Lara Brian1, Ben Warren1,2, Peter McAtee1, Jessica Rodrigues1, Niels Nieuwenhuizen1, Asher Pasha3, Karine M David2, Annette Richardson4, Nicholas J Provart3, Andrew C Allan1,2, Erika Varkonyi-Gasic1, Robert J Schaffer5,6. 1. The New Zealand Institute for Plant and Food Research Ltd (Plant & Food Research), Private Bag 92169, Auckland, 1146, New Zealand. 2. School of Biological Science, The University of Auckland, Private Bag 92019, Auckland, 1146, New Zealand. 3. Department of Cell & Systems Biology / Centre for the Analysis of Genome Evolution and Function, University of Toronto, 25 Willcocks St, Toronto, ON, M5S 3B2, Canada. 4. The New Zealand Institute for Plant and Food Research Ltd (Plant & Food Research), 121 Keri Downs Road, Kerikeri, 0294, New Zealand. 5. School of Biological Science, The University of Auckland, Private Bag 92019, Auckland, 1146, New Zealand. robert.schaffer@plantandfood.co.nz. 6. The New Zealand Institute for Plant and Food Research Ltd (Plant & Food Research), 55 Old Mill Road, Motueka, 7198, New Zealand. robert.schaffer@plantandfood.co.nz.
Abstract
BACKGROUND: Transcriptomic studies combined with a well annotated genome have laid the foundations for new understanding of molecular processes. Tools which visualise gene expression patterns have further added to these resources. The manual annotation of the Actinidia chinensis (kiwifruit) genome has resulted in a high quality set of 33,044 genes. Here we investigate gene expression patterns in diverse tissues, visualised in an Electronic Fluorescent Pictograph (eFP) browser, to study the relationship of transcription factor (TF) expression using network analysis. RESULTS: Sixty-one samples covering diverse tissues at different developmental time points were selected for RNA-seq analysis and an eFP browser was generated to visualise this dataset. 2839 TFs representing 57 different classes were identified and named. Network analysis of the TF expression patterns separated TFs into 14 different modules. Two modules consisting of 237 TFs were correlated with floral bud and flower development, a further two modules containing 160 TFs were associated with fruit development and maturation. A single module of 480 TFs was associated with ethylene-induced fruit ripening. Three "hub" genes correlated with flower and fruit development consisted of a HAF-like gene central to gynoecium development, an ERF and a DOF gene. Maturing and ripening hub genes included a KNOX gene that was associated with seed maturation, and a GRAS-like TF. CONCLUSIONS: This study provides an insight into the complexity of the transcriptional control of flower and fruit development, as well as providing a new resource to the plant community. The Actinidia eFP browser is provided in an accessible format that allows researchers to download and work internally.
BACKGROUND: Transcriptomic studies combined with a well annotated genome have laid the foundations for new understanding of molecular processes. Tools which visualise gene expression patterns have further added to these resources. The manual annotation of the Actinidia chinensis (kiwifruit) genome has resulted in a high quality set of 33,044 genes. Here we investigate gene expression patterns in diverse tissues, visualised in an Electronic Fluorescent Pictograph (eFP) browser, to study the relationship of transcription factor (TF) expression using network analysis. RESULTS: Sixty-one samples covering diverse tissues at different developmental time points were selected for RNA-seq analysis and an eFP browser was generated to visualise this dataset. 2839 TFs representing 57 different classes were identified and named. Network analysis of the TF expression patterns separated TFs into 14 different modules. Two modules consisting of 237 TFs were correlated with floral bud and flower development, a further two modules containing 160 TFs were associated with fruit development and maturation. A single module of 480 TFs was associated with ethylene-induced fruit ripening. Three "hub" genes correlated with flower and fruit development consisted of a HAF-like gene central to gynoecium development, an ERF and a DOF gene. Maturing and ripening hub genes included a KNOX gene that was associated with seed maturation, and a GRAS-like TF. CONCLUSIONS: This study provides an insight into the complexity of the transcriptional control of flower and fruit development, as well as providing a new resource to the plant community. The Actinidia eFP browser is provided in an accessible format that allows researchers to download and work internally.
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