Dataset Information

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

ABSTRACT: 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.

SUBMITTER: Moreira PA

PROVIDER: S-EPMC5077280 | biostudies-literature | 2016 Oct

REPOSITORIES: biostudies-literature

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Chloroplast sequence of treegourd (<i>Crescentia cujete</i>, Bignoniaceae) to study phylogeography and domestication.

Moreira Priscila Ambrósio PA Mariac Cédric C Scarcelli Nora N Couderc Marie M Rodrigues Doriane Picanço DP Clement Charles R CR Vigouroux Yves Y

Applications in plant sciences 20161018 10

<h4>Premise of the study</h4><i>Crescentia cujete</i> (Bignoniaceae) fruit rinds are traditionally used for storage vessels and handicrafts. We assembled its chloroplast genome and identified single-nucleotide polymorphisms (SNPs).<h4>Methods and results</h4>Using a genome skimming approach, the whole chloroplast of <i>C. cujete</i> 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 ...[more]

PMID: 27785381

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Project description:Bignoniaceae is a Pantropical plant family that is especially abundant in the Neotropics. Members of the Bignoniaceae are diverse in many ecosystems and represent key components of the Tropical flora. Despite the ecological importance of the Bignoniaceae and all the efforts to reconstruct the phylogeny of this group, whole chloroplast genome information has not yet been reported for any members of the family. Here, we report the complete chloroplast genome sequence of Tanaecium tetragonolobum (Jacq.) L.G. Lohmann, which was reconstructed using de novo and referenced-based assembly of single-end reads generated by shotgun sequencing of total genomic DNA in an Illumina platform. The gene order and organization of the chloroplast genome of T. tetragonolobum exhibits the general structure of flowering plants, and is similar to other Lamiales chloroplast genomes. The chloroplast genome of T. tetragonolobum is a circular molecule of 153,776 base pairs (bp) with a quadripartite structure containing two single copy regions, a large single copy region (LSC, 84,612 bp) and a small single copy region (SSC, 17,586 bp) separated by inverted repeat regions (IRs, 25,789 bp). In addition, the chloroplast genome of T. tetragonolobum has 38.3% GC content and includes 121 genes, of which 86 are protein-coding, 31 are transfer RNA, and four are ribosomal RNA. The chloroplast genome of T. tetragonolobum presents a total of 47 tandem repeats and 347 simple sequence repeats (SSRs) with mononucleotides being the most common and di-, tri-, tetra-, and hexanucleotides occurring with less frequency. The results obtained here were compared to other chloroplast genomes of Lamiales available to date, providing new insight into the evolution of chloroplast genomes within Lamiales. Overall, the evolutionary rates of genes in Lamiales are lineage-, locus-, and region-specific, indicating that the evolutionary pattern of nucleotide substitution in chloroplast genomes of flowering plants is complex. The discovery of tandem repeats within T. tetragonolobum and the presence of divergent regions between chloroplast genomes of Lamiales provides the basis for the development of markers at various taxonomic levels. The newly developed markers have the potential to greatly improve the resolution of molecular phylogenies.

Dataset Information

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

Publications

Chloroplast sequence of treegourd (<i>Crescentia cujete</i>, Bignoniaceae) to study phylogeography and domestication.

Similar Datasets

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