Data_Sheet_1_Mitochondrial Phylogenomics of Fagales Provides Insights Into Plant Mitogenome Mosaic Evolution.PDF

Fagales are an order of woody plants and comprise more than 1,100 species, most of which produce economically important timbers, nuts, and fruits. Their nuclear and plastid genomes are well-sequenced and provided valuable resources to study their phylogeny, breeding, resistance, etc. However, little is known about the mitochondrial genomes (mitogenomes), which hinder a full understanding of their genome evolution. In this study, we assembled complete mitogenomes of 23 species, covering five of the seven families of Fagales. These mitogenomes had similar gene sets but varied 2.4 times in size. The mitochondrial genes were highly conserved, and their capacity in phylogeny was challenging. The mitogenomic structure was extremely dynamic, and synteny among species was poor. Further analyses of the Fagales mitogenomes revealed extremely mosaic characteristics, with horizontal transfer (HGT)-like sequences from almost all seed plant taxa and even mitoviruses. The largest mitogenome, Carpinus cordata, did not have large amounts of specific sequences but instead contained a high proportion of sequences homologous to other Fagales. Independent and unequal transfers of third-party DNA, including nuclear genome and other resources, may partially account for the HGT-like fragments and unbalanced size expansions observed in Fagales mitogenomes. Supporting this, a mitochondrial plasmid-like of nuclear origin was found in Carpinus. Overall, we deciphered the last genetic materials of Fagales, and our large-scale analyses provide new insights into plant mitogenome evolution and size variation.

桦木纲（Fagales）为木本植物之一种，物种逾千一百，其中多数产出经济价值显著的木材、坚果与果实。其核基因组与质体基因组均已得到精细测序，为研究其系统发育、育种、抗性等提供了宝贵资源。然而，关于线粒体基因组（线粒体基因组），认知尚浅，这阻碍了对基因组进化的全面理解。在本研究中，我们对23种物种的线粒体基因组进行了组装，涵盖了桦木纲七大家族中的五家。这些线粒体基因组基因集相似，但大小相差达2.4倍。线粒体基因高度保守，其在系统发育中的应用极具挑战性。线粒体基因组结构极为动态，物种间同源性较差。对桦木纲线粒体基因组的进一步分析揭示了极为复杂的镶嵌特征，包括几乎所有种子植物类群乃至线粒体病毒的横向转移（HGT）类序列。最大的线粒体基因组——Carpinus cordata，不含有大量特异序列，反而含有大量与其它桦木纲同源的序列。第三方DNA的独立且不等量转移，包括核基因组及其他资源，可能部分解释了桦木纲线粒体基因组中观察到的HGT类片段和不平衡大小扩张。支持此观点的是，在Carpinus中发现了一种核起源的线粒体质粒。总体而言，我们解码了桦木纲的最后遗传物质，我们的大规模分析为植物线粒体基因组进化与大小变异提供了新的洞见。