Complete Chloroplast Genomes of <i>Saussurea katochaete</i>, <i>Saussurea superba</i>, and <i>Saussurea stella</i>: Genome Structures and Comparative and Phylogenetic Analyses
<i>Saussurea</i> plants are widely distributed in Asia and Europe; however, their complex phylogenetic relationships have led to many difficulties in phylogenetic studies and interspecific identification. In this study, we assembled, annotated, and analyzed the chloroplast genomes of thr...
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MDPI AG
2023-10-01
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| Series: | Genes |
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| author | Hui He Tao Wang Chuyu Tang Zhengfei Cao Xiaojian Pu Yuling Li Xiuzhang Li |
| author_facet | Hui He Tao Wang Chuyu Tang Zhengfei Cao Xiaojian Pu Yuling Li Xiuzhang Li |
| author_sort | Hui He |
| collection | DOAJ |
| description | <i>Saussurea</i> plants are widely distributed in Asia and Europe; however, their complex phylogenetic relationships have led to many difficulties in phylogenetic studies and interspecific identification. In this study, we assembled, annotated, and analyzed the chloroplast genomes of three <i>Saussurea</i> plants: <i>Saussurea katochaete</i>, <i>Saussurea superba</i>, and <i>Saussurea stella</i>. The results showed that the full-length sequences of the three <i>Saussurea</i> plants were 152,561 bp, 151,452 bp, and 152,293 bp, respectively, which represent the typical quadripartite structure, and the genomes were relatively conserved. The gene annotation results showed that the chloroplast genomes of <i>S. katochaete</i>, <i>S. superba</i>, and <i>S. stella</i> were annotated with 128, 124, and 127 unique genes, respectively, which included 83, 80, and 83 protein-coding genes (PCGs), respectively, 37, 36, and 36 tRNA genes, respectively, and 8 rRNA genes. Moreover, 46, 45, and 43 SSR loci, respectively, and nine highly variable regions (<i>rpl32-trnL-UAG</i>, <i>rpl32</i>, <i>ndhF-rpl32</i>, <i>ycf1</i>, <i>trnC-GCA-petN</i>, <i>trnC-GCA</i>, <i>rpcL</i>, <i>psbE-petL</i>, and <i>rpl16-trnG-UUG</i>) were identified and could be used as potential molecular markers for population identification and phylogenetic study of <i>Saussurea</i> plants. Phylogenetic analyses strongly support the sisterhood of <i>S. katochaete</i> with <i>S. superba</i> and <i>S. stella</i>, and are all clustered with <i>S. depsagensis</i>, <i>S. inversa</i>, <i>S. medusa</i>, and <i>S. gossipihora</i>, of which <i>S. gossipiphora</i> is most closely related. Additionally, the phylogenetic results indicate a high frequency of differentiation among different species of <i>Saussurea</i> plants, and many different species or genera are morphologically very different from each other, which may be related to certain genetic material in the chloroplasts. This study provides an important reference for the identification of <i>Saussurea</i> plants and studies their evolution and phylogenetics. |
| first_indexed | 2024-03-09T16:47:34Z |
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| id | doaj.art-118585ec1ee84a3e9fe9ae9c9fb3bfbe |
| institution | Directory Open Access Journal |
| issn | 2073-4425 |
| language | English |
| last_indexed | 2024-03-09T16:47:34Z |
| publishDate | 2023-10-01 |
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| spelling | doaj.art-118585ec1ee84a3e9fe9ae9c9fb3bfbe2023-11-24T14:43:39ZengMDPI AGGenes2073-44252023-10-011411200210.3390/genes14112002Complete Chloroplast Genomes of <i>Saussurea katochaete</i>, <i>Saussurea superba</i>, and <i>Saussurea stella</i>: Genome Structures and Comparative and Phylogenetic AnalysesHui He0Tao Wang1Chuyu Tang2Zhengfei Cao3Xiaojian Pu4Yuling Li5Xiuzhang Li6Qinghai Academy of Animal and Veterinary Science, Xining 810016, ChinaQinghai Academy of Animal and Veterinary Science, Xining 810016, ChinaQinghai Academy of Animal and Veterinary Science, Xining 810016, ChinaQinghai Academy of Animal and Veterinary Science, Xining 810016, ChinaQinghai Academy of Animal and Veterinary Science, Xining 810016, ChinaQinghai Academy of Animal and Veterinary