气候变化领域集成服务门户(CCPortal): Phylogenetic Analysis of Wild Pomegranate (Punica granatum L.) Based on Its Complete Chloroplast Genome from Tibet, China

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DOI	10.3390/agronomy13010126
	Phylogenetic Analysis of Wild Pomegranate (Punica granatum L.) Based on Its Complete Chloroplast Genome from Tibet, China
	Chen, Lide; Ren, Yuan; Zhao, Jun; Wang, Yuting; Liu, Xueqing; Zhao, Xueqing; Yuan, Zhaohe
发表日期	2023
EISSN	2073-4395
卷号	13 期号:1
英文摘要	Pomegranates (Punica granatum L.) are one of the most fashionable fruits and can be cultivated in both tropical and subtropical regions of the world. It is a shiny and attractive pome due to its cultivation. It belongs to the Lythraceae family. In this study, we analyzed the chloroplast genome of wild pomegranate based on whole genome shotgun sequences. In wild pomegranate, we found 158,645 bp in size, 132 genes containing 84 protein genes, 37 tRNA genes, 8 rRNA genes, and 36.92% of GC content, one infA and two duplicated ycf15 pseudogenes. Moreover, 21 chloroplast genes contained intros that are detected in a large single copy (LSC), small single copy (SSC), and two inverted repeats (IRA and IRB) regions, 17 of which were involved in single introns, while four genes (ycf3, rps12, clpP and rsp12) located in LSC, IRA, and IRB region. In total, 26,272 codons are found in protein-coding genes (PCGs); relative synonymous codon usage (RSCU) analysis revealed that the most abundant amino acid is leucine containing 2773 codons (10.55%), less abundant is methionine amino acid containing 1 codon (0.0032) in the PCGs. Furthermore, a total of 233 cpSSRs were identified in the wild pomegranate cp genome, and their distribution was analyzed in three regions, namely IR, LSC, and SSC. However, 155 cpSSR were found in the LSC (66.5%), followed by 40 cpSSR in the SSC (17.2%) and 38 cpSSR in the IR (16.3%) regions. Phylogenetic validation revealed that wild pomegranate is close to the pemphis acidula species. We believe that the cp genome allocates significant information promising for breeding research of wild pomegranate to Lythraceae.
关键词	wild pomegranate sequence repetition chloroplast genome sequence divergence phylogenetic analysis
英文关键词	GENETIC DIVERSITY; PHENOLIC-COMPOUNDS; SEQUENCE; ANTIOXIDANT; EVOLUTION; MARKERS; PEEL; ALIGNMENT
WOS研究方向	Agronomy ; Plant Sciences
WOS记录号	WOS:000914311000001
来源期刊	AGRONOMY-BASEL
文献类型	期刊论文
条目标识符	http://gcip.llas.ac.cn/handle/2XKMVOVA/283392
作者单位	Nanjing Forestry University
推荐引用方式 GB/T 7714	Chen, Lide,Ren, Yuan,Zhao, Jun,et al. Phylogenetic Analysis of Wild Pomegranate (Punica granatum L.) Based on Its Complete Chloroplast Genome from Tibet, China[J],2023,13(1).
APA	Chen, Lide.,Ren, Yuan.,Zhao, Jun.,Wang, Yuting.,Liu, Xueqing.,...&Yuan, Zhaohe.(2023).Phylogenetic Analysis of Wild Pomegranate (Punica granatum L.) Based on Its Complete Chloroplast Genome from Tibet, China.AGRONOMY-BASEL,13(1).
MLA	Chen, Lide,et al."Phylogenetic Analysis of Wild Pomegranate (Punica granatum L.) Based on Its Complete Chloroplast Genome from Tibet, China".AGRONOMY-BASEL 13.1(2023).