Comparative Phylogenetic Analysis of Ancient Korean Tea "Hadong Cheon-Nyeon Cha (<i>Camellia sinensis</i> var. <i>sinensis</i>)" Using Complete Chloroplast Genome Sequences
Wild teas are valuable genetic resources for studying evolution and breeding. Here, we report the complete chloroplast genome of the ancient Korean tea ‘Hadong Cheon-nyeon Cha’ (<i>C. sinensis</i> var. <i>sinensis</i>), which is known as the oldest tea tree in Korea. This stu...
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MDPI AG
2024-01-01
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| Online Access: | https://www.mdpi.com/1467-3045/46/2/69 |
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| author | Doobo Shim Seung Ho Jeon Jong Cheol Kim Dong-Kyung Yoon |
| author_facet | Doobo Shim Seung Ho Jeon Jong Cheol Kim Dong-Kyung Yoon |
| author_sort | Doobo Shim |
| collection | DOAJ |
| description | Wild teas are valuable genetic resources for studying evolution and breeding. Here, we report the complete chloroplast genome of the ancient Korean tea ‘Hadong Cheon-nyeon Cha’ (<i>C. sinensis</i> var. <i>sinensis</i>), which is known as the oldest tea tree in Korea. This study determined seven <i>Camellia sinensis</i> var. <i>sinenesis</i>, including Hadong Cheon-nyeon Cha (HCNC) chloroplast genome sequences, using Illumina sequencing technology via de novo assembly. The chloroplast genome sizes ranged from 157,019 to 157,114 bp and were organized into quadripartite regions with the typical chloroplast genomes. Further, differences in SNPs and InDels were detected across the seven chloroplast genomes through variance analysis. Principal component and phylogenetic analysis suggested that regional constraints, rather than functional constraints, strongly affected the sequence evolution of the cp genomes in this study. These genomic resources provide evolutionary insight into Korean tea plant cultivars and lay the foundation for a better understanding of the ancient Korean tea plant HCNC. |
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| spelling | doaj.art-a7fb0d1551a7424c9d521caaa1059a232024-02-23T15:12:34ZengMDPI AGCurrent Issues in Molecular Biology1467-30371467-30452024-01-014621091110610.3390/cimb46020069Comparative Phylogenetic Analysis of Ancient Korean Tea "Hadong Cheon-Nyeon Cha (<i>Camellia sinensis</i> var. <i>sinensis</i>)" Using Complete Chloroplast Genome SequencesDoobo Shim0Seung Ho Jeon1Jong Cheol Kim2Dong-Kyung Yoon3Institute of Hadong Green Tea, Hadong 52304, Republic of KoreaDepartment of Agricultural Life Science, College of Life Science and Natural Resources, Sunchon National University, Suncheon 57922, Republic of KoreaInstitute of Hadong Green Tea, Hadong 52304, Republic of KoreaDepartment of Southern Area Crop Science, National Institute of Crop Science, Rural Development Administration, Miryang 50424, Republic of KoreaWild teas are valuable genetic resources for studying evolution and breeding. Here, we report the complete chloroplast genome of the ancient Korean tea ‘Hadong Cheon-nyeon Cha’ (<i>C. sinensis</i> var. <i>sinensis</i>), which is known as the oldest tea tree in Korea. This study determined seven <i>Camellia sinensis</i> var. <i>sinenesis</i>, including Hadong Cheon-nyeon Cha (HCNC) chloroplast genome sequences, using Illumina sequencing technology via de novo assembly. The chloroplast genome sizes ranged from 157,019 to 157,114 bp and were organized into quadripartite regions with the typical chloroplast genomes. Further, differences in SNPs and InDels were detected across the seven chloroplast genomes through variance analysis. Principal component and phylogenetic analysis suggested that regional constraints, rather than functional constraints, strongly affected the sequence evolution of the cp genomes in this study. These genomic resources provide evolutionary insight into Korean tea plant cultivars and lay the foundation for a better understanding of the ancient Korean tea plant HCNC.https://www.mdpi.com/1467-3045/46/2/69<i>Camellia</i> (L.) <i>sinensis</i>chloroplast (cp) genomegenome assemblygenetic variationsphylogenetic analysis |
| spellingShingle | Doobo Shim Seung Ho Jeon Jong Cheol Kim Dong-Kyung Yoon Comparative Phylogenetic Analysis of Ancient Korean Tea "Hadong Cheon-Nyeon Cha (<i>Camellia sinensis</i> var. <i>sinensis</i>)" Using Complete Chloroplast Genome Sequences Current Issues in Molecular Biology <i>Camellia</i> (L.) <i>sinensis</i> chloroplast (cp) genome genome assembly genetic variations phylogenetic analysis |
| title | Comparative Phylogenetic Analysis of Ancient Korean Tea "Hadong Cheon-Nyeon Cha (<i>Camellia sinensis</i> var. <i>sinensis</i>)" Using Complete Chloroplast Genome Sequences |
| title_full | Comparative Phylogenetic Analysis of Ancient Korean Tea "Hadong Cheon-Nyeon Cha (<i>Camellia sinensis</i> var. <i>sinensis</i>)" Using Complete Chloroplast Genome Sequences |
| title_fullStr | Comparative Phylogenetic Analysis of Ancient Korean Tea "Hadong Cheon-Nyeon Cha (<i>Camellia sinensis</i> var. <i>sinensis</i>)" Using Complete Chloroplast Genome Sequences |
| title_full_unstemmed | Comparative Phylogenetic Analysis of Ancient Korean Tea "Hadong Cheon-Nyeon Cha (<i>Camellia sinensis</i> var. <i>sinensis</i>)" Using Complete Chloroplast Genome Sequences |
| title_short | Comparative Phylogenetic Analysis of Ancient Korean Tea "Hadong Cheon-Nyeon Cha (<i>Camellia sinensis</i> var. <i>sinensis</i>)" Using Complete Chloroplast Genome Sequences |
| title_sort | comparative phylogenetic analysis of ancient korean tea hadong cheon nyeon cha i camellia sinensis i var i sinensis i using complete chloroplast genome sequences |
| topic | <i>Camellia</i> (L.) <i>sinensis</i> chloroplast (cp) genome genome assembly genetic variations phylogenetic analysis |
| url | https://www.mdpi.com/1467-3045/46/2/69 |
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