College of Life Sciences, Shanxi Agricultural University, Taigu, Shanxi, 030801, China.
BMC Genomics. 2023 Nov 23;24(1):708. doi: 10.1186/s12864-023-09821-4.
Forsythia suspensa (Thunb.) Vahl is a valuable ornamental and medicinal plant. Although the nuclear and chloroplast genomes of F. suspensa have been published, its complete mitochondrial genome sequence has yet to be reported. In this study, the genomic DNA of F. suspensa yellowish leaf material was extracted, sequenced by using a mixture of Illumina Novaseq6000 short reads and Oxford Nanopore PromethION long reads, and the sequencing data were assembled and annotated.
The F. suspensa mitochondrial genome was obtained in the length of 535,692 bp with a circular structure, and the GC content was 44.90%. The genome contains 60 genes, including 36 protein-coding genes, 21 tRNA genes, and three rRNA genes. We further analyzed RNA editing of the protein-coding genes, relative synonymous codon usage, and sequence repeats based on the genomic data. There were 25 homologous sequences between F. suspensa mitochondria and chloroplast genome, which involved the transfer of 8 mitochondrial genes, and 9473 homologous sequences between mitochondrial and nuclear genomes. Analysis of the nucleic acid substitution rate, nucleic acid diversity, and collinearity of protein-coding genes of the F. suspensa mitochondrial genome revealed that the majority of genes may have undergone purifying selection, exhibiting a slower rate of evolution and a relatively conserved structure. Analysis of the phylogenetic relationships among different species revealed that F. suspensa was most closely related to Olea europaea subsp. Europaea.
In this study, we sequenced, assembled, and annotated a high-quality F. suspensa mitochondrial genome. The results of this study will enrich the mitochondrial genome data of Forsythia, lay a foundation for the phylogenetic development of Forsythia, and promote the evolutionary analysis of Oleaceae species.
连翘（Thunb.）Vahl 是一种有价值的观赏和药用植物。尽管连翘的核和叶绿体基因组已经发表，但尚未报道其完整的线粒体基因组序列。在这项研究中，从连翘黄色叶片材料中提取基因组 DNA，使用 Illumina Novaseq6000 短读和 Oxford Nanopore PromethION 长读混合测序，并对测序数据进行组装和注释。
获得的连翘线粒体基因组大小为 535692bp，呈环状结构，GC 含量为 44.90%。基因组包含 60 个基因，包括 36 个蛋白编码基因、21 个 tRNA 基因和 3 个 rRNA 基因。我们进一步基于基因组数据分析了蛋白编码基因的 RNA 编辑、相对同义密码子使用和序列重复。连翘线粒体与叶绿体基因组之间有 25 个同源序列，涉及 8 个线粒体基因的转移，线粒体与核基因组之间有 9473 个同源序列。对连翘线粒体基因组的核酸替代率、核酸多样性和蛋白编码基因的共线性分析表明，大多数基因可能经历了纯化选择，表现出较慢的进化速度和相对保守的结构。不同物种间的系统发育关系分析表明，连翘与油橄榄亚种。欧洲亚种最为密切相关。
本研究测序、组装和注释了高质量的连翘线粒体基因组。该研究结果将丰富连翘的线粒体基因组数据，为连翘的系统发育发展奠定基础，并促进木犀科物种的进化分析。
