Supplementary File S2. Table of the Fragaria vesca genes, identified by MapMan analysis, corresponding to the Fragaria x ananassa ethylene-related genes ...
Supplementary Information
Gene expression atlas of fruit ripening and transcriptome assembly from RNA-seq data in octoploid strawberry (Fragaria × ananassa)
José F. Sánchez-Sevilla, José G. Vallarino, Sonia Osorio, Aureliano Bombarely, David Posé, Catharina Merchante, Miguel A. Botella, Iraida Amaya, Victoriano Valpuesta
Supplementary File S1. Expression values, as FPKM, corresponding to the 28,574 XLOCs as described in Figure 2. Supplementary File S2. Table of the Fragaria vesca genes, identified by MapMan analysis, corresponding to the Fragaria x ananassa ethylene-related genes differentially expressed in achene in the transition from green (G) to white (W), as shown in Figure 4. Supplementary File S3. Table of the Fragaria vesca genes, identified by MapMan analysis, corresponding to the Fragaria x ananassa ethylene-related genes differentially expressed in achene in the transition from white (W) to turning (T), as shown in Figure 4. Supplementary File S4. Table of the Fragaria vesca genes, identified by MapMan analysis, corresponding to the Fragaria x ananassa ethylene-related genes differentially expressed in achene in the transition from turning (T) to red (R), as shown in Figure 4. Supplementary File S5. Table of the Fragaria vesca genes, identified by MapMan analysis, corresponding to the Fragaria x ananassa ethylene-related genes differentially expressed in receptacle in the transition from green (G) to white (W), as shown in Figure 4. Supplementary File S6. Table of the Fragaria vesca genes, identified by MapMan analysis, corresponding to the Fragaria x ananassa ethylene-related genes differentially expressed in receptacle in the transition from white (W) to turning (T), as shown in Figure 4. Supplementary File S7. Table of the Fragaria vesca genes, identified by MapMan analysis, corresponding to the Fragaria x ananassa ethylene-related genes differentially expressed in receptacle in the transition from turning (T) to red (R), as shown in Figure 4. Supplementary Files S8. Trinity isoforms for the 10 RNAseq samples are available d at www.ebi.ac.uk/ena, ref. PRJEB12420.RNASEQ, as: Transcriptome shotgun assembly (TSA) – UNANOTATED :HX2000058865
Transcriptome shotgun assembly (TSA) – UNANOTATED :HX2000058865 Transcriptome shotgun assembly (TSA) – UNANOTATED :HX2000058864 Transcriptome shotgun assembly (TSA) – UNANOTATED :HX2000058863 Transcriptome shotgun assembly (TSA) – UNANOTATED :HX2000058862 Transcriptome shotgun assembly (TSA) – UNANOTATED :HX2000058861 Transcriptome shotgun assembly (TSA) – UNANOTATED :HX2000058860 Transcriptome shotgun assembly (TSA) – UNANOTATED :HX2000058859 Transcriptome shotgun assembly (TSA) – UNANOTATED :HX2000058858 Transcriptome shotgun assembly (TSA) – UNANOTATED :HX2000058856 Transcriptome shotgun assembly (TSA) – UNANOTATED :HX2000058854 Supplementary File S9. MIRA contigs, are available at www.ebi.ac.uk/ena, ref. PRJEB12420.RNASEQ, as Transcriptome shotgun assembly (TSA) – UNANOTATED : HX2000059175
Supplementary figure S1: HeatMap of the Metabolism Overview corresponding to the DEGs (File S1) in the successive transitions from green (G), white (W), turning (T) and red (R), in the achene (A) and the receptacle (R), obtained from the MapMan analysis. Abbreviations of the pathways/cycles are CHO: carbohydrate: OPP: oxidative pentose phosphate; TCA: tricarboxylic acid. The color key indicates the log2 fold change between the transitions.
Green Achene - White Achene
White Achene - Turning Achene
Turning Achene - Red Achene
Green Receptacle - White Receptacle
White Receptacle - Turning Receptacle
Turning Receptacle - Red Receptacle
Supplementary figure S2: Dendrogram of the alignment of the mapped Fragaria vesca ERF genes with putative orthologues in Arabidopsis. Seaview v8_Incl_21047_Sec_ERF_anotados_REF_letras_en_At-Dnapars Wed Oct 19 16:54:23 2016
Dnapars, 3 best trees (100% consensus), 8913 steps, 414 sites (411 informative) gene13118_AtERF#063 gene11882_AtERF#037b gene32028_AtERF#064 gene25758_AtERF#037a gene21167_AtERF#103a gene16619_AtERF#099b gene32084_AtERF#061 gene11636_AtERF#004 gene15702_AtERF#001 gene21166_AtERF#080b gene10845_AtERF#103b gene21165_AtERF#099a gene03751_AtERF#071b gene25185_FaERF#131 gene28574_AtERF#075a gene04911_AtERF#099d gene16350_AtERF#056 gene22114_AtERF#060 gene32380_AtERF#026 gene05448_AtERF#075b gene07057_AtERF#071a gene08077_AtERF#091 gene04810_AtERF#041 gene11086_AtERF#072 gene13327_AtERF#025 gene15036_AtERF#003 gene11145_AtERF#012 gene09137_AtERF#006b gene03450_AtERF#104 gene10841_AtERF#100 gene21403_AtERF#076 gene12919_AtERF#017 gene23873_AtERF#006a gene27062_AtERF#022 gene11440_AtERF#099c gene17698_AtERF#053 gene29738_AtERF#080a gene00975_AtERF#078 gene17570_FaERF#130 gene21091_AtERF#110 gene07304_AtERF#113 gene27604_AtERF#108 gene08876_AtERF#039 gene21047_AtERF#045
Supplementary table S1: Summary of the mapping of the RNA seq reads on the Fragaria vesca genome (Fvb_genome).
Supplementary table S2: Summary of the mapping back of the RNA seq reads on the contigs assembled with the MIRA program, from the Trinity isoforms.
Supplementary table S3: List of the primer and conditions used for quantitative PCR assays.
