title: Seeing the forest for the trees: annotating small RNA producing genes in plants.
abstract: A key goal in genomics is the complete annotation of the expressed regions of the genome. In plants, substantial portions of the genome make regulatory small RNAs produced by Dicer-Like (DCL) proteins and utilized by Argonaute (AGO) proteins. These include miRNAs and various types of endogenous siRNAs. Small RNA-seq, enabled by cheap and fast DNA sequencing, has produced an enormous volume of data on plant miRNA and siRNA expression in recent years. In this review, we discuss recent progress in using small RNA-seq data to produce stable and reliable annotations of miRNA and siRNA genes in plants. In addition, we highlight key goals for the future of small RNA gene annotation in plants.
authors.affiliation: Department of Biology, Penn State University, University Park, PA 16802, USA; Plant Biology Intercollegiate Ph.D. Program, Penn State University, University Park, PA 16802, USA; Huck Institutes of the Life Sciences, Penn State University, University Park, PA 16802, USA.
authors.forename: Ceyda
authors.initials: C
authors.lastname: Coruh
authors.affiliation: Department of Biology, Penn State University, University Park, PA 16802, USA; Plant Biology Intercollegiate Ph.D. Program, Penn State University, University Park, PA 16802, USA; Huck Institutes of the Life Sciences, Penn State University, University Park, PA 16802, USA.
authors.forename: Saima
authors.initials: S
authors.lastname: Shahid
authors.affiliation: Department of Biology, Penn State University, University Park, PA 16802, USA; Plant Biology Intercollegiate Ph.D. Program, Penn State University, University Park, PA 16802, USA; Huck Institutes of the Life Sciences, Penn State University, University Park, PA 16802, USA. Electronic address: mja18@psu.edu.
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Axtell
mesh_terms: D017343:Genes, Plant; D006570:Heterochromatin / Q000378:metabolism; D035683:MicroRNAs / Q000235:genetics*; D058977:Molecular Sequence Annotation; D010944:Plants / Q000235:genetics*; D018749:RNA, Plant / Q000235:genetics*
chemical_list: D006570:Heterochromatin; D035683:MicroRNAs; D018749:RNA, Plant