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Twenty-one-nucleotide microRNAs (miRNAs) and 24-nucleotide Pol IV-dependent small interfering RNAs (p4-siRNAs) are the most abundant types of small RNAs in angiosperms. Some miRNAs are well conserved among different plant lineages, whereas others are less conserved, and it is not clear whether less-conserved miRNAs have the same functionality as the well(More)
Endogenous 24 nt short interfering RNAs (siRNAs), derived mostly from intergenic and repetitive genomic regions, constitute a major class of endogenous small RNAs in flowering plants. Accumulation of Arabidopsis thaliana 24 nt siRNAs requires the Dicer family member DCL3, and clear homologs of DCL3 exist in both flowering and non-flowering plants. However,(More)
microRNA156 (miR156) affects developmental timing in flowering plants. miR156 and its target relationships with members of the SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) gene family appear universally conserved in land plants, but the specific functions of miR156 outside of flowering plants are unknown. We find that miR156 promotes a developmental change(More)
High-throughput sequencing of small RNAs (sRNA-seq) is a popular method used to discover and annotate microRNAs (miRNAs), endogenous short interfering RNAs (siRNAs), and Piwi-associated RNAs (piRNAs). One of the key steps in sRNA-seq data analysis is alignment to a reference genome. sRNA-seq libraries often have a high proportion of reads that align to(More)
Rye (Secale cereale) is an important diploid (2n = 14, RR) crop species of the Triticeae and a better understanding of its organellar genome variation can aid in its improvement. Previous genetic analyses of rye focused on the nuclear genome. In the present study, the objective was to investigate the organellar genome diversity and relationships of 96(More)
Many plant small RNAs are sequence-specific negative regulators of target mRNAs and/or chromatin. In angiosperms, the two most abundant endogenous small RNA populations are usually 21-nucleotide microRNAs (miRNAs) and 24-nucleotide heterochromatic short interfering RNAs (siRNAs). Heterochromatic siRNAs are derived from repetitive regions and reinforce DNA(More)
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(More)
Zinc deficiency is a common problem leading to severe decreases in grain yield and has detrimental effects on nutritional quality in cereals. Wild emmer wheat, Triticum turgidum ssp. dicoccoides, exhibits a potential genetic resource for wheat improvement due to its compatibility with modern wheat. In this study, Zn deficiency response of wild progenitors(More)
Zhaorong Ma,a,b Ceyda Coruh,b,c and Michael J. Axtella,b,c,1 a Integrative Biosciences PhD Program in Bioinformatics and Genomics, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania 16802 b Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802 c Plant Biology PhD Program,(More)
microRNA156 (miR156) affects developmental timing in flowering plants. miR156 and its target relationships with members of the SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) gene family appear universally conserved in land plants, but the specific functions of miR156 outside of flowering plants are unknown. We find that miR156 promotes a developmental change(More)