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| Chloroplast genome of one brown seaweed, Saccharina japonica (Laminariales, Phaeophyta): Its structural features and phylogenetic analyses with other photosynthetic plastids | |
| Wang, Xiuliang; Shao, Zhanru; Fu, Wandong; Yao, Jianting; Hu, Qiuping; Duan, Delin; Duan, DL | |
| 2013-06-01 | |
| 发表期刊 | MARINE GENOMICS
 |
| ISSN | 1874-7787 |
| 卷号 | 10页码:1-9 |
| 文章类型 | Article |
| 摘要 | The chloroplast genome sequence of one brown seaweed, Saccharina japonica, was fully determined. It is characterized by 130,584 base pairs (bp) with a large and a small single-copy region (LSC and SSC), separated by two copies of inverted repeats (IR1 and IR2). The inverted repeat is 5015 bp long, and the sizes of SSC and LSC are 43,174 bp and 77,378 bp, respectively. The chloroplast genome of S. japonica consists of 139 protein-coding genes, 29 tRNA genes, and 3 ribosomal RNA genes. One intron was found in one tRNA-Leu gene in the chloroplast genome of S. japonica. Four types of overlapping genes were identified, ycf24 overlapped with ycf16 by 4 nucleotides (nt), ftrB overlapped with ycf12 by 6 nt, rpl4 and rpl23 overlapped by 8 nt, finally, psbC overlapped with psbD by 53 tit With two sets of concatenated plastid protein data, 40-protein dataset and 26-protein dataset, the chloroplast phylogenetic relationship among S. japonica and the other photosynthetic species was evaluated. We found that the chloroplast genomes of haptophyte, cryptophyte and heterokont were not resolved into one cluster by the 40-protein dataset with amino acid composition bias, although it was recovered with strong support by the 26-protein dataset. (C) 2012 Elsevier B.V. All rights reserved.; The chloroplast genome sequence of one brown seaweed, Saccharina japonica, was fully determined. It is characterized by 130,584 base pairs (bp) with a large and a small single-copy region (LSC and SSC), separated by two copies of inverted repeats (IR1 and IR2). The inverted repeat is 5015 bp long, and the sizes of SSC and LSC are 43,174 bp and 77,378 bp, respectively. The chloroplast genome of S. japonica consists of 139 protein-coding genes, 29 tRNA genes, and 3 ribosomal RNA genes. One intron was found in one tRNA-Leu gene in the chloroplast genome of S. japonica. Four types of overlapping genes were identified, ycf24 overlapped with ycf16 by 4 nucleotides (nt), ftrB overlapped with ycf12 by 6 nt, rpl4 and rpl23 overlapped by 8 nt, finally, psbC overlapped with psbD by 53 tit With two sets of concatenated plastid protein data, 40-protein dataset and 26-protein dataset, the chloroplast phylogenetic relationship among S. japonica and the other photosynthetic species was evaluated. We found that the chloroplast genomes of haptophyte, cryptophyte and heterokont were not resolved into one cluster by the 40-protein dataset with amino acid composition bias, although it was recovered with strong support by the 26-protein dataset. (C) 2012 Elsevier B.V. All rights reserved. |
| 关键词 | Photosynthetic Heterokont Saccharina Japonica Chloroplast Phylogenomic Molecular Phylogenetics |
| 学科领域 | Genetics & Heredity ; Marine & Freshwater Biology |
| DOI | 10.1016/j.margen.2012.12.002 |
| URL | 查看原文 |
| 收录类别 | SCI |
| 语种 | 英语 |
| WOS研究方向 | Genetics & Heredity ; Marine & Freshwater Biology |
| WOS类目 | Genetics & Heredity ; Marine & Freshwater Biology |
| WOS记录号 | WOS:000320080800001 |
| WOS关键词 | MAXIMUM-LIKELIHOOD ; CHLOROPHYLL-C ; NUCLEOTIDE-SEQUENCE ; CRYPTOPHYTE ALGA ; DNA ; INSIGHTS ; GENES ; TREE ; DINOFLAGELLATE ; EVOLUTION |
| WOS标题词 | Science & Technology ; Life Sciences & Biomedicine |
| 引用统计 | |
| 文献类型 | 期刊论文 |
| 条目标识符 | http://ir.qdio.ac.cn/handle/337002/16543 |
| 专题 | 实验海洋生物学重点实验室 |
| 通讯作者 | Duan, DL |
| 作者单位 | Chinese Acad Sci, Inst Oceanol, Key Lab Expt Marine Biol, Qingdao 266071, Peoples R China |
| 推荐引用方式 GB/T 7714 | Wang, Xiuliang,Shao, Zhanru,Fu, Wandong,et al. Chloroplast genome of one brown seaweed, Saccharina japonica (Laminariales, Phaeophyta): Its structural features and phylogenetic analyses with other photosynthetic plastids[J]. MARINE GENOMICS,2013,10:1-9. |
| APA | Wang, Xiuliang.,Shao, Zhanru.,Fu, Wandong.,Yao, Jianting.,Hu, Qiuping.,...&Duan, DL.(2013).Chloroplast genome of one brown seaweed, Saccharina japonica (Laminariales, Phaeophyta): Its structural features and phylogenetic analyses with other photosynthetic plastids.MARINE GENOMICS,10,1-9. |
| MLA | Wang, Xiuliang,et al."Chloroplast genome of one brown seaweed, Saccharina japonica (Laminariales, Phaeophyta): Its structural features and phylogenetic analyses with other photosynthetic plastids".MARINE GENOMICS 10(2013):1-9. |
| 条目包含的文件 | ||||||
| 文件名称/大小 | 文献类型 | 版本类型 | 开放类型 | 使用许可 | ||
| Chloroplast genome o（1248KB） | 限制开放 | CC BY-NC-SA | 浏览 | |||
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