干旱区生态环境知识资源中心(Arid): The Complete Chloroplast Genomes of Punica granatum and a Comparison with Other Species in Lythraceae

Arid

DOI	10.3390/ijms20122886
	The Complete Chloroplast Genomes of Punica granatum and a Comparison with Other Species in Lythraceae
	Yan, Ming 1,2; Zhao, Xueqing 1,2; Zhou, Jianqing 1,2; Huo, Yan 1,3; Ding, Yu 1,2; Yuan, Zhaohe 1,2
通讯作者	Yuan, Zhaohe
来源期刊	INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
EISSN	1422-0067
出版年	2019
卷号	20 期号:12
英文摘要	Pomegranates (Punica granatum L.) are one of the most popular fruit trees cultivated in arid and semi-arid tropics and subtropics. In this study, we determined and characterized three complete chloroplast (cp) genomes of P. granatum cultivars with different phenotypes using the genome skimming approach. The complete cp genomes of three pomegranate cultivars displayed the typical quadripartite structure of angiosperms, and their length ranged from 156,638 to 156,639 bp. They encoded 113 unique genes and 17 are duplicated in the inverted regions. We analyzed the sequence diversity of pomegranate cp genomes coupled with two previous reports. The results showed that the sequence diversity is extremely low and no informative sites were detected, which suggests that cp genome sequences may be not be suitable for investigating the genetic diversity of pomegranate genotypes. Further, we analyzed the codon usage pattern and identified the potential RNA editing sites. A comparative cp genome analysis with other species within Lythraceae revealed that the gene content and organization are highly conserved. Based on a site-specific model, 11 genes with positively selected sites were detected, and most of them were photosynthesis-related genes and genetic system-related genes. Together with previously released cp genomes of the order Myrtales, we determined the taxonomic position of P. granatum based on the complete chloroplast genomes. Phylogenetic analysis suggested that P. granatum form a single clade with other species from Lythraceae with a high support value. The complete cp genomes provides valuable information for understanding the phylogenetic position of P. gramatum in the order Myrtales.
英文关键词	pomegranate chloroplast genome sequence diversity site-specific selection phylogeny
类型	Article
语种	英语
国家	Peoples R China
开放获取类型	gold, Green Published, Green Submitted
收录类别	SCI-E
WOS记录号	WOS:000473756000036
WOS关键词	SYNONYMOUS CODON USAGE ; SELECTION ; SEQUENCE ; L. ; DIVERSITY ; EVOLUTION ; ORGANIZATION ; ANNOTATION ; PATTERNS ; PACKAGE
WOS类目	Biochemistry & Molecular Biology ; Chemistry, Multidisciplinary
WOS研究方向	Biochemistry & Molecular Biology ; Chemistry
资源类型	期刊论文
条目标识符	http://119.78.100.177/qdio/handle/2XILL650/216471
作者单位	1.Nanjing Forestry Univ, Coinnovat Ctr Sustainable Forestry Southern China, Nanjing 210037, Jiangsu, Peoples R China; 2.Nanjing Forestry Univ, Coll Forestry, Nanjing 210037, Jiangsu, Peoples R China; 3.Nanjing Forestry Univ, Coll Landscape Architecture, Nanjing 210037, Jiangsu, Peoples R China
推荐引用方式 GB/T 7714	Yan, Ming,Zhao, Xueqing,Zhou, Jianqing,et al. The Complete Chloroplast Genomes of Punica granatum and a Comparison with Other Species in Lythraceae[J],2019,20(12).
APA	Yan, Ming,Zhao, Xueqing,Zhou, Jianqing,Huo, Yan,Ding, Yu,&Yuan, Zhaohe.(2019).The Complete Chloroplast Genomes of Punica granatum and a Comparison with Other Species in Lythraceae.INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES,20(12).
MLA	Yan, Ming,et al."The Complete Chloroplast Genomes of Punica granatum and a Comparison with Other Species in Lythraceae".INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES 20.12(2019).