Science, Xining 810016, ChinaState Key Laboratory of Plateau Ecology and Agriculture, Qinghai Academy of Animal and Veterinary Sciences, Qinghai University, Xining 810016, China<i>Saussurea</i> plants are widely distributed in Asia and Europe; however, their complex phylogenetic relationships have led to many difficulties in phylogenetic studies and interspecific identification. In this study, we assembled, annotated, and analyzed the chloroplast genomes of three <i>Saussurea</i> plants: <i>Saussurea katochaete</i>, <i>Saussurea superba</i>, and <i>Saussurea stella</i>. The results showed that the full-length sequences of the three <i>Saussurea</i> plants were 152,561 bp, 151,452 bp, and 152,293 bp, respectively, which represent the typical quadripartite structure, and the genomes were relatively conserved. The gene annotation results showed that the chloroplast genomes of <i>S. katochaete</i>, <i>S. superba</i>, and <i>S. stella</i> were annotated with 128, 124, and 127 unique genes, respectively, which included 83, 80, and 83 protein-coding genes (PCGs), respectively, 37, 36, and 36 tRNA genes, respectively, and 8 rRNA genes. Moreover, 46, 45, and 43 SSR loci, respectively, and nine highly variable regions (<i>rpl32-trnL-UAG</i>, <i>rpl32</i>, <i>ndhF-rpl32</i>, <i>ycf1</i>, <i>trnC-GCA-petN</i>, <i>trnC-GCA</i>, <i>rpcL</i>, <i>psbE-petL</i>, and <i>rpl16-trnG-UUG</i>) were identified and could be used as potential molecular markers for population identification and phylogenetic study of <i>Saussurea</i> plants. Phylogenetic analyses strongly support the sisterhood of <i>S. katochaete</i> with <i>S. superba</i> and <i>S. stella</i>, and are all clustered with <i>S. depsagensis</i>, <i>S. inversa</i>, <i>S. medusa</i>, and <i>S. gossipihora</i>, of which <i>S. gossipiphora</i> is most closely related. Additionally, the phylogenetic results indicate a high frequency of differentiation among different species of <i>Saussurea</i> plants, and many different species or genera are morphologically very different from each other, which may be related to certain genetic material in the chloroplasts. This study provides an important reference for the identification of <i>Saussurea</i> plants and studies their evolution and phylogenetics.https://www.mdpi.com/2073-4425/14/11/2002<i>Saussurea</i>chloroplast genomephylogenetic analysissequence variationmolecular markers |
| spellingShingle | Hui He Tao Wang Chuyu Tang Zhengfei Cao Xiaojian Pu Yuling Li Xiuzhang Li Complete Chloroplast Genomes of <i>Saussurea katochaete</i>, <i>Saussurea superba</i>, and <i>Saussurea stella</i>: Genome Structures and Comparative and Phylogenetic Analyses Genes <i>Saussurea</i> chloroplast genome phylogenetic analysis sequence variation molecular markers |
| title | Complete Chloroplast Genomes of <i>Saussurea katochaete</i>, <i>Saussurea superba</i>, and <i>Saussurea stella</i>: Genome Structures and Comparative and Phylogenetic Analyses |
| title_full | Complete Chloroplast Genomes of <i>Saussurea katochaete</i>, <i>Saussurea superba</i>, and <i>Saussurea stella</i>: Genome Structures and Comparative and Phylogenetic Analyses |
| title_fullStr | Complete Chloroplast Genomes of <i>Saussurea katochaete</i>, <i>Saussurea superba</i>, and <i>Saussurea stella</i>: Genome Structures and Comparative and Phylogenetic Analyses |
| title_full_unstemmed | Complete Chloroplast Genomes of <i>Saussurea katochaete</i>, <i>Saussurea superba</i>, and <i>Saussurea stella</i>: Genome Structures and Comparative and Phylogenetic Analyses |
| title_short | Complete Chloroplast Genomes of <i>Saussurea katochaete</i>, <i>Saussurea superba</i>, and <i>Saussurea stella</i>: Genome Structures and Comparative and Phylogenetic Analyses |
| title_sort | complete chloroplast genomes of i saussurea katochaete i i saussurea superba i and i saussurea stella i genome structures and comparative and phylogenetic analyses |
| topic | <i>Saussurea</i> chloroplast genome phylogenetic analysis sequence variation molecular markers |
| url | https://www.mdpi.com/2073-4425/14/11/2002 |
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