The Draft Genome Sequence of Tabebuia impetiginosa, an Ecologically Keystone High Value Timber Species of the American Neotropics

Tabebuia impetiginosa (common name "Ipê") (Bignoniaceae) is a highly valued neotropical timber species regarded as the "new mahogany" for its dense, rot-resistant wood, exported largely to North America for residential decking. It is the second most expensive timber and the most logged species in Brazil, currently under significant illegal trading pressure. With a widespread disjunct distribution throughout the seasonally dry forest of South and Mesoamerica, it has served as a keystone species for ecological studies. With a two-fold objective of accelerating breeding endeavors and better powered population genomics investigations, we have generated a draft assembly of its 970 Mbp genome. Following processing, 281,671,476 high-quality reads, ~41Gb of data, were used for genome assembly. The MaSuRCA pipeline resulted in 647,390,007 bp assembled in 185,988 scaffolds with N50 of 18,883bp, covering ~67% of the genome. The longest scaffold was 261,687 bp while 64,303 scaffolds were >1Kb and 17,331 >10kb. RNA-Seq data were assembled combining reference guided and de novo approaches: 75,062,940 (96.5%) high-quality reads were successfully mapped onto the assembly and only 2,747,697 failed to be placed. Only 55,447 (<0.07%) of the RNA-Seq reads were mapped to different scaffolds in the draft indicating the high confidence of the assembled fraction of the genome and completeness of the gene content space. Integrative analysis of the gene content resulted in 26,124 sequences annotated as gene models, and 25,034 of them successfully aligned back on the draft genome (30% coverage and 95% identity), 24,884 sequences representing putative gene structures produced by hit against NCBI nr protein database with e-value < 1e-5. A preliminary and rather conservative SNP discovery job was carried out based on a pooled whole-genome shotgun sample of six unrelated trees. Filtering for depth of coverage 12-90X and ≥2 reads of the alternative allele a total of 46,834 high-quality SNPs were detected.