Jiangsu Academy of Forestry, 109 Danyang Road, Dongshanqiao, Nanjing, 211153, China.
Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, 210037, Nanjing, China.
BMC Plant Biol. 2023 Aug 14;23(1):393. doi: 10.1186/s12870-023-04377-7.
Ilex metabaptista is a woody tree species with strong waterlogging tolerance and is also admired as a landscape plant with high development prospects and scientific research value. Unfortunately, populations of this species have declined due to habitat loss. Thus, it is a great challenge for us to efficiently protect I. metabaptista resources from extinction. Molecular biology research can provide the scientific basis for the conservation of species. However, the study of I. metabaptista genetics is still in its infancy. To date, no mitochondrial genome (mitogenome) in the genus Ilex has been analysed in detail.
The mitogenome of I. metabaptista was assembled based on the reads from Illumina and Nanopore sequencing platforms; it was a typical circular DNA molecule of 529,560 bp with a GC content of 45.61% and contained 67 genes, including 42 protein-coding genes, 22 tRNA genes, and 3 rRNA genes. Repeat sequence analysis and prediction of RNA editing sites revealed a total of 286 dispersed repeats, 140 simple repeats, 18 tandem repeats, and 543 RNA editing sites. Analysis of codon usage showed that codons ending in A/T were preferred. Gene migration was observed to occur between the mitogenome and chloroplast genome via the detection of homologous fragments. In addition, Ka/Ks analysis revealed that most of the protein-coding genes in the mitogenome had undergone negative selection, and only the ccmB gene had undergone potential positive selection in most asterids. Nucleotide polymorphism analysis revealed the variation in each gene, with atp9 being the most notable. Furthermore, comparative analysis showed that the GC contents were conserved, but the sizes and structure of mitogenomes varied greatly among asterids. Phylogenetic analysis based on the mitogenomes reflected the exact evolutionary and taxonomic status of I. metabaptista.
In this study, we sequenced and annotated the mitogenome of I. metabaptista and compared it with the mitogenomes of other asterids, which provided essential background information for further understanding of the genetics of this plant and helped lay the foundation for future studies on molecular breeding of I. metabaptista.
冬青科植物喜树是一种具有较强耐水淹能力的木本植物，也是一种具有较高开发前景和科研价值的景观植物。然而，由于栖息地的丧失，该物种的数量已经减少。因此，有效地保护喜树资源免受灭绝是我们面临的巨大挑战。分子生物学研究可以为物种保护提供科学依据。然而，喜树的遗传学研究仍处于起步阶段。迄今为止，还没有对冬青属的线粒体基因组（mitogenome）进行详细分析。
基于 Illumina 和 Nanopore 测序平台的reads 组装了喜树的线粒体基因组；它是一个典型的 529560bp 的圆形 DNA 分子，GC 含量为 45.61%，包含 67 个基因，包括 42 个蛋白质编码基因、22 个 tRNA 基因和 3 个 rRNA 基因。重复序列分析和 RNA 编辑位点预测共发现 286 个散布重复序列、140 个简单重复序列、18 个串联重复序列和 543 个 RNA 编辑位点。密码子使用分析表明，终止密码子偏好 A/T。通过同源片段的检测，发现线粒体基因组和叶绿体基因组之间存在基因迁移。此外，Ka/Ks 分析表明，线粒体基因组中的大多数蛋白质编码基因经历了负选择，而只有 ccmB 基因在大多数类植物中经历了潜在的正选择。核苷酸多态性分析显示了每个基因的变化，其中 atp9 最为显著。此外，比较分析表明，GC 含量是保守的，但类植物的线粒体基因组大小和结构差异很大。基于线粒体基因组的系统发育分析反映了喜树的准确进化和分类地位。
本研究对喜树的线粒体基因组进行了测序和注释，并与其他类植物的线粒体基因组进行了比较，为进一步了解该植物的遗传学提供了必要的背景信息，为今后喜树的分子育种研究奠定了基础。
