Files in this data supplement:
- Supporting Information: Figures S1-S5, Tables S1-S9, and Files S1-S12 (PDF, 1 MB)
- Figure S1: Flowchart for GCclassif. (PDF, 350 KB)
- Figure S2: The genome sorted by descending scaffold size and placed in 100 bins. (PDF, 624 KB)
- Figure S3: Multiple Sequence Alignment between genes predicted to be within a gene family where the units are measured in base pairs. (PDF, 398 KB)
- Figure S4: Tandem repeat content of the genomic sequence in bin 1 of the genome. (PDF, 348 KB)
- Figure S5: Intronic repeats. (PDF, 402 KB)
- Table S1: Orthologous proteins from the PLAZA project aligned to the Pinus taeda versions 1.01 genome. (PDF, 324 KB)
- Table S2: Summary of MAKER Gene Annotations. (PDF, 314 KB)
- Table S3: Gain/Loss Protein Matrix Table (PDF, 325 KB)
- Table S4: Summary of tandem repeat content in Pinus taeda. (PDF, 431 KB)
- Table S5: A comparison of the most common tandem period in Picea abies, Picea glauca and Pinus taeda. (PDF, 428 KB)
- Table S6: Summary of hits to the PlantSat database. (PDF, 317 KB)
- Table S7: Repeat summary. (PDF, 339 KB)
- Table S8: High Copy Full-Length Elements. (PDF, 335 KB)
- Table S9: High Coverage Elements. (PDF, 335 KB)
- File S1: Methodology of the loblolly transcriptome (PDF, 325 KB)
- File S2: Accession numbers and additional details for alignment data sets (.xls, 3.2 MB)
- File S3: An explanation of PIER and GCclassif (PDF, 325 KB)
- File S4: Annotations for MAKER-derived gene models (.xlsx, 11 MB)
- File S5: Transcript notations including introns > 20Kbp (.xlsx, 203 KB)
- File S6: Gene Families Greater than or equal to 2 (.xlsx, 1.1 MB)
- File S7: Genes with Annotations (.xlsx, 13.7 MB)
- File S8: Conifer-Specific families (.xlsx, 114 KB)
- File S9: Multiple Sequence Alignments related to Figure S2 (PDF, 325 KB)
- File S10: Overview of tandem content in Arabidopsis thaliana, Vitis vinifera, Selaginella moellendorffii, Cucumis sativus, Populus trichocarpa, Picea glauca, Picea abies and Amborella trichopoda (.xlsx, 17 KB)
- File S11: Tri/tetra nucleotide motifs and frequency (.xlsx, 48 KB)
- File S12: Full Repeat Summary for Similarity Search Applied to Intronic Sequence (.xlsx, 30 KB)