Comparative genomics of 11 complete chloroplast genomes of Senecioneae (Asteraceae) species: DNA barcodes and phylogenetics
文献类型：期刊论文
| 作者 | Gichira, Andrew Wanyoike1,2,3; Avoga, Sheila1,2,3; Li, Zhizhong1,2; Hu, Guangwan3,4; Wang, Qingfeng3,4; Chen, Jinming1 |
| 刊名 | BOTANICAL STUDIES
 |
| 出版日期 | 2019-08-22 |
| 卷号 | 60期号:1页码:17 |
| 关键词 | Senecio Dendrosenecio Endemic Chloroplast genome Codon usage Microsatellites DNA barcodes Phylogenomics |
| DOI | 10.1186/s40529-019-0265-y |
| 英文摘要 | Background Majority of the species within Senecioneae are classified in Senecio, making it the tribe's largest genus. Certain intergeneric relationships within the tribe are vaguely defined, with the genus Senecio being partly linked to this ambiguity. Infrageneric relationships within Senecio remain largely unknown and consequently, the genus has undergone continuous expansion and contraction over the recent past due to addition and removal of taxa. Dendrosenecio, an endemic genus in Africa, is one of its segregate genera. To heighten the understanding of species divergence and phylogeny within the tribe, the complete chloroplast genomes of the first five Senecio and six Dendrosenecio species were sequenced and analyzed in this study. Results The entire length of the complete chloroplast genomes was 150 kb and 151 kb in Dendrosenecio and Senecio respectively. Characterization of the 11 chloroplast genomes revealed a significant degree of similarity particularly in their organization, gene content, repetitive sequence composition and patterns of codon usage. The chloroplast genomes encoded an equal number of unique genes out of which 80 were protein-coding genes, 30 transfer ribonucleic acid, and four ribosomal ribonucleic acid genes. Based on comparative sequence analyses, the level of divergence was lower in Dendrosenecio. A total of 331 and 340 microsatellites were detected in Senecio and Dendrosenecio, respectively. Out of which, 25 and five chloroplast microsatellites (cpSSR) were identified as potentially valuable molecular markers. Also, through whole chloroplast genome comparisons and DNA polymorphism tests, ten divergent hotspots were identified. Potential primers were designed creating genomic tools to further molecular studies within the tribe. Intergeneric relationships within the tribe were firmly resolved using genome-scale dataset in partitioned and unpartitioned schemes. Two main clades, corresponding to two subtribes within the Senecioneae, were formed with the genus Ligularia forming a single clade while the other had Dendrosenecio, Pericallis, Senecio and Jacobaea. A sister relationship was revealed between Dendrosenecio and Pericallis whereas Senecio, and Jacobaea were closely placed in a different clade. Conclusion Besides emphasizing on the potential of chloroplast genome data in resolving intergeneric relationships within Senecioneae, this study provides genomic resources to facilitate species identification and phylogenetic reconstructions within the respective genera. |
| 资助项目 | Sino Africa Joint Research Center[Y323771W07] ; Sino Africa Joint Research Center[SAJC201322] ; CAS-TWAS |
| WOS研究方向 | Plant Sciences |
| 语种 | 英语 |
| WOS记录号 | WOS:000482740700001 |
| 出版者 | SPRINGEROPEN |
| 源URL | [http://202.127.146.157/handle/2RYDP1HH/7369]  |
| 专题 | 中国科学院武汉植物园 |
| 通讯作者 | Wang, Qingfeng; Chen, Jinming |
| 作者单位 | 1.Chinese Acad Sci, Key Lab Aquat Bot & Watershed Ecol, Wuhan Bot Garden, Wuhan 430074, Hubei, Peoples R China 2.Univ Chinese Acad Sci, Beijing 100049, Peoples R China 3.Chinese Acad Sci, Sino Africa Joint Res Ctr, Wuhan 430074, Hubei, Peoples R China 4.Chinese Acad Sci, Key Lab Plant Germplasm Enhancement & Specialty A, Wuhan Bot Garden, Wuhan 430074, Hubei, Peoples R China |
| 推荐引用方式 GB/T 7714 | Gichira, Andrew Wanyoike,Avoga, Sheila,Li, Zhizhong,et al. Comparative genomics of 11 complete chloroplast genomes of Senecioneae (Asteraceae) species: DNA barcodes and phylogenetics[J]. BOTANICAL STUDIES,2019,60(1):17. |
| APA | Gichira, Andrew Wanyoike,Avoga, Sheila,Li, Zhizhong,Hu, Guangwan,Wang, Qingfeng,&Chen, Jinming.(2019).Comparative genomics of 11 complete chloroplast genomes of Senecioneae (Asteraceae) species: DNA barcodes and phylogenetics.BOTANICAL STUDIES,60(1),17. |
| MLA | Gichira, Andrew Wanyoike,et al."Comparative genomics of 11 complete chloroplast genomes of Senecioneae (Asteraceae) species: DNA barcodes and phylogenetics".BOTANICAL STUDIES 60.1(2019):17. |
入库方式： OAI收割
来源：武汉植物园
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