Plastids and mitochondria are endosymbiotic organelles that store genetic information. The genomes of these organelles generally exhibit contrasting patterns regarding genome architecture and genetic content. However, they have similar genetic features in Selaginellaceae, and little is known about what causes parallel evolution. Here, we document the multipartite plastid genomes (plastomes) and the highly divergent mitochondrial genomes (mitogenomes) from spikemoss obtained by combining short‐ and long‐reads. The 188‐kb multipartite plastome has three ribosomal operon copies in the master genomic conformation, creating the alternative subgenomic conformation composed of 110‐ and 78‐kb subgenomes. The long‐read data indicated that the two different genomic conformations were present in almost equal proportions in the plastomes of Selaginella nipponica. The mitogenome of S. nipponica was assembled into 27 contigs with a total size of 110 kb. All contigs contained directly arranged repeats at both ends, which introduced multiple conformations. Our results showed that plastomes and mitogenomes share high tRNA losses, GC‐biased nucleotides, elevated substitution rates and complicated organization. The exploration of nuclear‐encoded organelle DNA replication, recombination and repair proteins indicated that, several single‐targeted proteins, particularly plastid‐targeted recombinase A1, have been lost in Selaginellaceae; conversely, the dual‐targeted proteins remain intact. According to the reported function of recombinase A1, we propose that the plastomes of spikemoss often fail to pair homologous sequences during recombination, and the dual‐targeted proteins play a key role in the convergent genetic features of plastomes and mitogenomes. Our results provide a distinctive evolutionary pattern of the organelle genomes in Selaginellaceae and evidence of their convergent evolution.

中文翻译：

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卷柏科中与细胞核基因组相关的细胞器基因组的独特进化模式

质体和线粒体是存储遗传信息的内共生细胞器。这些细胞器的基因组通常表现出关于基因组结构和遗传含量的对比模式。然而，它们在卷柏科中具有相似的遗传特征，而导致平行进化的原因鲜为人知。在这里，我们记录了通过结合短读和长读获得的穗状花序的多部分质体基因组（质体组）和高度发散的线粒体基因组（有丝分裂基因组）。188kb多部分质体组在主基因组构象中具有3个核糖体操纵子拷贝，从而形成了由110kb和78kb亚基因组组成的替代亚基因组构象。长期读取的数据表明，两种不同的基因组构象以几乎相等的比例存在于卷柏卷柏。的线粒体基因S.蓣被组装成27个重叠群，总大小为110 kb。所有重叠群在其两端均包含直接排列的重复序列，从而引入了多个构象。我们的结果表明，质体组和有丝分裂组共享高的tRNA损失，GC偏向核苷酸，升高的取代率和复杂的组织。对核编码细胞器DNA复制，重组和修复蛋白的探索表明，卷柏中已经丢失了几种单靶蛋白，特别是质体靶向重组酶A1。相反，双重靶向蛋白保持完整。根据报道的重组酶A1的功能，我们提出，穗苔藓的质体通常在重组过程中无法配对同源序列，双靶蛋白在质体组和有丝分裂组的融合遗传特征中起关键作用。我们的结果提供了卷柏科细胞器基因组的独特进化模式，以及它们趋同进化的证据。