Identification of evolutionary relationships and DNA markers in the medicinally important genus Fritillaria based on chloroplast genomics
The genus Fritillaria has attracted great attention because of its medicinal and ornamental values. At least three reasons, including the accurate discrimination between various Fritillaria species, protection and sustainable development of rare Fritillaria resources as well as understanding of rela...
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PeerJ Inc.
2021-12-01
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| author | Tian Zhang Sipei Huang Simin Song Meng Zou Tiechui Yang Weiwei Wang Jiayu Zhou Hai Liao |
| author_facet | Tian Zhang Sipei Huang Simin Song Meng Zou Tiechui Yang Weiwei Wang Jiayu Zhou Hai Liao |
| author_sort | Tian Zhang |
| collection | DOAJ |
| description | The genus Fritillaria has attracted great attention because of its medicinal and ornamental values. At least three reasons, including the accurate discrimination between various Fritillaria species, protection and sustainable development of rare Fritillaria resources as well as understanding of relationship of some perplexing species, have prompted phylogenetic analyses and development of molecular markers for Fritillaria species. Here we determined the complete chloroplast (CP) genomes for F. unibracteata, F. przewalskii, F. delavayi, and F. sinica through Illumina sequencing, followed by de novo assembly. The lengths of the genomes ranged from 151,076 in F. unibracteata to 152,043 in F. przewalskii. Those CP genomes displayed a typical quadripartite structure, all including a pair of inverted repeats (26,078 to 26,355 bp) separated by the large single-copy (81,383 to 81,804 bp) and small single-copy (17,537 to 17,569 bp) regions. Fritillaria przewalskii, F. delavayi, and F. sinica equivalently encoded 133 unique genes consisting of 38 transfer RNA genes, eight ribosomal RNA genes, and 87 protein coding genes, whereas F. unibracteata contained 132 unique genes due to absence of the rps16 gene. Subsequently, comparative analysis of the complete CP genomes revealed that ycf1, trnL, trnF, ndhD, trnN-trnR, trnE-trnT, trnN, psbM-trnD, atpI, and rps19 to be useful molecular markers in taxonomic studies owning to their interspecies variations. Based on the comprehensive CP genome data collected from 53 species in Fritillaria and Lilium genera, a phylogenomic study was carried out with three Cardiocrinum species and five Amana species as outgroups. The results of the phylogenetic analysis showed that Fritillaria was a sister to Lilium, and the interspecies relationships within subgenus Fritillaria were well resolved. Furthermore, phylogenetic analysis based on the CP genome was proved to be a promising method in selecting potential novel medicinal resources to substitute current medicinal species that are on the verge of extinction. |
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| language | English |
| last_indexed | 2024-03-09T06:38:58Z |
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| spelling | doaj.art-21b68e9e0ef94502bfe8d42b900063982023-12-03T10:53:43ZengPeerJ Inc.PeerJ2167-83592021-12-019e1261210.7717/peerj.12612Identification of evolutionary relationships and DNA markers in the medicinally important genus Fritillaria based on chloroplast genomicsTian Zhang0Sipei Huang1Simin Song2Meng Zou3Tiechui Yang4Weiwei Wang5Jiayu Zhou6Hai Liao7School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, Sichuan, ChinaSchool of Life Science and Engineering, Southwest Jiaotong University, Chengdu, Sichuan, ChinaSchool of Life Science and Engineering, Southwest Jiaotong University, Chengdu, Sichuan, ChinaSchool of Life Science and Engineering, Southwest Jiaotong University, Chengdu, Sichuan, ChinaQinghai lvkang Biological Development Co., Ltd, Xining, Qinghai, ChinaSchool of Life Science and Engineering, Southwest Jiaotong University, Chengdu, Sichuan, ChinaSchool of Life Science and Engineering, Southwest Jiaotong University, Chengdu, Sichuan, ChinaSchool of Life Science and Engineering, Southwest Jiaotong University, Chengdu, Sichuan, ChinaThe genus Fritillaria has attracted great attention because of its medicinal and ornamental values. At least three reasons, including the accurate discrimination between various Fritillaria species, protection and sustainable development of rare Fritillaria resources as well as understanding of relationship of some perplexing species, have prompted phylogenetic analyses and development of molecular markers for Fritillaria species. Here we determined the complete chloroplast (CP) genomes for F. unibracteata, F. przewalskii, F. delavayi, and F. sinica through Illumina sequencing, followed by de novo assembly. The lengths of the genomes ranged from 151,076 in F. unibracteata to 152,043 in F. przewalskii. Those CP genomes displayed a typical quadripartite structure, all including a pair of inverted repeats (26,078 to 26,355 bp) separated by the large single-copy (81,383 to 81,804 bp) and small single-copy (17,537 to 17,569 bp) regions. Fritillaria przewalskii, F. delavayi, and F. sinica equivalently encoded 133 unique genes consisting of 38 transfer RNA genes, eight ribosomal RNA genes, and 87 protein coding genes, whereas F. unibracteata contained 132 unique genes due to absence of the rps16 gene. Subsequently, comparative analysis of the complete CP genomes revealed that ycf1, trnL, trnF, ndhD, trnN-trnR, trnE-trnT, trnN, psbM-trnD, atpI, and rps19 to be useful molecular markers in taxonomic studies owning to their interspecies variations. Based on the comprehensive CP genome data collected from 53 species in Fritillaria and Lilium genera, a phylogenomic study was carried out with three Cardiocrinum species and five Amana species as outgroups. The results of the phylogenetic analysis showed that Fritillaria was a sister to Lilium, and the interspecies relationships within subgenus Fritillaria were well resolved. Furthermore, phylogenetic analysis based on the CP genome was proved to be a promising method in selecting potential novel medicinal resources to substitute current medicinal species that are on the verge of extinction.https://peerj.com/articles/12612.pdfChloroplast genomicDNA markersFritillariaPhylogenetic analysisSpecies-specific identification |
| spellingShingle | Tian Zhang Sipei Huang Simin Song Meng Zou Tiechui Yang Weiwei Wang Jiayu Zhou Hai Liao Identification of evolutionary relationships and DNA markers in the medicinally important genus Fritillaria based on chloroplast genomics PeerJ Chloroplast genomic DNA markers Fritillaria Phylogenetic analysis Species-specific identification |
| title | Identification of evolutionary relationships and DNA markers in the medicinally important genus Fritillaria based on chloroplast genomics |
| title_full | Identification of evolutionary relationships and DNA markers in the medicinally important genus Fritillaria based on chloroplast genomics |
| title_fullStr | Identification of evolutionary relationships and DNA markers in the medicinally important genus Fritillaria based on chloroplast genomics |
| title_full_unstemmed | Identification of evolutionary relationships and DNA markers in the medicinally important genus Fritillaria based on chloroplast genomics |
| title_short | Identification of evolutionary relationships and DNA markers in the medicinally important genus Fritillaria based on chloroplast genomics |
| title_sort | identification of evolutionary relationships and dna markers in the medicinally important genus fritillaria based on chloroplast genomics |
| topic | Chloroplast genomic DNA markers Fritillaria Phylogenetic analysis Species-specific identification |
| url | https://peerj.com/articles/12612.pdf |
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