Supplemental Material for Minio et al., 2018

<p>File S1: Iso-Seq reconstructed transcriptome (FASTA format)</p><p>File S2: databases used for InterProScan search of functional domains</p><p>File S3: parameters used for MAKER-P annotation</p><p>File S4: parameters used in PASA for annotation polishing </p><p>File S5: association of Iso-Seq reconstructed transcripts with gene loci in the Cabernet Sauvignon genome</p><p>File S6: biological process GO tree of the Iso-Seq reconstructed transcriptome</p><p>File S7: cellular component GO tree of the Iso-Seq reconstructed transcriptome</p><p>File S8: molecular function GO tree of the Iso-Seq reconstructed transcriptome </p><p>File S9: biological process GO tree of the protein-coding genes predicted in the Cabernet Sauvignon genome</p><p>File S10: cellular component GO tree of the protein-coding genes predicted in the Cabernet Sauvignon genome</p><p>File S11: molecular function GO tree of the protein-coding genes predicted on the Cabernet Sauvignon genome</p><p>File S12: distribution and classification of alternative splicing events annotated on the Cabernet Sauvignon genome</p><p>Figure S1: Soluble solids content of Cabernet Sauvignon berries at four different growth stages. For each biological replicate, soluble solid measurement (°Brix) was performed using two technical replicates.</p><p>Figure S2: Evaluation of the impact of the expression level on Iso-Seq sequence accuracy</p><p>Figure S3: Cabernet Sauvignon genome annotation pipeline. The diagram represents the workflow used to produce the gene annotation of Cabernet Sauvignon genome.</p><p>Table S1: Weather conditions during the sampling of Cabernet Sauvignon berries.</p><p>Table S2: Soluble solids content (°Brix) of Cabernet Sauvignon berries at the four developmental stages.</p><p>Table S3: Sequences of the oligo dT barcodes used for the construction of the Iso-Seq SMRTBell libraries.</p><p>Table S4: Iso-Seq read sequencing and standard PacBio clustering pipeline statistics.</p><p>Table S5: Short-read sequencing, filtering and mapping results.</p><p>Table S6: Repetitive content identification statistics.</p><p>Table S7: Experimental evidences used for MAKER annotation.</p><p>Table S8: Gene and transcript annotation statistics.</p><p>Table S9: RFAM categories identified in Cabernet Sauvignon genome.</p><p>Table S10: Groups of ISNT isoforms and annotated gene loci based on sequence clustering approach.</p><p>Table S11: Functional annotation of the reconstructed ISNT.</p><p>Table S12: Functional annotation of the cultivar-specific ISNT isoforms.</p><p>Table S13: Functional annotation of the Cabernet Sauvignon genome.</p><p>Table S14: Functional annotation of the Cabernet Sauvignon private gene loci.</p><p>Table S15: RNA-seq analysis of the 16 berry samples using the Iso-Seq non-redundant transcriptome (ISNT) as reference. </p><p>Table S16: RNA-seq analysis of the 16 berry samples using the Cabernet Sauvignon genome as reference. </p><p>Table S17: Expression and differential expression analysis of the clustered ISNT transcripts. </p>