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Park JM, Koo J. The complete chloroplast genome sequence of Berchemia racemosa Siebold & Zucc. (Rhamnaceae), a rare plant species in Korea. Mitochondrial DNA B Resour 2023; 8:69-72. [PMID: 36620322 PMCID: PMC9817123 DOI: 10.1080/23802359.2022.2161329] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Berchemia racemosa Siebold & Zucc., 1845 is a rare species distributed in restricted areas in the western Korean peninsula. In this study, the complete chloroplast genome (plastome) of B. racemosa was sequenced and assembled by Illumina paired-end sequencing. The plastome of B. racemosa was 161,187 bp in length and was quadripartite in structure, including a large single-copy (LSC) region of 89,503 bp, a small single-copy (SSC) region of 18,214 bp, and two inverted repeats of 26,735 bp. The GC content was 37.2%. The plastome of B. racemosa contains 130 genes, including eight ribosomal RNA (rRNA) genes, 37 transfer RNA (tRNA) genes, and 85 protein-coding genes. Phylogenetic analysis using complete genome sequences showed that B. racemosa is most closely related to Berchemia flavescens.
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Affiliation(s)
- Joon Moh Park
- Forest Resource Research Division, Jeollabuk-do Forest Environment Research Institute, Jinan, South Korea
| | - Jachoon Koo
- Division of Science Education and Institute of Fusion Science, College of Education, Jeonbuk National University, Jeonju, South Korea,CONTACT Jachoon Koo Division of Science Education and Institute of Fusion Science, College of Education, Jeonbuk National University, Jeonju, South Korea
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Wu X, Luo D, Zhang Y, Yang C, Crabbe MJC, Zhang T, Li G. Comparative Genomic and Phylogenetic Analysis of Chloroplast Genomes of Hawthorn (Crataegus spp.) in Southwest China. Front Genet 2022; 13:900357. [PMID: 35860470 PMCID: PMC9289535 DOI: 10.3389/fgene.2022.900357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Accepted: 06/15/2022] [Indexed: 11/21/2022] Open
Abstract
The hawthorns (Crataegus spp.) are widely distributed and famous for their edible and medicinal values. There are ∼18 species and seven varieties of hawthorn in China distributed throughout the country. We now report the chloroplast genome sequences from C. scabrifolia, C. chungtienensis and C. oresbia, from the southwest of China and compare them with the previously released six species in Crataegus and four species in Rosaceae. The chloroplast genome structure of Crataegus is typical and can be divided into four parts. The genome sizes are between 159,654 and 159,898bp. The three newly sequenced chloroplast genomes encode 132 genes, including 85 protein-coding genes, 37 tRNA genes, and eight rRNA genes. Comparative analysis of the chloroplast genomes revealed six divergent hotspot regions, including ndhA, rps16-trnQ-UUG, ndhF-rpl32, rps16-psbK, trnR-UCU-atpA and rpl32-trnL-UAG. According to the correlation and co-occurrence analysis of repeats with indels and SNPs, the relationship between them cannot be ignored. The phylogenetic tree constructed based on the complete chloroplast genome and intergenic region sequences indicated that C. scabrifolia has a different origin from C. chungtienensis and C. oresbia. We support the placement of C. hupehensis, C. cuneata, C. scabrifolia in C. subg. Crataegus and C. kansuensis, C. oresbia, C. kansuensis in C. subg. Sanguineae. In addition, based on the morphology, geographic distribution and phylogenetic relationships of C. chungtienensis and C. oresbia, we speculate that these two species may be the same species. In conclusion, this study has enriched the chloroplast genome resources of Crataegus and provided valuable information for the phylogeny and species identification of this genus.
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Affiliation(s)
- Xien Wu
- College of Chinese Material Medica, Yunnan University of Chinese Medicine, Kunming, China
| | - Dengli Luo
- College of Chinese Material Medica, Yunnan University of Chinese Medicine, Kunming, China
| | - Yingmin Zhang
- College of Chinese Material Medica, Yunnan University of Chinese Medicine, Kunming, China
| | - Congwei Yang
- College of Chinese Material Medica, Yunnan University of Chinese Medicine, Kunming, China
| | - M. James C. Crabbe
- Wolfson College, Oxford University, Oxford, United Kingdom
- Institute of Biomedical and Environmental Science and Technology, School of Life Sciences, University of Bedfordshire, Luton, United Kingdom
- School of Life Sciences, Shanxi University, Taiyuan, China
| | - Ticao Zhang
- College of Chinese Material Medica, Yunnan University of Chinese Medicine, Kunming, China
- *Correspondence: Ticao Zhang, ; Guodong Li,
| | - Guodong Li
- College of Chinese Material Medica, Yunnan University of Chinese Medicine, Kunming, China
- *Correspondence: Ticao Zhang, ; Guodong Li,
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