Complete plastome sequencing resolves taxonomic relationships among species of Calligonum L. (Polygonaceae) in China
Abstract Background Calligonum (Polygonaceae) is distributed from southern Europe through northern Africa to central Asia, and is typically found in arid, desert regions. Previous studies have revealed that standard DNA barcodes fail to discriminate Calligonum species. In this study, the complete pl...
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| Format: | Article |
| Language: | English |
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BMC
2020-06-01
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| Series: | BMC Plant Biology |
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| Online Access: | http://link.springer.com/article/10.1186/s12870-020-02466-5 |
| _version_ | 1828485763567714304 |
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| author | Feng Song Ting Li Kevin S. Burgess Ying Feng Xue-Jun Ge |
| author_facet | Feng Song Ting Li Kevin S. Burgess Ying Feng Xue-Jun Ge |
| author_sort | Feng Song |
| collection | DOAJ |
| description | Abstract Background Calligonum (Polygonaceae) is distributed from southern Europe through northern Africa to central Asia, and is typically found in arid, desert regions. Previous studies have revealed that standard DNA barcodes fail to discriminate Calligonum species. In this study, the complete plastid genomes (plastome) for 32 accessions of 21 Calligonum species is sequenced to not only generate the first complete plastome sequence for the genus Calligonum but to also 1) Assess the ability of the complete plastome sequence to discern species within the group, and 2) screen the plastome sequence for a cost-effective DNA barcode that can be used in future studies to resolve taxonomic relationships within the group. Results The whole plastomes of Calligonum species possess a typical quadripartite structure. The size of the Calligonum plastome is approximately 161 kilobase pairs (kbp), and encodes 113 genes, including 79 protein-coding genes, 30 tRNA genes, and four rRNA genes. Based on ML phylogenetic tree analyses, the complete plastome has higher species identification (78%) than combinations of standard DNA barcodes (rbcL + matK + nrITS, 56%). Five newly screened gene regions (ndhF, trnS-G, trnC-petN, ndhF-rpl32, rpl32-trnL) had high species resolution, where ndhF and trnS-G were able to distinguish the highest proportion of Calligonum species (56%). Conclusions The entire plastid genome was the most effective barcode for the genus Calligonum, although other gene regions showed great potential as taxon-specific barcodes for species identification in Calligonum. |
| first_indexed | 2024-12-11T09:21:06Z |
| format | Article |
| id | doaj.art-14a4b004c70e412b9e73cf33304e66fb |
| institution | Directory Open Access Journal |
| issn | 1471-2229 |
| language | English |
| last_indexed | 2024-12-11T09:21:06Z |
| publishDate | 2020-06-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Plant Biology |
| spelling | doaj.art-14a4b004c70e412b9e73cf33304e66fb2022-12-22T01:13:16ZengBMCBMC Plant Biology1471-22292020-06-0120111510.1186/s12870-020-02466-5Complete plastome sequencing resolves taxonomic relationships among species of Calligonum L. (Polygonaceae) in ChinaFeng Song0Ting Li1Kevin S. Burgess2Ying Feng3Xue-Jun Ge4University of Chinese Academy of SciencesUniversity of Chinese Academy of SciencesDepartment of Biology, Columbus State University, University System of GeorgiaState Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of SciencesKey Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of SciencesAbstract Background Calligonum (Polygonaceae) is distributed from southern Europe through northern Africa to central Asia, and is typically found in arid, desert regions. Previous studies have revealed that standard DNA barcodes fail to discriminate Calligonum species. In this study, the complete plastid genomes (plastome) for 32 accessions of 21 Calligonum species is sequenced to not only generate the first complete plastome sequence for the genus Calligonum but to also 1) Assess the ability of the complete plastome sequence to discern species within the group, and 2) screen the plastome sequence for a cost-effective DNA barcode that can be used in future studies to resolve taxonomic relationships within the group. Results The whole plastomes of Calligonum species possess a typical quadripartite structure. The size of the Calligonum plastome is approximately 161 kilobase pairs (kbp), and encodes 113 genes, including 79 protein-coding genes, 30 tRNA genes, and four rRNA genes. Based on ML phylogenetic tree analyses, the complete plastome has higher species identification (78%) than combinations of standard DNA barcodes (rbcL + matK + nrITS, 56%). Five newly screened gene regions (ndhF, trnS-G, trnC-petN, ndhF-rpl32, rpl32-trnL) had high species resolution, where ndhF and trnS-G were able to distinguish the highest proportion of Calligonum species (56%). Conclusions The entire plastid genome was the most effective barcode for the genus Calligonum, although other gene regions showed great potential as taxon-specific barcodes for species identification in Calligonum.http://link.springer.com/article/10.1186/s12870-020-02466-5CalligonumDNA barcodesPlastid genomeSpecies resolution |
| spellingShingle | Feng Song Ting Li Kevin S. Burgess Ying Feng Xue-Jun Ge Complete plastome sequencing resolves taxonomic relationships among species of Calligonum L. (Polygonaceae) in China BMC Plant Biology Calligonum DNA barcodes Plastid genome Species resolution |
| title | Complete plastome sequencing resolves taxonomic relationships among species of Calligonum L. (Polygonaceae) in China |
| title_full | Complete plastome sequencing resolves taxonomic relationships among species of Calligonum L. (Polygonaceae) in China |
| title_fullStr | Complete plastome sequencing resolves taxonomic relationships among species of Calligonum L. (Polygonaceae) in China |
| title_full_unstemmed | Complete plastome sequencing resolves taxonomic relationships among species of Calligonum L. (Polygonaceae) in China |
| title_short | Complete plastome sequencing resolves taxonomic relationships among species of Calligonum L. (Polygonaceae) in China |
| title_sort | complete plastome sequencing resolves taxonomic relationships among species of calligonum l polygonaceae in china |
| topic | Calligonum DNA barcodes Plastid genome Species resolution |
| url | http://link.springer.com/article/10.1186/s12870-020-02466-5 |
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