Classification of Isatis indigotica Fortune and Isatis tinctoria Linnaeus via comparative analysis of chloroplast genomes
Abstract Background Isatis tinctoria Linnaeus and Isatis indigotica Fortune are very inconsistent in their morphological characteristics, but the Flora of China treats them as the same species. In this work, a new technology that differs from conventional barcodes is developed to prove that they are...
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| Format: | Article |
| Language: | English |
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BMC
2023-08-01
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| Series: | BMC Genomics |
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| Online Access: | https://doi.org/10.1186/s12864-023-09534-8 |
| _version_ | 1827724403782189056 |
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| author | Yong Su Man Zhang Qiaosheng Guo Min Wei Hongzhuan Shi Tao Wang Zhengzhou Han Huihui Liu Chang Liu Jianmin Huang |
| author_facet | Yong Su Man Zhang Qiaosheng Guo Min Wei Hongzhuan Shi Tao Wang Zhengzhou Han Huihui Liu Chang Liu Jianmin Huang |
| author_sort | Yong Su |
| collection | DOAJ |
| description | Abstract Background Isatis tinctoria Linnaeus and Isatis indigotica Fortune are very inconsistent in their morphological characteristics, but the Flora of China treats them as the same species. In this work, a new technology that differs from conventional barcodes is developed to prove that they are different species and to clarify their classification. Results and methods I. indigotica was indistinguishable from I. tinctoria when using ITS2. CPGAVAS2 was used to construct the chloroplast genomes. MAFFT and DnaSP were used to calculate nucleotide polymorphism, the chloroplast genomes of the two have high diversity in the rpl32 ~ trnL-UAG short region. When using this region as a mini barcode, it was found that there are obvious differences in the base numbers of I. tinctoria and different ploidy I. indigotica were found, but diploid and tetraploid I. indigotica had the same number of bases. Moreover, the reconstruction of the maximum likelihood (ML) tree, utilizing the mini-barcode, demonstrated that I. tinctoria and both diploid and tetraploid I. indigotica are located on distinct branches. The genome size of tetraploid I. indigotica was approximately 643.773 MB, the heterozygosity rate was approximately 0.98%, and the repeat sequence content was approximately 90.43%. This species has a highly heterozygous, extremely repetitive genome. Conclusion A new method was established to differentiate between I. indigotica and I. tinctoria. Furthermore, this approach provides a reference and basis for the directional breeding of Isatis. |
| first_indexed | 2024-03-10T22:15:20Z |
| format | Article |
| id | doaj.art-5dd1d9746902474280c17d89074351e5 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-03-10T22:15:20Z |
| publishDate | 2023-08-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-5dd1d9746902474280c17d89074351e52023-11-19T12:28:26ZengBMCBMC Genomics1471-21642023-08-0124111210.1186/s12864-023-09534-8Classification of Isatis indigotica Fortune and Isatis tinctoria Linnaeus via comparative analysis of chloroplast genomesYong Su0Man Zhang1Qiaosheng Guo2Min Wei3Hongzhuan Shi4Tao Wang5Zhengzhou Han6Huihui Liu7Chang Liu8Jianmin Huang9Institute of Chinese Medicinal Materials, Nanjing Agricultural UniversityInstitute of Chinese Medicinal Materials, Nanjing Agricultural UniversityInstitute of Chinese Medicinal Materials, Nanjing Agricultural UniversityInstitute of Chinese Medicinal Materials, Nanjing Agricultural UniversityInstitute of Chinese Medicinal Materials, Nanjing Agricultural UniversityInstitute of Chinese Medicinal Materials, Nanjing Agricultural UniversityChina Resources Sanjiu Medical & Pharmaceutical Co., LtdChina Resources Sanjiu Medical & Pharmaceutical Co., LtdInstitute of Chinese Medicinal Materials, Nanjing Agricultural UniversityInstitute of Chinese Medicinal Materials, Nanjing Agricultural UniversityAbstract Background Isatis tinctoria Linnaeus and Isatis indigotica Fortune are very inconsistent in their morphological characteristics, but the Flora of China treats them as the same species. In this work, a new technology that differs from conventional barcodes is developed to prove that they are different species and to clarify their classification. Results and methods I. indigotica was indistinguishable from I. tinctoria when using ITS2. CPGAVAS2 was used to construct the chloroplast genomes. MAFFT and DnaSP were used to calculate nucleotide polymorphism, the chloroplast genomes of the two have high diversity in the rpl32 ~ trnL-UAG short region. When using this region as a mini barcode, it was found that there are obvious differences in the base numbers of I. tinctoria and different ploidy I. indigotica were found, but diploid and tetraploid I. indigotica had the same number of bases. Moreover, the reconstruction of the maximum likelihood (ML) tree, utilizing the mini-barcode, demonstrated that I. tinctoria and both diploid and tetraploid I. indigotica are located on distinct branches. The genome size of tetraploid I. indigotica was approximately 643.773 MB, the heterozygosity rate was approximately 0.98%, and the repeat sequence content was approximately 90.43%. This species has a highly heterozygous, extremely repetitive genome. Conclusion A new method was established to differentiate between I. indigotica and I. tinctoria. Furthermore, this approach provides a reference and basis for the directional breeding of Isatis.https://doi.org/10.1186/s12864-023-09534-8Chloroplast genomeGermplasmIsatis indigotica FortuneAutotetraploid |
| spellingShingle | Yong Su Man Zhang Qiaosheng Guo Min Wei Hongzhuan Shi Tao Wang Zhengzhou Han Huihui Liu Chang Liu Jianmin Huang Classification of Isatis indigotica Fortune and Isatis tinctoria Linnaeus via comparative analysis of chloroplast genomes BMC Genomics Chloroplast genome Germplasm Isatis indigotica Fortune Autotetraploid |
| title | Classification of Isatis indigotica Fortune and Isatis tinctoria Linnaeus via comparative analysis of chloroplast genomes |
| title_full | Classification of Isatis indigotica Fortune and Isatis tinctoria Linnaeus via comparative analysis of chloroplast genomes |
| title_fullStr | Classification of Isatis indigotica Fortune and Isatis tinctoria Linnaeus via comparative analysis of chloroplast genomes |
| title_full_unstemmed | Classification of Isatis indigotica Fortune and Isatis tinctoria Linnaeus via comparative analysis of chloroplast genomes |
| title_short | Classification of Isatis indigotica Fortune and Isatis tinctoria Linnaeus via comparative analysis of chloroplast genomes |
| title_sort | classification of isatis indigotica fortune and isatis tinctoria linnaeus via comparative analysis of chloroplast genomes |
| topic | Chloroplast genome Germplasm Isatis indigotica Fortune Autotetraploid |
| url | https://doi.org/10.1186/s12864-023-09534-8 |
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