Identification and profiling of narrow-leafed lupin (Lupinus angustifolius) microRNAs during seed development
dc.contributor.author | DeBoer, Kathleen | |
dc.contributor.author | Melser, Su | |
dc.contributor.author | Sperschneider, Jana | |
dc.contributor.author | Kamphuis, Lars G. | |
dc.contributor.author | Garg, Gagan | |
dc.contributor.author | Gao, Ling-Ling | |
dc.contributor.author | Frick, Karen | |
dc.contributor.author | Singh, Karam B. | |
dc.date.accessioned | 2019-02-27T00:43:12Z | |
dc.date.available | 2019-02-27T00:43:12Z | |
dc.date.issued | 2019-02-14 | |
dc.date.updated | 2019-02-17T09:06:07Z | |
dc.description.abstract | Background: 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. | en_AU |
dc.description.sponsorship | 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. | en_AU |
dc.format | 16 pages | en_AU |
dc.format.mimetype | application/pdf | en_AU |
dc.identifier.uri | http://hdl.handle.net/1885/156518 | |
dc.language.iso | en_AU | en_AU |
dc.publisher | BioMed Central | en_AU |
dc.rights | The Author(s) | en_AU |
dc.rights.license | This 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. | en_AU |
dc.rights.uri | (http://creativecommons.org/licenses/by/4.0/) | en_AU |
dc.source | BMC Genomics | en_AU |
dc.subject | Gene silencing | en_AU |
dc.subject | Legume | en_AU |
dc.subject | Lupin | en_AU |
dc.subject | microRNAs | en_AU |
dc.subject | Seed development | en_AU |
dc.subject | Small RNAs | en_AU |
dc.title | Identification and profiling of narrow-leafed lupin (Lupinus angustifolius) microRNAs during seed development | en_AU |
dc.type | Journal article | en_AU |
dcterms.accessRights | Open Access | en_AU |
dcterms.dateAccepted | 2019-02-07 | |
local.bibliographicCitation.issue | 1 | en_AU |
local.bibliographicCitation.startpage | 135 | en_AU |
local.contributor.affiliation | DeBoer, Kathleen, The UWA Institute of Agriculture, University of Western Australia | en_AU |
local.contributor.affiliation | Melser, Su, CSIRO Agriculture and Food | en_AU |
local.contributor.affiliation | Melser, Su, Present address: INSERM U1215, Neurocentre Magendie | en_AU |
local.contributor.affiliation | Sperschneider, Jana, Centre for Genomics, Metabolomics and Bioinformatics (CGMB), The Australian National University | en_AU |
local.contributor.affiliation | Kamphuis, Lars G., The UWA Institute of Agriculture, University of Western Australia | en_AU |
local.contributor.affiliation | Kamphuis, Lars G., CSIRO Agriculture and Food | en_AU |
local.contributor.affiliation | Kamphuis, Lars G., Curtin University, Centre for Crop and Disease Management, Department of Environment and Agriculture | en_AU |
local.contributor.affiliation | Garg, Gagan, CSIRO Agriculture and Food | en_AU |
local.contributor.affiliation | Gao, Ling-Ling, CSIRO Agriculture and Food | en_AU |
local.contributor.affiliation | Frick, Karen, The UWA Institute of Agriculture, University of Western Australia | en_AU |
local.contributor.affiliation | Frick, Karen, CSIRO Agriculture and Food | en_AU |
local.contributor.affiliation | Frick, Karen, The School of Plant Biology, University of Western Australia | en_AU |
local.contributor.affiliation | Singh, Karam B., The UWA Institute of Agriculture, University of Western Australia | en_AU |
local.contributor.affiliation | Singh, Karam B., CSIRO Agriculture and Food | en_AU |
local.contributor.affiliation | Singh, Karam B., Curtin University, Centre for Crop and Disease Management, Department of Environment and Agriculture | en_AU |
local.contributor.authoruid | T1698 | en_AU |
local.description.notes | Imported from Springer Nature | en_AU |
local.identifier.citationvolume | 20 | en_AU |
local.identifier.doi | 10.1186/s12864-019-5521-8 | en_AU |
local.identifier.essn | 1471-2164 | en_AU |
local.identifier.uidSubmittedBy | u4579722 | en_AU |
local.publisher.url | https://www.biomedcentral.com/ | en_AU |
local.type.status | Published Version | en_AU |
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