College of Biology and Agriculture, Jiamusi University, Jiamusi, 154007, Heilongjiang, China.
Affiliated Stomatological Hospital, Jiamusi University, Jiamusi, 154002, Heilongjiang, China.
BMC Genomics. 2024 Aug 8;25(1):773. doi: 10.1186/s12864-024-10680-w.
Fritillaria ussuriensis is an endangered medicinal plant known for its notable therapeutic properties. Unfortunately, its population has drastically declined due to the destruction of forest habitats. Thus, effectively protecting F. ussuriensis from extinction poses a significant challenge. A profound understanding of its genetic foundation is crucial. To date, research on the complete mitochondrial genome of F. ussuriensis has not yet been reported.
The complete mitochondrial genome of F. ussuriensis was sequenced and assembled by integrating PacBio and Illumina sequencing technologies, revealing 13 circular chromosomes totaling 737,569 bp with an average GC content of 45.41%. A total of 55 genes were annotated in this mitogenome, including 2 rRNA genes, 12 tRNA genes, and 41 PCGs. The mitochondrial genome of F. ussuriensis contained 192 SSRs and 4,027 dispersed repeats. In the PCGs of F. ussuriensis mitogenome, 90.00% of the RSCU values exceeding 1 exhibited a preference for A-ended or U-ended codons. In addition, 505 RNA editing sites were predicted across these PCGs. Selective pressure analysis suggested negative selection on most PCGs to preserve mitochondrial functionality, as the notable exception of the gene nad3 showed positive selection. Comparison between the mitochondrial and chloroplast genomes of F. ussuriensis revealed 20 homologous fragments totaling 8,954 bp. Nucleotide diversity analysis revealed the variation among genes, and gene atp9 was the most notable. Despite the conservation of GC content, mitogenome sizes varied significantly among six closely related species, and colinear analysis confirmed the lack of conservation in their genomic structures. Phylogenetic analysis indicated a close relationship between F. ussuriensis and Lilium tsingtauense.
In this study, we sequenced and annotated the mitogenome of F. ussuriensis and compared it with the mitogenomes of other closely related species. In addition to genomic features and evolutionary position, this study also provides valuable genomic resources to further understand and utilize this medicinal plant.
贝母属乌苏里贝母是一种具有显著治疗特性的濒危药用植物。然而，由于森林生境的破坏，其种群数量急剧减少。因此，有效地保护乌苏里贝母免受灭绝是一项重大挑战。深入了解其遗传基础至关重要。迄今为止，尚未报道过乌苏里贝母完整的线粒体基因组研究。
通过整合 PacBio 和 Illumina 测序技术，对乌苏里贝母的完整线粒体基因组进行了测序和组装，共测序得到 13 条环状染色体，总长 737569bp，平均 GC 含量为 45.41%。该线粒体基因组共注释了 55 个基因，包括 2 个 rRNA 基因、12 个 tRNA 基因和 41 个 PCGs。乌苏里贝母线粒体基因组包含 192 个 SSR 和 4027 个散布重复序列。在乌苏里贝母线粒体基因组的 PCGs 中，90.00%的 RSCU 值大于 1 的基因偏好 A 端或 U 端密码子。此外，还预测到这些 PCGs 中有 505 个 RNA 编辑位点。选择压力分析表明，大多数 PCGs 受到负选择以保持线粒体功能，而 nad3 基因是一个显著的例外，表现出正选择。与乌苏里贝母的线粒体和叶绿体基因组进行比较，发现 20 个同源片段，总长 8954bp。核苷酸多样性分析揭示了基因之间的变异，其中基因 atp9 最为显著。尽管 GC 含量保持保守，但六个密切相关物种的线粒体基因组大小差异显著，共线性分析证实它们的基因组结构没有保守性。系统发育分析表明，乌苏里贝母与青岛百合关系密切。
本研究对乌苏里贝母的线粒体基因组进行了测序和注释，并与其他近缘物种的线粒体基因组进行了比较。除了基因组特征和进化位置外，本研究还为进一步了解和利用这种药用植物提供了有价值的基因组资源。
