Characterization of the complete chloroplast genome of Syringa oblata Lindl. from China and analysis of genome structures, comparative, phylogenetic relationships

Abstract

Abstract Syringa oblata is a flowering tree endemic to China, which has high medicinal and economic value. Comparative genomic analysis is necessary to elucidate the variation and phylogenetic relationships among Syringa species. An Illumina NovaSeq 6000 sequencing platform was used to sequence the whole genome of Syringa oblata plastomes in this study, and sequence assembly, annotation and characterization were performed by bioinformatics analysis, and a phylogenetic tree using Maximum Likelihood (ML) was constructed. A total of 155,668 bp was contained in the genome, which comprised two inverted repeats (IR) of 25,733 bp each, separated by a small single copy (SSC) region of 17,926 bp and a large single copy (LSC) region of 86 bp. There is a total GC content of 37.9% in the chloroplast genome, while the GC content in each region of SSC, LSC, and IR is 36.0%, 32.1%, and 43.2%. The genome contains 132 genes, including 88 protein-coding genes (CDS), 36 tRNA genes and 8 rRNA. There are seven protein-coding genes in the IR region, seven tRNA genes, and four rRNA genes. There was the most abundance of leucine and the least abundance of tryptophan among all amino acids. We detected 36 simple sequence repeats (SSRs) in the repeat structure analysis which included 32 mononucleotides (p1), 1 dinucleotide (p2), 1 trinucleotide (p3), 1 tetranucleotides (p4), and 1 complex nucleotide were explored, in the S. oblata chloroplast genome. In addition, we identified 50 long repeats, comprising 21 forward repeats, 28 palindromic repeats, and 1 complementary repeat. A phylogenetic analysis suggested that S. oblata (MW464119) is closely related to Syringa vulgaris (MG255768). It is anticipated that our results will be useful to further species identification, population genetic analysis, and biological research on Syringa oblata in the future.