Comparative chloroplast genome analysis of Sambucus L. (Viburnaceae): inference for phylogenetic relationships among the closely related Sambucus adnata Wall. ex DC Sambucus javanica Blume
Sambucus L. is found in the family Viburnaceae (syn. Adoxaceae) and encompasses approximately 29 accepted species. The complex morphology of these species has caused continued confusion concerning their nomenclature, classification, and identification. Despite previous attempts to resolve taxonomic...
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Frontiers Media S.A.
2023-06-01
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| Series: | Frontiers in Plant Science |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fpls.2023.1179510/full |
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| author | Emmanuel Nyongesa Waswa Emmanuel Nyongesa Waswa Emmanuel Nyongesa Waswa Elijah Mbandi Mkala Elijah Mbandi Mkala Elijah Mbandi Mkala Wyclif Ochieng Odago Wyclif Ochieng Odago Wyclif Ochieng Odago Sara Getachew Amenu Sara Getachew Amenu Sara Getachew Amenu Elizabeth Syowai Mutinda Elizabeth Syowai Mutinda Elizabeth Syowai Mutinda Samuel Wamburu Muthui Samuel Wamburu Muthui Samuel Wamburu Muthui Shi-Xiong Ding Shi-Xiong Ding Shi-Xiong Ding Guang-Wan Hu Guang-Wan Hu Guang-Wan Hu Qing-Feng Wang Qing-Feng Wang Qing-Feng Wang |
| author_facet | Emmanuel Nyongesa Waswa Emmanuel Nyongesa Waswa Emmanuel Nyongesa Waswa Elijah Mbandi Mkala Elijah Mbandi Mkala Elijah Mbandi Mkala Wyclif Ochieng Odago Wyclif Ochieng Odago Wyclif Ochieng Odago Sara Getachew Amenu Sara Getachew Amenu Sara Getachew Amenu Elizabeth Syowai Mutinda Elizabeth Syowai Mutinda Elizabeth Syowai Mutinda Samuel Wamburu Muthui Samuel Wamburu Muthui Samuel Wamburu Muthui Shi-Xiong Ding Shi-Xiong Ding Shi-Xiong Ding Guang-Wan Hu Guang-Wan Hu Guang-Wan Hu Qing-Feng Wang Qing-Feng Wang Qing-Feng Wang |
| author_sort | Emmanuel Nyongesa Waswa |
| collection | DOAJ |
| description | Sambucus L. is found in the family Viburnaceae (syn. Adoxaceae) and encompasses approximately 29 accepted species. The complex morphology of these species has caused continued confusion concerning their nomenclature, classification, and identification. Despite previous attempts to resolve taxonomic complexities in the Sambucus genus, there are still unclear phylogenetic relationships among several species. In this study, the newly obtained plastome of Sambucus williamsii Hance. as well as the populations of Sambucus canadensis L., Sambucus javanica Blume, and Sambucus adnata Wall. ex DC were sequenced, and their sizes, structural similarity, gene order, gene number, and guanine–cytosine (GC) contents were analyzed. The phylogenetic analyses were conducted using the whole chloroplast genomes and protein-coding genes (PCGs). The findings revealed that the chloroplast genomes of Sambucus species exhibited typical quadripartite double-stranded DNA molecules. Their lengths ranged from 158,012 base pairs (bp) (S. javanica) to 158,716 bp (S. canadensis L). Each genome comprised a pair of inverted repeats (IRs), which separated the large single-copy (LSC) and small single-copy (SSC) regions. In addition, the plastomes contained 132 genes, encompassing 87 protein-coding, 37 tRNA, and four rRNA genes. In the simple sequence repeat (SSR) analysis, A/T mononucleotides had the highest proportion, with the most repetitive sequences observed in S. williamsii. The comparative genome analyses showed high similarities in structure, order, and gene contents. The hypervariable regions in the studied chloroplast genomes were trnT-GGU, trnF-GAA, psaJ, trnL-UAG, ndhF, and ndhE, which may be used as candidate barcodes for species discrimination in Sambucus genus. Phylogenetic analyses supported the monophyly of Sambucus and revealed the separation of S. javanica and S. adnata populations. Sambucus chinensis Lindl. was nested within S. javanica in the same clade, collaborating their conspecific treatment. These outcomes indicate that the chloroplast genome of Sambucus plants is a valuable genetic resource for resolving taxonomic discrepancies at the lower taxonomic levels and can be applied in molecular evolutionary studies. |
