地黄是一种重要的药用植物,具有巨大的科学研究价值。然而,其线粒体基因组(有丝分裂基因组)尚未被表征。在这里,基于全基因组Illumina短读数和PacBioHiFi读数,通过从头组装策略,我们获得了R.chingii的完整有丝分裂基因组。我们进行了比较基因组分析,发现,与显示高度结构保守性的质体基因组(质体)相比,金鸡有丝分裂基因组结构相对复杂,显示了一个复杂的环形结构,有16个连接,由于五个重复序列。金吉丝裂原基因组为783,161bp,GC含量为44.8%,包含77个基因,包含47个蛋白质编码基因(CDS),27个tRNA基因,和3个rRNA基因。我们计数了47个CDS中的579个RNA编辑事件,并在R.chingi有丝分裂基因组的所有CDS中的12,828个密码子中。此外,在有丝分裂基因组和质体之间发现了24个独特的序列转移片段,包括8个有丝分裂基因组CDS基因和16个质体CDS基因,对应于2.39%的五味子有丝分裂基因组。有丝分裂基因组有更短但更共线的区域,通过比较非寄生R.chingii的细胞器来证明,半寄生中国,和Orobanchaceae家族中的全寄生虫斑叶。此外,从非寄生到全寄生物种,虫草科物种的有丝分裂基因组中的基因组大小并未逐渐减小。相反,最小的有丝分裂基因组是在半寄生虫中发现的。大小为225,612bp。这些发现填补了药用植物R.chingii的有丝分裂组学研究的空白,促进木管科细胞器基因组研究的进展,为分子育种提供线索。
Rehmannia chingii is an important medicinal plant with immense value in scientific research. However, its mitochondrial genome (mitogenome) has not yet been characterized. Herein, based on whole-genome Illumina short reads and PacBio HiFi reads, we obtained the complete mitogenome of R. chingii through a de novo assembly strategy. We carried out comparative genomic analyses and found that, in comparison with the plastid genome (plastome) showing a high degree of structural conservation, the R. chingii mitogenome structure is relatively complex, showing an intricate ring structure with 16 connections, owing to five repetitive sequences. The R. chingii mitogenome was 783,161 bp with a GC content of 44.8% and contained 77 genes, comprising 47 protein-coding genes (CDS), 27 tRNA genes, and 3 rRNA genes. We counted 579 RNA editing events in 47 CDS and 12,828 codons in all CDSs of the R. chingii mitogenome. Furthermore, 24 unique sequence transfer fragments were found between the mitogenome and plastome, comprising 8 mitogenome CDS genes and 16 plastome CDS genes, corresponding to 2.39% of the R. chingii mitogenome. Mitogenomes had shorter but more collinear regions, evidenced by a comparison of the organelles of non-parasitic R. chingii, hemiparasitic Pedicularis chinensis, and holoparasitic Aeginetia indica in the
Orobanchaceae family. Moreover, from non-parasitic to holoparasitic species, the genome size in the mitogenomes of
Orobanchaceae species did not decrease gradually. Instead, the smallest mitogenome was found in the hemiparasitic species P. chinensis, with a size of 225,612 bp. The findings fill the gap in the mitogenome research of the medicinal plant R. chingii, promote the progress of the organelle genome research of the
Orobanchaceae family, and provide clues for molecular breeding.