Department of Biology, New Mexico State University.
Department of Biology, Hobart and William Smith Colleges, Geneva, New York.
Genome Biol Evol. 2018 Sep 1;10(9):2501-2517. doi: 10.1093/gbe/evy179.
Reconstructions of vascular plant mitochondrial genomes (mt-genomes) are notoriously complicated by rampant recombination that has resulted in comparatively few plant mt-genomes being available. The dearth of plant mitochondrial resources has limited our understanding of mt-genome structural diversity, complex patterns of RNA editing, and the origins of novel mt-genome elements. Here, we use an efficient long read (PacBio) iterative assembly pipeline to generate mt-genome assemblies for Leucaena trichandra (Leguminosae: Caesalpinioideae: mimosoid clade), providing the first assessment of non-papilionoid legume mt-genome content and structure to date. The efficiency of the assembly approach facilitated the exploration of alternative structures that are common place among plant mitochondrial genomes. A compact version (729 kbp) of the recovered assemblies was used to investigate sources of mt-genome size variation among legumes and mt-genome sequence similarity to the legume associated root holoparasite Lophophytum. The genome and an associated suite of transcriptome data from select species of Leucaena permitted an in-depth exploration of RNA editing in a diverse clade of closely related species that includes hybrid lineages. RNA editing in the allotetraploid, Leucaena leucocephala, is consistent with co-option of nearly equal maternal and paternal C-to-U edit components, generating novel combinations of RNA edited sites. A preliminary investigation of L. leucocephala C-to-U edit frequencies identified the potential for a hybrid to generate unique pools of alleles from parental variation through edit frequencies shared with one parental lineage, those intermediate between parents, and transgressive patterns.
植物线粒体基因组（mt-genomes）的重建由于猖獗的重组而变得异常复杂，导致可用的植物 mt-genomes 相对较少。植物线粒体资源的匮乏限制了我们对 mt 基因组结构多样性、复杂的 RNA 编辑模式以及新的 mt 基因组元件起源的理解。在这里，我们使用高效的长读（PacBio）迭代组装管道为 Leucaena trichandra（豆科：金虎尾科：含羞草亚科）生成 mt 基因组组装，这是迄今为止对非豆科豆科 mt 基因组内容和结构的首次评估。组装方法的效率促进了对替代结构的探索，这些替代结构在植物线粒体基因组中很常见。从回收的组装体中得到一个紧凑的版本（729 kbp），用于研究豆科植物 mt 基因组大小变异的来源和与豆科相关的根全寄生植物 Lophophytum 的 mt 基因组序列相似性。从 Leucaena 的选定物种中获得的基因组和相关转录组数据套件允许在包括杂种谱系在内的密切相关的多样化物种中深入研究 RNA 编辑。在异源四倍体 Leucaena leucocephala 中的 RNA 编辑与几乎相等的母本和父本 C 到 U 编辑成分的共选择一致，产生了新的 RNA 编辑位点组合。对 L. leucocephala C 到 U 编辑频率的初步研究表明，杂种有可能通过与一个亲本谱系共享的编辑频率、介于父母之间的编辑频率以及过渡模式，从亲本变异中产生独特的等位基因池。
