Open AccessChloroplast sequence of treegourd ( Crescentia cujete , Bignoniaceae) to study phylogeography and domestication
Author(s) -
Moreira Priscila Ambrósio,
Mariac Cédric,
Scarcelli Nora,
Couderc Marie,
Rodrigues Doriane Picanço,
Clement Charles R.,
Vigouroux Yves
Publication year - 2016
Publication title -
applications in plant sciences
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.64
H-Index - 23
ISSN - 2168-0450
DOI - 10.3732/apps.1600048
Subject(s) - biology , phylogeography , bignoniaceae , single nucleotide polymorphism , nucleotide diversity , chloroplast dna , chloroplast , evolutionary biology , genome , whole genome sequencing , genetic diversity , genetics , phylogenetics , botany , gene , haplotype , genotype , population , sociology , demography
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.