DOI: 10.6084/m9.figshare.16305312
title: Supplementary Tables (1-9 and 11-23)

description: Supplementary tables (1-9 & 11-23) for <i>Communications Biology</i> manuscript entitled: The genome of a dipterocarp <i>Shorea leprosula</i> highlights the ecological relevance of drought in aseasonal tropical rainforests.Supplementary Table 1. Features of the Illumina libraries and read mapping to the genome assembly.Supplementary Table 2. RNA-Seq data of multiple organs of <i>Shorea leprosula</i> sequenced on an Illumina instrument used for genome quality assessment, gene prediction and gene annotation.Supplementary Table 3. Repeat and TE content of the <i>Shorea leprosula</i> genome, determined with RepeatMasker using RepeatModeler library.Supplementary Table 4. Summary of the predicted <i>S. leprosula</i> genes.Supplementary Table 5. Criteria for determining the reliability of gene models.Supplementary Table 6. Details of the <i>S. leprosula</i> individuals sequenced on an Illumina instrument in a 2 x 101 bp module used for whole-genome resequencing study.Supplementary Table 7. Details of the other dipterocarp species sequenced on an Illumina instrument in a 2 x 101 bp module used for whole-genome resequencing and the mapping ratio.Supplementary Table 8. Nucleotide diversity (p), Watterson's theta (<i>q</i><sub>W</sub>) and Tajima's D of the conserved genes.Supplementary Table 9. The order and the directions of the <i>S. leprosula</i> scaffolds used for the dotplot.Supplementary Table 11. RNA-Seq data for ten other dipterocarp species.Supplementary Table 12. List of the <i>Shorea leprosula</i> gene IDs, the posterior median age estimates of WGD, and their 95% high posterior densities of each family under the 2 different settings.Supplementary Table 13. Calibration settings for phylogenetic dating.Supplementary Table 14. The gene ontology (GO) enrichment test reveals that a large number of drought related genes retained their paralogous pairs after the duplication event.Supplementary Table 15. <i>Shorea leprosula</i> duplicated pairs conserved in all four Dipterocarpaceae (<i>S. leprosula</i>, <i>S. platycarpa</i>, <i>Dryobalanops aromatica</i>, and <i>Neobalanocarpus heimii</i>). Each row contains the <i>S. leprosula</i> WGD-derived paralogs.Supplementary Table 16. The gene ontology (GO) enrichment test using the conserved gene set among the resequenced <i>S. leprosula</i>, <i>S. platycarpa</i>, <i>Dryobalanops aromatica</i> and <i>N. heimii</i>.Supplementary Table 17. The gene ontology (GO) enrichment test using the tandemly duplicated gene set in <i>S. leprosula</i>.Supplementary Table 18. RNA-Seq data for <i>S. leprosula</i> drought experiment. Three leaf samples were collected for each treatment (before and after "no-irrigation" stress) and sequenced on an Illumina instrument in a 2 x 125 bp module.Supplementary Table 19. List of differentially expressed genes (up-regulated). Expression values of each replicates in control and drought condition (columns F to Q).Supplementary Table 20. List of differentially expressed genes (down-regulated). Expression values of each replicates in control and drought condition (columns F to Q).Supplementary Table 21. Up-regulated GO terms involved in drought experiment conducted on <i>S. leprosula</i> seedlings.Supplementary Table 22. Down-regulated GO terms involved in drought experiment conducted on <i>S. leprosula</i> seedlings.Supplementary Table 23. Comparisons between the tandemly duplicated genes and the differentially expressed genes under the drought condition.<br>