| first_indexed | 2024-03-13T05:08:38Z |
| format | Article |
| id | doaj.art-1e7e1fba6b4d4bc09851b064c8dfa96e |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-03-13T05:08:38Z |
| publishDate | 2023-06-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj.art-1e7e1fba6b4d4bc09851b064c8dfa96e2023-06-16T06:06:39ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2023-06-011410.3389/fpls.2023.11795101179510Comparative chloroplast genome analysis of Sambucus L. (Viburnaceae): inference for phylogenetic relationships among the closely related Sambucus adnata Wall. ex DC Sambucus javanica BlumeEmmanuel Nyongesa Waswa0Emmanuel Nyongesa Waswa1Emmanuel Nyongesa Waswa2Elijah Mbandi Mkala3Elijah Mbandi Mkala4Elijah Mbandi Mkala5Wyclif Ochieng Odago6Wyclif Ochieng Odago7Wyclif Ochieng Odago8Sara Getachew Amenu9Sara Getachew Amenu10Sara Getachew Amenu11Elizabeth Syowai Mutinda12Elizabeth Syowai Mutinda13Elizabeth Syowai Mutinda14Samuel Wamburu Muthui15Samuel Wamburu Muthui16Samuel Wamburu Muthui17Shi-Xiong Ding18Shi-Xiong Ding19Shi-Xiong Ding20Guang-Wan Hu21Guang-Wan Hu22Guang-Wan Hu23Qing-Feng Wang24Qing-Feng Wang25Qing-Feng Wang26Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, ChinaSino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, ChinaBotany Department, University of Chinese Academy of Sciences, Beijing, ChinaKey Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, ChinaSino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, ChinaBotany Department, University of Chinese Academy of Sciences, Beijing, ChinaKey Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, ChinaSino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, ChinaBotany Department, University of Chinese Academy of Sciences, Beijing, ChinaKey Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, ChinaSino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, ChinaBotany Department, University of Chinese Academy of Sciences, Beijing, ChinaKey Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, ChinaSino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, ChinaBotany Department, University of Chinese Academy of Sciences, Beijing, ChinaKey Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, ChinaSino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, ChinaBotany Department, University of Chinese Academy of Sciences, Beijing, ChinaKey Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, ChinaSino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, ChinaBotany Department, University of Chinese Academy of Sciences, Beijing, ChinaKey Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, ChinaSino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, ChinaBotany Department, University of Chinese Academy of Sciences, Beijing, ChinaKey Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, ChinaSino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, ChinaBotany Department, University of Chinese Academy of Sciences, Beijing, ChinaSambucus L. is found in the family Viburnaceae (syn. Adoxaceae) and encompasses approximately 29 accepted species. The complex morphology of these species has caused continued confusion concerning their nomenclature, classification, and identification. Despite previous attempts to resolve taxonomic complexities in the Sambucus genus, there are still unclear phylogenetic relationships among several species. In this study, the newly obtained plastome of Sambucus williamsii Hance. as well as the populations of Sambucus canadensis L., Sambucus javanica Blume, and Sambucus adnata Wall. ex DC were sequenced, and their sizes, structural similarity, gene order, gene number, and guanine–cytosine (GC) contents were analyzed. The phylogenetic analyses were conducted using the whole chloroplast genomes and protein-coding genes (PCGs). The findings revealed that the chloroplast genomes of Sambucus species exhibited typical quadripartite double-stranded DNA molecules. Their lengths ranged from 158,012 base pairs (bp) (S. javanica) to 158,716 bp (S. canadensis L). Each genome comprised a pair of inverted repeats (IRs), which separated the large single-copy (LSC) and small single-copy (SSC) regions. In addition, the plastomes contained 132 genes, encompassing 87 protein-coding, 37 tRNA, and four rRNA genes. In the simple sequence repeat (SSR) analysis, A/T mononucleotides had the highest proportion, with the most repetitive sequences observed in S. williamsii. The comparative genome analyses showed high similarities in structure, order, and gene contents. The hypervariable regions in the studied chloroplast genomes were trnT-GGU, trnF-GAA, psaJ, trnL-UAG, ndhF, and ndhE, which may be used as candidate barcodes for species discrimination in Sambucus genus. Phylogenetic analyses supported the monophyly of Sambucus and revealed the separation of S. javanica and S. adnata populations. Sambucus chinensis Lindl. was nested within S. javanica in the same clade, collaborating their conspecific treatment. These outcomes indicate that the chloroplast genome of Sambucus plants is a valuable genetic resource for resolving taxonomic discrepancies at the lower taxonomic levels and can be applied in molecular evolutionary studies.https://www.frontiersin.org/articles/10.3389/fpls.2023.1179510/fullchloroplastgenomesphylogenytaxonomySambucusViburnaceae |
| spellingShingle | Emmanuel Nyongesa Waswa Emmanuel Nyongesa Waswa Emmanuel Nyongesa Waswa Elijah Mbandi Mkala Elijah Mbandi Mkala Elijah Mbandi Mkala Wyclif Ochieng Odago Wyclif Ochieng Odago Wyclif Ochieng Odago Sara Getachew Amenu Sara Getachew Amenu Sara Getachew Amenu Elizabeth Syowai Mutinda Elizabeth Syowai Mutinda Elizabeth Syowai Mutinda Samuel Wamburu Muthui Samuel Wamburu Muthui Samuel Wamburu Muthui Shi-Xiong Ding Shi-Xiong Ding Shi-Xiong Ding Guang-Wan Hu Guang-Wan Hu Guang-Wan Hu Qing-Feng Wang Qing-Feng Wang Qing-Feng Wang Comparative chloroplast genome analysis of Sambucus L. (Viburnaceae): inference for phylogenetic relationships among the closely related Sambucus adnata Wall. ex DC Sambucus javanica Blume Frontiers in Plant Science chloroplast genomes phylogeny taxonomy Sambucus Viburnaceae |
| title | Comparative chloroplast genome analysis of Sambucus L. (Viburnaceae): inference for phylogenetic relationships among the closely related Sambucus adnata Wall. ex DC Sambucus javanica Blume |
| title_full | Comparative chloroplast genome analysis of Sambucus L. (Viburnaceae): inference for phylogenetic relationships among the closely related Sambucus adnata Wall. ex DC Sambucus javanica Blume |
| title_fullStr | Comparative chloroplast genome analysis of Sambucus L. (Viburnaceae): inference for phylogenetic relationships among the closely related Sambucus adnata Wall. ex DC Sambucus javanica Blume |
| title_full_unstemmed | Comparative chloroplast genome analysis of Sambucus L. (Viburnaceae): inference for phylogenetic relationships among the closely related Sambucus adnata Wall. ex DC Sambucus javanica Blume |
| title_short | Comparative chloroplast genome analysis of Sambucus L. (Viburnaceae): inference for phylogenetic relationships among the closely related Sambucus adnata Wall. ex DC Sambucus javanica Blume |
| title_sort | comparative chloroplast genome analysis of sambucus l viburnaceae inference for phylogenetic relationships among the closely related sambucus adnata wall ex dc sambucus javanica blume |
| topic | chloroplast genomes phylogeny taxonomy Sambucus Viburnaceae |
| url | https://www.frontiersin.org/articles/10.3389/fpls.2023.1179510/full |
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