DeBoer, KathleenMelser, SuSperschneider, JanaKamphuis, Lars G.Garg, GaganGao, Ling-LingFrick, KarenSingh, Karam B.2019-02-272019-02-27http://hdl.handle.net/1885/156518Background: Whilst information regarding small RNAs within agricultural crops is increasing, the miRNA composition of the nutritionally valuable pulse narrow-leafed lupin (Lupinus angustifolius) remains unknown. Results: By conducting a genome- and transcriptome-wide survey we identified 7 Dicer-like and 16 Argonaute narrow-leafed lupin genes, which were highly homologous to their legume counterparts. We identified 43 conserved miRNAs belonging to 16 families, and 13 novel narrow-leafed lupin-specific miRNAs using high-throughput sequencing of small RNAs from foliar and root and five seed development stages. We observed up-regulation of members of the miRNA families miR167, miR399, miR156, miR319 and miR164 in narrow-leafed lupin seeds, and confirmed expression of miR156, miR166, miR164, miR1507 and miR396 using quantitative RT-PCR during five narrow-leafed lupin seed development stages. We identified potential targets for the conserved and novel miRNAs and were able to validate targets of miR399 and miR159 using 5′ RLM-RACE. The conserved miRNAs are predicted to predominately target transcription factors and 93% of the conserved miRNAs originate from intergenic regions. In contrast, only 43% of the novel miRNAs originate from intergenic regions and their predicted targets were more functionally diverse. Conclusion: This study provides important insights into the miRNA gene regulatory networks during narrow-leafed lupin seed development.Su Melser was the recipient of a CSIRO OCE Post-doctoral fellowship. Karen Frick was the recipient of a GRDC PhD scholarship (GRS10935). We thank CSIRO and UWA for financial support. We also acknowledge the use of the Illumina MiSeq purchased using the ARC LIEF grant LE110100188.16 pagesapplication/pdfen-AUThe Author(s)(http://creativecommons.org/licenses/by/4.0/)Gene silencingLegumeLupinmicroRNAsSeed developmentSmall RNAs2019-02-1410.1186/s12864-019-5521-82019-02-17This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.