Genetic Insights into the Extremely Dwarf <i>Hibiscus syriacus</i> var. <i>micranthus</i>: Complete Chloroplast Genome Analysis and Development of a Novel dCAPS Marker
This study explored the chloroplast (cp) genomes of three <i>Hibiscus syriacus</i> (HS) specimens endemic to Korea possessing unique ornamental and conservation values: the dwarf <i>H. syriacus</i> var. <i>micranthus</i> (HSVM), renowned for its small stature and...
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| Format: | Article |
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MDPI AG
2024-03-01
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| Series: | Current Issues in Molecular Biology |
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| Online Access: | https://www.mdpi.com/1467-3045/46/3/173 |
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| author | Soon-Ho Kwon Hae-Yun Kwon Hanna Shin |
| author_facet | Soon-Ho Kwon Hae-Yun Kwon Hanna Shin |
| author_sort | Soon-Ho Kwon |
| collection | DOAJ |
| description | This study explored the chloroplast (cp) genomes of three <i>Hibiscus syriacus</i> (HS) specimens endemic to Korea possessing unique ornamental and conservation values: the dwarf <i>H. syriacus</i> var. <i>micranthus</i> (HSVM), renowned for its small stature and breeding potential; HS ‘Tamra’, a cultivar from Korea’s southernmost islands, noteworthy for its distinctive beauty; and HS Natural Monument no. 521 (N.M.521), a specimen of significant lifespan and height. Given the scarcity of evolutionary studies on these specimens, we assembled and analyzed their cp genomes. We successfully assembled genomes spanning 160,000 to 160,100 bp and identified intraspecific variants. Among these, a unique ATA 3-mer insertion in the <i>trnL-UAA</i> region was identified in HSVM, highlighting its value as a genetic resource. Leveraging this finding, we developed a novel InDel dCAPS marker, which was validated across 43 cultivars, enhancing our ability to distinguish HSVM and its derivatives from other HS cultivars. Phylogenetic analysis involving 23 Malvaceae species revealed that HSVM forms a clade with woody <i>Hibiscus</i> species, closely associating with N.M.520, which may suggest a shared ancestry or parallel evolutionary paths. This investigation advances our understanding of the genetic diversity in Korean HS and offers robust tools for accurate cultivar identification, aiding conservation and breeding efforts. |
| first_indexed | 2024-04-24T18:25:35Z |
| format | Article |
| id | doaj.art-5a81d7df8b5e4d718e78650b5d39d0be |
| institution | Directory Open Access Journal |
| issn | 1467-3037 1467-3045 |
| language | English |
| last_indexed | 2024-04-24T18:25:35Z |
| publishDate | 2024-03-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Current Issues in Molecular Biology |
| spelling | doaj.art-5a81d7df8b5e4d718e78650b5d39d0be2024-03-27T13:31:31ZengMDPI AGCurrent Issues in Molecular Biology1467-30371467-30452024-03-014632757277110.3390/cimb46030173Genetic Insights into the Extremely Dwarf <i>Hibiscus syriacus</i> var. <i>micranthus</i>: Complete Chloroplast Genome Analysis and Development of a Novel dCAPS MarkerSoon-Ho Kwon0Hae-Yun Kwon1Hanna Shin2Department of Forest Bio-Resources, National Institute of Forest Science, Suwon 16631, Republic of KoreaForest Medicinal Resources Research Center, National Institute of Forest Science, Yeongju 36040, Republic of KoreaDepartment of Forest Bio-Resources, National Institute of Forest Science, Suwon 16631, Republic of KoreaThis study explored the chloroplast (cp) genomes of three <i>Hibiscus syriacus</i> (HS) specimens endemic to Korea possessing unique ornamental and conservation values: the dwarf <i>H. syriacus</i> var. <i>micranthus</i> (HSVM), renowned for its small stature and breeding potential; HS ‘Tamra’, a cultivar from Korea’s southernmost islands, noteworthy for its distinctive beauty; and HS Natural Monument no. 521 (N.M.521), a specimen of significant lifespan and height. Given the scarcity of evolutionary studies on these specimens, we assembled and analyzed their cp genomes. We successfully assembled genomes spanning 160,000 to 160,100 bp and identified intraspecific variants. Among these, a unique ATA 3-mer insertion in the <i>trnL-UAA</i> region was identified in HSVM, highlighting its value as a genetic resource. Leveraging this finding, we developed a novel InDel dCAPS marker, which was validated across 43 cultivars, enhancing our ability to distinguish HSVM and its derivatives from other HS cultivars. Phylogenetic analysis involving 23 Malvaceae species revealed that HSVM forms a clade with woody <i>Hibiscus</i> species, closely associating with N.M.520, which may suggest a shared ancestry or parallel evolutionary paths. This investigation advances our understanding of the genetic diversity in Korean HS and offers robust tools for accurate cultivar identification, aiding conservation and breeding efforts.https://www.mdpi.com/1467-3045/46/3/173<i>Hibiscus syriacus</i> var. <i>micranthus</i>chloroplast genomedCAPS marker<i>trnL-UAA</i> p8 regiondwarf |
| spellingShingle | Soon-Ho Kwon Hae-Yun Kwon Hanna Shin Genetic Insights into the Extremely Dwarf <i>Hibiscus syriacus</i> var. <i>micranthus</i>: Complete Chloroplast Genome Analysis and Development of a Novel dCAPS Marker Current Issues in Molecular Biology <i>Hibiscus syriacus</i> var. <i>micranthus</i> chloroplast genome dCAPS marker <i>trnL-UAA</i> p8 region dwarf |
| title | Genetic Insights into the Extremely Dwarf <i>Hibiscus syriacus</i> var. <i>micranthus</i>: Complete Chloroplast Genome Analysis and Development of a Novel dCAPS Marker |
| title_full | Genetic Insights into the Extremely Dwarf <i>Hibiscus syriacus</i> var. <i>micranthus</i>: Complete Chloroplast Genome Analysis and Development of a Novel dCAPS Marker |
| title_fullStr | Genetic Insights into the Extremely Dwarf <i>Hibiscus syriacus</i> var. <i>micranthus</i>: Complete Chloroplast Genome Analysis and Development of a Novel dCAPS Marker |
| title_full_unstemmed | Genetic Insights into the Extremely Dwarf <i>Hibiscus syriacus</i> var. <i>micranthus</i>: Complete Chloroplast Genome Analysis and Development of a Novel dCAPS Marker |
| title_short | Genetic Insights into the Extremely Dwarf <i>Hibiscus syriacus</i> var. <i>micranthus</i>: Complete Chloroplast Genome Analysis and Development of a Novel dCAPS Marker |
| title_sort | genetic insights into the extremely dwarf i hibiscus syriacus i var i micranthus i complete chloroplast genome analysis and development of a novel dcaps marker |
| topic | <i>Hibiscus syriacus</i> var. <i>micranthus</i> chloroplast genome dCAPS marker <i>trnL-UAA</i> p8 region dwarf |
| url | https://www.mdpi.com/1467-3045/46/3/173 |
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