Plastid genome of Chenopodium petiolare from Trujillo, Peru

The Peruvian Andean region is an important center for plant domestication. However, to date, there have been few genetic studies on native grain, which limits our understanding of their genetic diversity and the development of new genetic studies for their breeding. Herein, we revealed the plastid g...

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Bibliographic Details
Published in:BMC research notes 2024-03, Vol.17 (1), p.69-69, Article 69
Main Authors: Aliaga, Flavio, Zapata-Cruz, Mario, Valverde-Zavaleta, Silvia Ana
Format: Article
Language:English
Subjects:
Acids
Analysis
Bioinformatics
Chenopodiaceae
Chenopodium
Chenopodium - genetics
Chenopodium petiolare
Chloroplast genome
Chloroplasts
Chromosomes
Conservation genetics
Cytosine
Data Note
DNA
Domestication
Evolution
Gene duplication
Genes
Genetic aspects
Genetic diversity
Genetic research
Genome, Chloroplast
Genome, Plastid
Genomes
Genomics
Grain
Herbs
Introns
Inverted repeat
Lomas del Cerro Campana
Mitochondrial DNA
Nucleotide sequence
Peru
Phylogenetics
Phylogeny
Plant Breeding
Plastid genome
Proteins
Quinoa
Ribosomal RNA
RNA polymerase
rRNA
Transfer RNA
Trees
Trujillo
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Summary:The Peruvian Andean region is an important center for plant domestication. However, to date, there have been few genetic studies on native grain, which limits our understanding of their genetic diversity and the development of new genetic studies for their breeding. Herein, we revealed the plastid genome of Chenopodium petiolare to expand our knowledge of its molecular markers, evolutionary studies, and conservation genetics. Total genomic DNA was extracted from fresh leaves (voucher: USM  :MHN333570). The DNA was sequenced using Illumina Novaseq 6000 (Macrogen Inc., Seoul, Republic of Korea) and reads 152,064 bp in length, with a large single-copy region of 83,520 bp and small single-copy region of 18,108 bp were obtained. These reads were separated by a pair of inverted repeat regions (IR) of 25,218 bp, and the overall guanine and cytosine (GC) was 37.24%. The plastid genome contains 130 genes (111 genes were unique and 19 genes were found duplicated in each IR region), including 86 protein-coding genes, 36 transfer RNA-coding genes, eight ribosomal RNA-coding genes, and 25 genes with introns (21 genes with one intron and four genes with two introns). The phylogenetic tree reconstructed based on single-copy orthologous genes and maximum likelihood analysis indicated that Chenopodium petiolare is most closely related to Chenopodium quinoa.
ISSN:1756-0500
1756-0500
DOI:10.1186/s13104-024-06705-y