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The complete chloroplast genome of the lipstick tree, Bixa Orellana (Bixaceae).

ABSTRACT: Bixa orellana is a small tree known for its red, oil-soluble pigment contained in the seed coat that is used as a natural dye and food coloring. In this study, we assembled and characterized the complete chloroplast genome of B. orellana as a resource for future genetic studies. With a total length of 159,825?bp, the chloroplast genome comprised of a large single-copy (LSC) region of 89,476?bp, a small single-copy (SSC) region of 19,617?bp, and two inverted repeat (IR) regions of 25,356?bp each. A total of 127 genes were predicted, consisting of 83 protein-coding genes, 36 tRNA genes, and 8 rRNA genes. Phylogenetic analysis confirmed the position of B. orellana within the order Malvales.

SUBMITTER: Dai S

PROVIDER: S-EPMC7510647 | biostudies-literature | 2019

REPOSITORIES: biostudies-literature

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The complete chloroplast genome of the lipstick tree, Bixa Orellana (Bixaceae).

Dai Seping S Li Xuwen X Ni Jianzhong J Ruan Lin L Zhou Renchao R Ng Wei Lun WL

Mitochondrial DNA. Part B, Resources 20181121 1

Bixa orellana is a small tree known for its red, oil-soluble pigment contained in the seed coat that is used as a natural dye and food coloring. In this study, we assembled and characterized the complete chloroplast genome of B. orellana as a resource for future genetic studies. With a total length of 159,825 bp, the chloroplast genome comprised of a large single-copy (LSC) region of 89,476 bp, a small single-copy (SSC) region of 19,617 bp, and two inverted repeat (IR) regions of 2 ...[more]

PMID: 33365401

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Project description:BackgroundFull chloroplast genomes provide high resolution taxonomic discrimination between closely related plant species and are quickly replacing single and multi-locus barcoding regions as reference materials of choice for DNA based taxonomic annotation of plants. Bixa orellana, commonly known as "achiote" and "annatto" is a plant used for both human and animal foods and was thus identified for full chloroplast sequencing for the Center for Veterinary Medicine (CVM) Complete Chloroplast Animal Feed database. This work was conducted in collaboration with the Instituto de Medicina Tradicional (IMET) in Iquitos, Peru. There is a wide range of color variation in pods of Bixa orellana for which genetic loci that distinguish phenotypes have not yet been identified. Here we apply whole chloroplast genome sequencing of "red" and "yellow" individuals of Bixa orellana to provide high quality reference genomes to support kmer database development for use identifying this plant from complex mixtures using shotgun data. Additionally, we describe chloroplast gene content, synteny and phylogeny, and identify an indel and snp that may be associated with seed pod color.ResultsFully assembled chloroplast genomes were produced for both red and yellow Bixa orellana accessions (158,918 and 158,823 bp respectively). Synteny and gene content was identical to the only other previously reported full chloroplast genome of Bixa orellana (NC_041550). We observed a 17 base pair deletion at position 58,399-58,415 in both accessions, relative to NC_041550 and a 6 bp deletion at position 75,531-75,526 and a snp at position 86,493 in red Bixa orellana.ConclusionsOur data provide high quality reference genomes of individuals of red and yellow Bixa orellana to support kmer based identity markers for use with shotgun sequencing approaches for rapid, precise identification of Bixa orellana from complex mixtures. Kmer based phylogeny of full chloroplast genomes supports monophylly of Bixaceae consistent with alignment based approaches. A potentially discriminatory indel and snp were identified that may be correlated with the red phenotype.

Dataset Information

The complete chloroplast genome of the lipstick tree, Bixa Orellana (Bixaceae).

Publications

The complete chloroplast genome of the lipstick tree, <i>Bixa Orellana</i> (Bixaceae).

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