Chloroplast sequence of treegourd (Crescentia cujete, Bignoniaceae) to study phylogeography and domestication(1)

PREMISE OF THE STUDY: Crescentia cujete (Bignoniaceae) fruit rinds are traditionally used for storage vessels and handicrafts. We assembled its chloroplast genome and identified single-nucleotide polymorphisms (SNPs). METHODS AND RESULTS: Using a genome skimming approach, the whole chloroplast of C. cujete was assembled using 3,106,928 sequence reads of 150 bp. The chloroplast is 154,662 bp in length, structurally divided into a large single copy region (84,788 bp), a small single copy region (18,299 bp), and two inverted repeat regions (51,575 bp) with 88 genes annotated. By resequencing the whole chloroplast, we identified 66 SNPs in C. cujete (N = 30) and 68 SNPs in C. amazonica (N = 6). Nucleotide diversity was estimated at 1.1 × 10(−3) and 3.5 × 10(−3) for C. cujete and C. amazonica, respectively. CONCLUSIONS: This broadened C. cujete genetic toolkit will be important to study the origin, domestication, diversity, and phylogeography of treegourds in the Neotropics.