Distinctive evolutionary pattern of organelle genomes linked to the nuclear genome in Selaginellaceae
Distinctive evolutionary pattern of organelle genomes linked to the nuclear genome in Selaginellaceae
复制标题
卷柏科细胞器基因组与核基因组相关的独特进化模式
DOI：
10.1111/tpj.15028
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发表时间：
2020-11-17
期刊：
影响因子：
7.2
通讯作者：
Xiang, Qiao-Ping
中科院分区：
文献类型：
--
作者：
Kang, Jong-Soo;Zhang, Hong-Rui;Xiang, Qiao-Ping
质体和线粒体是储存遗传信息的内共生细胞器。这些细胞器的基因组通常在基因组结构和遗传内容方面表现出截然不同的模式。然而，它们在卷柏科中具有相似的遗传特征，并且对导致平行进化的原因知之甚少。在这里，我们记录了多部质体基因组（质体组）和高度分化的线粒体基因组（有丝分裂基因组）从穗藓通过结合短读和长读获得。188 kb的多部质体体在主基因组构象中有三个核糖体操纵子拷贝，形成由110和78 kb亚基因组组成的备选亚基因组构象。长时间读取的数据表明，这两种不同的基因组构象在日本卷柏的质体中几乎相同的比例存在。nipponica有丝分裂基因组被组装成27个contigs，总大小为110 kb。所有的contigs在两端都含有直接排列的重复序列，这就引入了多重构象。我们的研究结果表明，质体和有丝分裂基因组具有高tRNA损失，gc偏向核苷酸，高取代率和复杂的组织。对核编码的细胞器DNA复制、重组和修复蛋白的研究表明，卷柏科植物中丢失了一些单目标蛋白，特别是质体靶向重组酶A1；相反，双靶蛋白保持完整。根据报道的重组酶A1的功能，我们提出在重组过程中，刺藓的质体往往不能配对同源序列，双靶蛋白在质体和有丝分裂基因组的趋同遗传特征中起关键作用。我们的研究结果提供了卷柏科细胞器基因组的独特进化模式和趋同进化的证据。
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.