Chloroplast sequence of treegourd (Crescentia cujete, Bignoniaceae) to study phylogeography and domestication1

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.