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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....
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Botanical Society of America
2016
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5077280/ https://www.ncbi.nlm.nih.gov/pubmed/27785381 http://dx.doi.org/10.3732/apps.1600048 |
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author | Moreira, Priscila Ambrósio Mariac, Cédric Scarcelli, Nora Couderc, Marie Rodrigues, Doriane Picanço Clement, Charles R. Vigouroux, Yves |
author_facet | Moreira, Priscila Ambrósio Mariac, Cédric Scarcelli, Nora Couderc, Marie Rodrigues, Doriane Picanço Clement, Charles R. Vigouroux, Yves |
author_sort | Moreira, Priscila Ambrósio |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-5077280 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2016 |
publisher | Botanical Society of America |
record_format | MEDLINE/PubMed |
spelling | pubmed-50772802016-10-26 Chloroplast sequence of treegourd (Crescentia cujete, Bignoniaceae) to study phylogeography and domestication(1) Moreira, Priscila Ambrósio Mariac, Cédric Scarcelli, Nora Couderc, Marie Rodrigues, Doriane Picanço Clement, Charles R. Vigouroux, Yves Appl Plant Sci Genomic Resources Note 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. Botanical Society of America 2016-10-18 /pmc/articles/PMC5077280/ /pubmed/27785381 http://dx.doi.org/10.3732/apps.1600048 Text en © 2016 Moreira et al. Published by the Botanical Society of America http://creativecommons.org/licenses/by-nc/4.0/ This work is licensed under a Creative Commons Attribution License (CC-BY-NC-SA). |
spellingShingle | Genomic Resources Note Moreira, Priscila Ambrósio Mariac, Cédric Scarcelli, Nora Couderc, Marie Rodrigues, Doriane Picanço Clement, Charles R. Vigouroux, Yves Chloroplast sequence of treegourd (Crescentia cujete, Bignoniaceae) to study phylogeography and domestication(1) |
title | Chloroplast sequence of treegourd (Crescentia cujete, Bignoniaceae) to study phylogeography and domestication(1) |
title_full | Chloroplast sequence of treegourd (Crescentia cujete, Bignoniaceae) to study phylogeography and domestication(1) |
title_fullStr | Chloroplast sequence of treegourd (Crescentia cujete, Bignoniaceae) to study phylogeography and domestication(1) |
title_full_unstemmed | Chloroplast sequence of treegourd (Crescentia cujete, Bignoniaceae) to study phylogeography and domestication(1) |
title_short | Chloroplast sequence of treegourd (Crescentia cujete, Bignoniaceae) to study phylogeography and domestication(1) |
title_sort | chloroplast sequence of treegourd (crescentia cujete, bignoniaceae) to study phylogeography and domestication(1) |
topic | Genomic Resources Note |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5077280/ https://www.ncbi.nlm.nih.gov/pubmed/27785381 http://dx.doi.org/10.3732/apps.1600048 |
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