干旱区生态环境知识资源中心(Arid): Decoding first complete chloroplast genome of toothbrush tree (Salvadora persica L.): insight into genome evolution, sequence divergence and phylogenetic relationship within Brassicales

Arid

DOI	10.1186/s12864-021-07626-x
	Decoding first complete chloroplast genome of toothbrush tree (Salvadora persica L.): insight into genome evolution, sequence divergence and phylogenetic relationship within Brassicales
	Khan, Abdul Latif; Asaf, Sajjad; Lubna; Al-Rawahi, Ahmed; Al-Harrasi, Ahmed
通讯作者	Asaf, S ; Al-Harrasi, A (corresponding author), Univ Nizwa, Nat & Med Sci Res Ctr, Nizwa 616, Oman.
来源期刊	BMC GENOMICS
ISSN	1471-2164
出版年	2021
卷号	22 期号:1
英文摘要	Background Salvadora persica L. (Toothbrush tree - Miswak; family-Salvadoraceae) grows in the arid-land ecosystem and possesses economic and medicinal importance. The species, genus and the family have no genomic datasets available specifically on chloroplast (cp) genomics and taxonomic evolution. Herein, we have sequenced the complete chloroplast genome of S. persica for the first time and compared it with 11 related specie's cp genomes from the order Brassicales. Results The S. persica cp genome was 153,379 bp in length containing a sizeable single-copy region (LSC) of 83,818 bp which separated from the small single-copy region (SSC) of 17,683 bp by two inverted repeats (IRs) each 25,939 bp. Among these genomes, the largest cp genome size (160,600 bp) was found in M. oleifera, while in S. persica it was the smallest (153,379 bp). The cp genome of S. persica encoded 131 genes, including 37 tRNA genes, eight rRNA genes and 86 protein-coding genes. Besides, S. persica contains 27 forward, 36 tandem and 19 palindromic repeats. The S. persica cp genome had 154 SSRs with the highest number in the LSC region. Complete cp genome comparisons showed an overall high degree of sequence resemblance between S. persica and related cp genomes. Some divergence was observed in the intergenic spaces of other species. Phylogenomic analyses of 60 shared genes indicated that S. persica formed a single clade with A. tetracantha with high bootstrap values. The family Salvadoraceae is closely related to Capparaceae and Petadiplandraceae rather than to Bataceae and Koberliniacaea. Conclusion The current genomic datasets provide pivotal genetic resources to determine the phylogenetic relationships, genome evolution and future genetic diversity-related studies of S. persica in complex angiosperm families.
英文关键词	Salvadoraceae Sequencing Repeat analysis Divergence Phylogenomics InDel SNP Chloroplast
类型	Article
语种	英语
开放获取类型	gold, Green Published
收录类别	SCI-E
WOS记录号	WOS:000645650700001
WOS关键词	INVERTED REPEAT ; MEDICINAL-PLANT ; DNA ; ORGANIZATION ; MARKERS ; GENES ; POLYMORPHISM ; SOFTWARE
WOS类目	Biotechnology & Applied Microbiology ; Genetics & Heredity
WOS研究方向	Biotechnology & Applied Microbiology ; Genetics & Heredity
资源类型	期刊论文
条目标识符	http://119.78.100.177/qdio/handle/2XILL650/349728
作者单位	[Khan, Abdul Latif; Asaf, Sajjad; Al-Rawahi, Ahmed; Al-Harrasi, Ahmed] Univ Nizwa, Nat & Med Sci Res Ctr, Nizwa 616, Oman; [Lubna] Abdul Wali Khan Univ, Dept Bot, Garden Campus, Mardan 23200, Pakistan
推荐引用方式 GB/T 7714	Khan, Abdul Latif,Asaf, Sajjad,Lubna,et al. Decoding first complete chloroplast genome of toothbrush tree (Salvadora persica L.): insight into genome evolution, sequence divergence and phylogenetic relationship within Brassicales[J],2021,22(1).
APA	Khan, Abdul Latif,Asaf, Sajjad,Lubna,Al-Rawahi, Ahmed,&Al-Harrasi, Ahmed.(2021).Decoding first complete chloroplast genome of toothbrush tree (Salvadora persica L.): insight into genome evolution, sequence divergence and phylogenetic relationship within Brassicales.BMC GENOMICS,22(1).
MLA	Khan, Abdul Latif,et al."Decoding first complete chloroplast genome of toothbrush tree (Salvadora persica L.): insight into genome evolution, sequence divergence and phylogenetic relationship within Brassicales".BMC GENOMICS 22.1(2021).