The newly developed single nucleotide polymorphism (SNP) markers for a potentially medicinal plant, Crepidiastrum denticulatum (Asteraceae), inferred from complete chloroplast genome data
Autor: | Joonhyung Jung, JongYoung Hyun, Joo-Hwan Kim, Seok Jeong Yoon, Keedon Park, Hoang Dang Khoa Do, Chae-Jin Lim |
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Rok vydání: | 2018 |
Předmět: |
0301 basic medicine
Chloroplasts Single-nucleotide polymorphism Genomics Biology Asteraceae Genes Plant Genome Polymorphism Single Nucleotide DNA sequencing Evolution Molecular 03 medical and health sciences 0302 clinical medicine Phylogenomics Genetics Genome Chloroplast Molecular Biology Gene Phylogeny Plants Medicinal High-Throughput Nucleotide Sequencing General Medicine Sequence Analysis DNA 030104 developmental biology Chloroplast DNA Genetic marker 030220 oncology & carcinogenesis Biomarkers Genome Plant |
Zdroj: | Molecular biology reports. 46(3) |
ISSN: | 1573-4978 |
Popis: | Medicinal effects of Crepidiastrum denticulatum have been previously reported. However, the genomic resources of this species and its applications have not been studied. In this study, based on the next generation sequencing method (Miseq sequencing system), we characterize the chloroplast genome of C. denticulatum which contains a large single copy (84,112 bp) and a small single copy (18,519 bp), separated by two inverted repeat regions (25,074 bp). This genome consists of 80 protein-coding gene, 30 tRNAs, and four rRNAs. Notably, the trnT_GGU is pseudogenized because of a small insertion within the coding region. Comparative genomic analysis reveals a high similarity among Asteraceae taxa. However, the junctions between LSC, SSC, and IRs locate in different positions within rps19 and ycf1 among examined species. Also, we describe a newly developed single nucleotide polymorphism (SNP) marker for C. denticulatum based on amplification‐refractory mutation system (ARMS) technique. The markers, inferred from SNP in rbcL and matK genes, show effectiveness to recognize C. denticulatum from other related taxa through simple PCR protocol. The chloroplast genome-based molecular markers are effective to distinguish a potentially medicinal species, C. denticulatum, from other related taxa. Additionally, the complete chloroplast genome of C. denticulatum provides initial genomic data for further studies on phylogenomics, population genetics, and evolutionary history of Crepidiastrum as well as other taxa in Asteraceae. |
Databáze: | OpenAIRE |
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