Chloroplast genome of one brown seaweed, Saccharina japonica (Laminariales, Phaeophyta): Its structural features and phylogenetic analyses with other photosynthetic plastids

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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
刊名	MARINE GENOMICS
	2013-06-01
卷号	10 页码:1-9
关键词	Photosynthetic heterokont Saccharina japonica Chloroplast Phylogenomic Molecular phylogenetics
ISSN号	1874-7787
通讯作者	Duan, DL
中文摘要	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.
英文摘要	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.
学科主题	Genetics & Heredity ; Marine & Freshwater Biology
WOS标题词	Science & Technology ; Life Sciences & Biomedicine
类目[WOS]	Genetics & Heredity ; Marine & Freshwater Biology
研究领域[WOS]	Genetics & Heredity ; Marine & Freshwater Biology
关键词[WOS]	MAXIMUM-LIKELIHOOD ; CHLOROPHYLL-C ; NUCLEOTIDE-SEQUENCE ; CRYPTOPHYTE ALGA ; DNA ; INSIGHTS ; GENES ; TREE ; DINOFLAGELLATE ; EVOLUTION
收录类别	SCI
原文出处	10.1016/j.margen.2012.12.002
语种	英语
WOS记录号	WOS:000320080800001
公开日期	2014-07-17
内容类型	期刊论文
源URL	[http://ir.qdio.ac.cn/handle/337002/16543]
专题	海洋研究所_实验海洋生物学重点实验室
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, Delin.(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.