Phylogenetic Analysis of Wild Pomegranate (Punica granatum L.) Based on Its Complete Chloroplast Genome from Tibet, China

• Published in: Agronomy (Basel) Vol. 13; no. 1; p. 126
• Main Authors: Chen, Lide, Ren, Yuan, Zhao, Jun, Wang, Yuting, Liu, Xueqing, Zhao, Xueqing, Yuan, Zhaohe
• Format: Journal Article
• Language: English
• Published: Basel MDPI AG 01-01-2023
• Subjects: Amino acids; Bioinformatics; chloroplast genome; Chloroplasts; Codons; Collaboration; Cultivars; Evolution & development; Flavonoids; Fruits; Gene banks; Gene sequencing; Genes; Genomes; Introns; Leucine; Lythraceae; Methionine; phylogenetic analysis; Phylogenetics; Phylogeny; Physiology; Pomegranates; Proteins; Pseudogenes; Punica granatum; rRNA; sequence divergence; sequence repetition; Software; Trees; tRNA; wild pomegranate; Iran; Tibet; United States > US; China
• ISSN: 2073-4395; 2073-4395
• DOI: 10.3390/agronomy13010126

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.