Additional file 1 of Long read sequencing to reveal the full complexity of a plant transcriptome by targeting both standard and long workflows
Creators: name: Al-Dossary, Othman
name: Furtado, Agnelo
name: KharabianMasouleh, Ardashir
name: Alsubaie, Bader
name: Al-Mssallem, Ibrahim
name: Henry, Robert J.
Publisher: name: figshare
Year: 2024
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 1: Figure S1. Distribution of unique transcript isoforms from the long workflow across genes with CDS length between one to three thousand base pairs. Common transcript isoforms derived from SW and LW mapped to each of the CDS sequences are shown as blue bars and had a percentage of 36.3%, the unique transcripts isoforms derived from the SW are shown as black bars and had a percentage of 26.6%, while the unique transcripts isoforms derived from the LW and shown as orange bars had a percentage of 37.1%. Across all the isoforms, the average ratio of unique isoforms generated by LW / total isoforms by the SW generated isoforms was 0.65. Transcript isoforms shown here are non-redundant CD-Hit CCS sequences at 99% similarity. Mapping was undertaken using the “enable long-read spliced alignment” option in Minimap2 and executed via the CLC Genomics Workbench. Figure S2. Distribution of unique transcript isoforms from the long workflow across genes with CDS length between three to five thousand base pairs. Common transcript isoforms derived from SW and LW mapped to each of the CDS sequences are shown as blue bars and had a percentage of 26.9%, the unique transcripts isoforms derived from the SW are shown as black bars and had a percentage of 25.2%, while the unique transcripts isoforms derived from the LW and shown as orange bars had a percentage of 47.9%. Across all the isoforms, the average ratio of unique isoforms generated by LW / total isoforms by the SW generated isoforms was 1.0. Transcript isoforms shown here are non-redundant Cd-Hit CCS sequences at 99% similarity. Mapping was undertaken using the “enable long-read spliced alignment” option in Minimap2 and executed via the CLC Genomics Workbench. Figure S3. BUSCO v.5.1.2 analysis of four different datasets (long, standard, merged, and non-redundant Cd-Hit) for jojoba (Simmondsia chinensis) transcriptome Iso-Seq reference using the viridiplantae_odb10 dataset. The x-axis describes the percentage of complete and single copy, complete and duplicated, fragmented and missing BUSCO and the y-axis show. Figure S4. Number of transcript isoforms aligned to the InterProScan (IPS) families during the jojoba (Simmondsia chinensis) annotation. Figure S5. Gene Ontology (GO) classification of the jojoba (Simmondsia chinensis) Iso-Seq transcriptome reference (A) biological process, (B) molecular function, (C) cellular component. Figure S6. The top 11 KEGG pathways enrichment in the jojoba (Simmondsia chinensis) transcriptome Iso-Seq transcripts reference. Figure S7. Coding potential sequences for the non-redundant (Cd-Hit) jojoba (Simmondsia chinensis) transcriptome Iso-Seq reference including the four categories complete, 5’ potential, 3’ potential, and internal. Figure S8. Coding potential sequences for the novel isoforms in the jojoba (Simmondsia chinensis) transcriptome Iso-Seq reference including the four categories complete, 5’ potential, 3’ potential, and internal. Table S4. BUSCO analysis of four different datasets (long, standard, merged, and non-redundant Cd-Hit) for jojoba (Simmondsia chinensis) transcriptome Iso-Seq reference using the viridiplantae_odb10 dataset. Table S5. Default settings of consensus circular sequence (CCS) analysis used for jojoba (Simmondsia chinensis) Iso-Seq sequencing process. Table S6. Default settings of isoform sequencing (Iso-Seq) analysis used for jojoba (Simmondsia chinensis) water-stress RNA transcript isoforms. Table S7. Sequence coverage percentage for isoforms aligned to four jojoba (Simmondsia chinensis) apetala genes sequence.