Phylogenomic Analysis of Two Species of <i>Parasenecio</i> and Comparative Analysis within Tribe Senecioneae (Asteraceae)
The genus of <i>Parasenecio</i> (Senecioneae) comprises about 70 species of high medicinal value. In this study, the plastomes of <i>Parasenecio palmatisectus</i> and <i>P. latipes</i> were newly sequenced using high-throughput sequencing technology and compared w...
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| Formato: | Artigo |
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MDPI AG
2023-04-01
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| Colecção: | Diversity |
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| Acesso em linha: | https://www.mdpi.com/1424-2818/15/4/563 |
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| author | Xiaofeng Liu Junjia Luo Mingke Zhang Qiang Wang Jie Liu Die Wu Zhixi Fu |
| author_facet | Xiaofeng Liu Junjia Luo Mingke Zhang Qiang Wang Jie Liu Die Wu Zhixi Fu |
| author_sort | Xiaofeng Liu |
| collection | DOAJ |
| description | The genus of <i>Parasenecio</i> (Senecioneae) comprises about 70 species of high medicinal value. In this study, the plastomes of <i>Parasenecio palmatisectus</i> and <i>P. latipes</i> were newly sequenced using high-throughput sequencing technology and compared with those of eight other species in Senecioneae. The complete chloroplast (cp) genomes were 151,185 bp in <i>P. latipes</i> with 37.5% GC and 151,263 bp in <i>P. palmatisectus</i> with 37.5% GC. We predicted 133 genes, including 37 tRNA genes, 86 protein-coding genes, 8 rRNA genes, and 2 pseudogenes (<i>ycf1</i> and <i>rps19</i>). A comparative genomic analysis showed that the complete cp genome sequences of <i>Parasenecio</i> species and their related species were relatively conserved. A total of 49 to 61 simple sequence repeats (SSRs) and 34 to 46 interspersed repeat sequences were identified in the 10 Senecioneae species of plastomes. Within the tribe Senecioneae, single-copy regions were more variable than inverted repeats regions, and the intergenic regions were more variable than the coding regions. Two genic regions (<i>ycf1</i> and <i>ccsA</i>) and four intergenic regions (<i>trnC-GCA-petN</i>, <i>ycf1-trnN-GUU</i>, <i>psaI-ycf4</i>, and <i>rpl32-trnL-UAG</i>) were identified as highly valuable plastid markers. A phylogenetic analysis under maximum likelihood revealed that the two <i>Parasenecio</i> species are sister to the genera of <i>Ligularia</i> and <i>Sinosenecio</i> in the tribe Senecioneae. This study also contributes to the super-barcode, phylogenetic, and evolutionary studies of <i>Parasenecio</i> plants. |
| first_indexed | 2024-03-11T05:04:59Z |
| format | Article |
| id | doaj.art-5a05db5447554dec94b2107f44e78de5 |
| institution | Directory Open Access Journal |
| issn | 1424-2818 |
| language | English |
| last_indexed | 2024-03-11T05:04:59Z |
| publishDate | 2023-04-01 |
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| record_format | Article |
| series | Diversity |
| spelling | doaj.art-5a05db5447554dec94b2107f44e78de52023-11-17T18:57:23ZengMDPI AGDiversity1424-28182023-04-0115456310.3390/d15040563Phylogenomic Analysis of Two Species of <i>Parasenecio</i> and Comparative Analysis within Tribe Senecioneae (Asteraceae)Xiaofeng Liu0Junjia Luo1Mingke Zhang2Qiang Wang3Jie Liu4Die Wu5Zhixi Fu6Key Laboratory of Land Resources Evaluation and Monitoring in Southwest, Sichuan Normal University, Ministry of Education, Chengdu 610066, ChinaCollege of Life Sciences, Sichuan Normal University, Chengdu 610101, ChinaCollege of Life Sciences, Sichuan Normal University, Chengdu 610101, ChinaSchool of Computer Science, Sichuan Normal University, Chengdu 610101, ChinaSchool of Computer Science, Sichuan Normal University, Chengdu 610101, ChinaSchool of Computer Science, Sichuan Normal University, Chengdu 610101, ChinaKey Laboratory of Land Resources Evaluation and Monitoring in Southwest, Sichuan Normal University, Ministry of Education, Chengdu 610066, ChinaThe genus of <i>Parasenecio</i> (Senecioneae) comprises about 70 species of high medicinal value. In this study, the plastomes of <i>Parasenecio palmatisectus</i> and <i>P. latipes</i> were newly sequenced using high-throughput sequencing technology and compared with those of eight other species in Senecioneae. The complete chloroplast (cp) genomes were 151,185 bp in <i>P. latipes</i> with 37.5% GC and 151,263 bp in <i>P. palmatisectus</i> with 37.5% GC. We predicted 133 genes, including 37 tRNA genes, 86 protein-coding genes, 8 rRNA genes, and 2 pseudogenes (<i>ycf1</i> and <i>rps19</i>). A comparative genomic analysis showed that the complete cp genome sequences of <i>Parasenecio</i> species and their related species were relatively conserved. A total of 49 to 61 simple sequence repeats (SSRs) and 34 to 46 interspersed repeat sequences were identified in the 10 Senecioneae species of plastomes. Within the tribe Senecioneae, single-copy regions were more variable than inverted repeats regions, and the intergenic regions were more variable than the coding regions. Two genic regions (<i>ycf1</i> and <i>ccsA</i>) and four intergenic regions (<i>trnC-GCA-petN</i>, <i>ycf1-trnN-GUU</i>, <i>psaI-ycf4</i>, and <i>rpl32-trnL-UAG</i>) were identified as highly valuable plastid markers. A phylogenetic analysis under maximum likelihood revealed that the two <i>Parasenecio</i> species are sister to the genera of <i>Ligularia</i> and <i>Sinosenecio</i> in the tribe Senecioneae. This study also contributes to the super-barcode, phylogenetic, and evolutionary studies of <i>Parasenecio</i> plants.https://www.mdpi.com/1424-2818/15/4/563<i>Parasenecio</i>chloroplast genomecomparative genomicsplastome phylogeny |
| spellingShingle | Xiaofeng Liu Junjia Luo Mingke Zhang Qiang Wang Jie Liu Die Wu Zhixi Fu Phylogenomic Analysis of Two Species of <i>Parasenecio</i> and Comparative Analysis within Tribe Senecioneae (Asteraceae) Diversity <i>Parasenecio</i> chloroplast genome comparative genomics plastome phylogeny |
| title | Phylogenomic Analysis of Two Species of <i>Parasenecio</i> and Comparative Analysis within Tribe Senecioneae (Asteraceae) |
| title_full | Phylogenomic Analysis of Two Species of <i>Parasenecio</i> and Comparative Analysis within Tribe Senecioneae (Asteraceae) |
| title_fullStr | Phylogenomic Analysis of Two Species of <i>Parasenecio</i> and Comparative Analysis within Tribe Senecioneae (Asteraceae) |
| title_full_unstemmed | Phylogenomic Analysis of Two Species of <i>Parasenecio</i> and Comparative Analysis within Tribe Senecioneae (Asteraceae) |
| title_short | Phylogenomic Analysis of Two Species of <i>Parasenecio</i> and Comparative Analysis within Tribe Senecioneae (Asteraceae) |
| title_sort | phylogenomic analysis of two species of i parasenecio i and comparative analysis within tribe senecioneae asteraceae |
| topic | <i>Parasenecio</i> chloroplast genome comparative genomics plastome phylogeny |
| url | https://www.mdpi.com/1424-2818/15/4/563 |
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