PDF(Pubmed)
Abstract：
BACKGROUND: 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.
RESULTS: 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.
CONCLUSIONS: 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.
RESULTS: 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.
CONCLUSIONS: 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.
摘要：
背景：贝母是一种濒危药用植物，以其显着的治疗特性而闻名。不幸的是,由于森林栖息地的破坏，其人口急剧下降。因此，有效地保护乌苏里氏菌免于灭绝是一个重大挑战。对其遗传基础的深刻理解至关重要。迄今为止,关于乌苏里的完整线粒体基因组的研究尚未见报道。
结果：通过整合PacBio和Illumina测序技术，对乌苏里氏菌的完整线粒体基因组进行了测序和组装，显示13条环状染色体，总计737,569bp，平均GC含量为45.41％。共有55个基因被注释在这个有丝分裂基因组中，包括2个rRNA基因,12个tRNA基因，和41个PCGs。乌苏里氏菌的线粒体基因组包含192个SSR和4,027个分散重复序列。在ussuriensis的PCGs中，超过1的RSCU值的90.00%表现出对A末端或U末端密码子的偏好。此外,在这些PCG中预测了505个RNA编辑位点。选择性压力分析表明，对大多数PCGs进行负选择以保持线粒体功能，作为基因nad3的显着例外，显示阳性选择。乌苏里氏菌线粒体和叶绿体基因组之间的比较揭示了20个同源片段，总计8,954bp。核苷酸多样性分析揭示了基因之间的变异，基因atp9最为显著。尽管保留了GC含量，有丝分裂体大小在六个密切相关的物种中差异显著，共线性分析证实了它们的基因组结构缺乏保守性。系统发育分析表明，乌苏里百合与百合有密切关系。
结论：在这项研究中，我们测序并注释了乌苏里氏菌的有丝分裂基因组，并将其与其他密切相关物种的有丝分裂基因组进行了比较。除了基因组特征和进化位置，本研究也为进一步了解和利用该药用植物提供了宝贵的基因组资源。
结果：通过整合PacBio和Illumina测序技术，对乌苏里氏菌的完整线粒体基因组进行了测序和组装，显示13条环状染色体，总计737,569bp，平均GC含量为45.41％。共有55个基因被注释在这个有丝分裂基因组中，包括2个rRNA基因,12个tRNA基因，和41个PCGs。乌苏里氏菌的线粒体基因组包含192个SSR和4,027个分散重复序列。在ussuriensis的PCGs中，超过1的RSCU值的90.00%表现出对A末端或U末端密码子的偏好。此外,在这些PCG中预测了505个RNA编辑位点。选择性压力分析表明，对大多数PCGs进行负选择以保持线粒体功能，作为基因nad3的显着例外，显示阳性选择。乌苏里氏菌线粒体和叶绿体基因组之间的比较揭示了20个同源片段，总计8,954bp。核苷酸多样性分析揭示了基因之间的变异，基因atp9最为显著。尽管保留了GC含量，有丝分裂体大小在六个密切相关的物种中差异显著，共线性分析证实了它们的基因组结构缺乏保守性。系统发育分析表明，乌苏里百合与百合有密切关系。
结论：在这项研究中，我们测序并注释了乌苏里氏菌的有丝分裂基因组，并将其与其他密切相关物种的有丝分裂基因组进行了比较。除了基因组特征和进化位置，本研究也为进一步了解和利用该药用植物提供了宝贵的基因组资源。
