Supplemental Material for Minio et al., 2018

File S1: Iso-Seq reconstructed transcriptome (FASTA format)

File S2: databases used for InterProScan search of functional domains

File S3: parameters used for MAKER-P annotation

File S4: parameters used in PASA for annotation polishing

File S5: association of Iso-Seq reconstructed transcripts with gene loci in the Cabernet Sauvignon genome

File S6: biological process GO tree of the Iso-Seq reconstructed transcriptome

File S7: cellular component GO tree of the Iso-Seq reconstructed transcriptome

File S8: molecular function GO tree of the Iso-Seq reconstructed transcriptome

File S9: biological process GO tree of the protein-coding genes predicted in the Cabernet Sauvignon genome

File S10: cellular component GO tree of the protein-coding genes predicted in the Cabernet Sauvignon genome

File S11: molecular function GO tree of the protein-coding genes predicted on the Cabernet Sauvignon genome

File S12: distribution and classification of alternative splicing events annotated on the Cabernet Sauvignon genome

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.

Figure S2: Evaluation of the impact of the expression level on Iso-Seq sequence accuracy

Figure S3: Cabernet Sauvignon genome annotation pipeline. The diagram represents the workflow used to produce the gene annotation of Cabernet Sauvignon genome.

Table S1: Weather conditions during the sampling of Cabernet Sauvignon berries.

Table S2: Soluble solids content (°Brix) of Cabernet Sauvignon berries at the four developmental stages.

Table S3: Sequences of the oligo dT barcodes used for the construction of the Iso-Seq SMRTBell libraries.

Table S4: Iso-Seq read sequencing and standard PacBio clustering pipeline statistics.

Table S5: Short-read sequencing, filtering and mapping results.

Table S6: Repetitive content identification statistics.

Table S7: Experimental evidences used for MAKER annotation.

Table S8: Gene and transcript annotation statistics.

Table S9: RFAM categories identified in Cabernet Sauvignon genome.

Table S10: Groups of ISNT isoforms and annotated gene loci based on sequence clustering approach.

Table S11: Functional annotation of the reconstructed ISNT.

Table S12: Functional annotation of the cultivar-specific ISNT isoforms.

Table S13: Functional annotation of the Cabernet Sauvignon genome.

Table S14: Functional annotation of the Cabernet Sauvignon private gene loci.

Table S15: RNA-seq analysis of the 16 berry samples using the Iso-Seq non-redundant transcriptome (ISNT) as reference.

Table S16: RNA-seq analysis of the 16 berry samples using the Cabernet Sauvignon genome as reference.

Table S17: Expression and differential expression analysis of the clustered ISNT transcripts.