-acting siRNA pathways were characterized and confirmed with distinct features. Our work identified novel miRNA-FBX networks in F. vesca and shed light on the evolution of miRNAs/phased small interfering RNA networks that regulate large gene families in higher plants.
authors.affiliation: United States Department of Agriculture-Agricultural Research Service-Appalachian Fruit Research Station, Kearneysville, West Virginia 25430 (R.X., Zo.L.);Delaware Biotechnology Institute and Department of Plant and Soil Sciences, University of Delaware, Newark, Delaware 19711 (R.X., B.C.M.); andDepartment of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742 (S.Y., Zh.L.).
authors.forename: Rui
authors.identifier: http://orcid.org/0000-0003-2409-1181
authors.initials: R
authors.lastname: Xia
authors.affiliation: United States Department of Agriculture-Agricultural Research Service-Appalachian Fruit Research Station, Kearneysville, West Virginia 25430 (R.X., Zo.L.);Delaware Biotechnology Institute and Department of Plant and Soil Sciences, University of Delaware, Newark, Delaware 19711 (R.X., B.C.M.); andDepartment of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742 (S.Y., Zh.L.).
authors.forename: Songqing
authors.initials: S
authors.lastname: Ye
authors.affiliation: United States Department of Agriculture-Agricultural Research Service-Appalachian Fruit Research Station, Kearneysville, West Virginia 25430 (R.X., Zo.L.);Delaware Biotechnology Institute and Department of Plant and Soil Sciences, University of Delaware, Newark, Delaware 19711 (R.X., B.C.M.); andDepartment of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742 (S.Y., Zh.L.).
authors.forename: Zongrang
authors.identifier: http://orcid.org/0000-0002-8677-2743
authors.initials: Z
authors.lastname: Liu
authors.affiliation: United States Department of Agriculture-Agricultural Research Service-Appalachian Fruit Research Station, Kearneysville, West Virginia 25430 (R.X., Zo.L.);Delaware Biotechnology Institute and Department of Plant and Soil Sciences, University of Delaware, Newark, Delaware 19711 (R.X., B.C.M.); andDepartment of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742 (S.Y., Zh.L.).
authors.forename: Blake C
authors.identifier: http://orcid.org/0000-0003-3436-6097
authors.initials: BC
authors.lastname: Meyers
authors.affiliation: United States Department of Agriculture-Agricultural Research Service-Appalachian Fruit Research Station, Kearneysville, West Virginia 25430 (R.X., Zo.L.);Delaware Biotechnology Institute and Department of Plant and Soil Sciences, University of Delaware, Newark, Delaware 19711 (R.X., B.C.M.); andDepartment of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742 (S.Y., Zh.L.) zliu@umd.edu.
authors.forename: Zhongchi
authors.identifier: http://orcid.org/0000-0001-9969-9381
authors.initials: Z
authors.lastname: Liu
mesh_terms: D001483:Base Sequence; D017124:Conserved Sequence / Q000235:genetics; D004171:Diploidy; D019143:Evolution, Molecular; D035264:Flowers / Q000235:genetics; D031985:Fragaria / Q000235:genetics*; D005638:Fruit / Q000235:genetics; D020440:Gene Duplication; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D053263:Gene Regulatory Networks; D017343:Genes, Plant; D035683:MicroRNAs / Q000235:genetics* / Q000378:metabolism; D008957:Models, Genetic; D008969:Molecular Sequence Data; D059372:Nucleotide Motifs; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D034741:RNA, Small Interfering / Q000378:metabolism*
chemical_list: D035683:MicroRNAs; D012333:RNA, Messenger; D034741:RNA, Small Interfering