Liu Hui, Zhao Wei, Zhang Ren-Gang, Mao Jian-Feng, Wang Xiao-Ru
National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.
Department of Ecology and Environmental Science, Umeå Plant Science Centre, Umeå University, Umeå, Sweden.
Front Genet. 2022 May 25;13:867736. doi: 10.3389/fgene.2022.867736. eCollection 2022.
Among the three genomes in plant cells, the mitochondrial genome (mitogenome) is the least studied due to complex recombination and intergenomic transfer. In gymnosperms only ∼20 mitogenomes have been released thus far, which hinders a systematic investigation into the tempo and mode of mitochondrial DNA evolution in seed plants. Here, we report the complete mitogenome sequence of (Cupressaceae). This mitogenome is assembled as two circular-mapping chromosomes with a size of ∼2.6 Mb and which contains 32 protein-coding genes, three rRNA and seven tRNA genes, and 1,068 RNA editing sites. Repetitive sequences, including dispersed repeats, transposable elements (TEs), and tandem repeats, made up 23% of the genome. Comparative analyses with 17 other mitogenomes representing the five gymnosperm lineages revealed a 30-fold difference in genome size, 80-fold in repetitive content, and 230-fold in substitution rate. We found dispersed repeats are highly associated with mitogenome expansion ( = 0.99), and most of them were accumulated during recent duplication events. Syntenic blocks and shared sequences between mitogenomes decay rapidly with divergence time ( = 0.53), with the exceptions of Ginkgo and Cycads which retained conserved genome structure over long evolutionary time. Our phylogenetic analysis supports a sister group relationship of Cupressophytes and Gnetophytes; both groups are unique in that they lost 8-12 protein-coding genes, of which 4-7 intact genes are likely transferred to nucleus. These two clades also show accelerated and highly variable substitution rates relative to other gymnosperms. Our study highlights the dynamic and enigmatic evolution of gymnosperm mitogenomes.
在植物细胞的三个基因组中，线粒体基因组（mitogenome）由于复杂的重组和基因组间转移而研究最少。在裸子植物中，迄今为止仅公布了约20个线粒体基因组，这阻碍了对种子植物线粒体DNA进化的速度和模式进行系统研究。在此，我们报告了柏科植物（Cupressaceae）的完整线粒体基因组序列。该线粒体基因组组装成两个环状映射染色体，大小约为2.6 Mb，包含32个蛋白质编码基因、3个rRNA基因和7个tRNA基因，以及1068个RNA编辑位点。重复序列，包括分散重复序列、转座元件（TEs）和串联重复序列，占基因组的23%。与代表五个裸子植物谱系的其他17个线粒体基因组进行比较分析，发现基因组大小相差30倍，重复含量相差80倍，替代率相差230倍。我们发现分散重复序列与线粒体基因组扩展高度相关（r = 0.99），并且它们中的大多数是在最近的复制事件中积累的。线粒体基因组之间的共线性区域和共享序列随分歧时间迅速衰减（r = 0.53），银杏和苏铁除外，它们在漫长的进化时间里保留了保守的基因组结构。我们的系统发育分析支持柏类植物和买麻藤类植物的姐妹群关系；这两个类群的独特之处在于它们丢失了8 - 12个蛋白质编码基因，其中4 - 7个完整基因可能转移到了细胞核中。相对于其他裸子植物，这两个分支也显示出加速且高度可变的替代率。我们的研究突出了裸子植物线粒体基因组的动态和神秘进化。
