PacBio-Based Mitochondrial Genome Assembly of Leucaena trichandra (Leguminosae) and an Intrageneric Assessment of Mitochondrial RNA Editing

Abstract

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.

Assembly and Analysis of the Complete Mitochondrial Genome of Capsella bursa-pastoris

“…Plant mitochondrial DNA (mtDNA) contains many repeats as well as inserts of nuclear and chloroplast origin, which makes mitogenome assembly difficult [8]. However, the development of long-read third-generation sequencing technologies (PacBio in particular) improves and simplifies assembly of such complex molecules, greatly facilitating the research of plant mitogenomes [9][10][11][12][13].…”

Organellar Genome Variation and Genetic Diversity of Chinese Pyropia yezoensis

“…This technology has been successfully applied to a wide range of experiments including whole-genome sequencing, targeted sequencing, RNA sequencing, and epigenetics (Filichkin et al, 2018;Sun et al, 2018;Suzuki et al, 2018;Zhou et al, 2018). PacBio has been successfully used in many mitochondrial and chloroplast genomic projects (Chen et al, 2015;Xiang et al, 2016;Peccoud et al, 2017;Kovar et al, 2018). However, errors in reference genomes, which could be carried over by reference-based assembly approaches, misled subsequent studies of mutation detection and molecular evolution (Sloan et al, 2018).…”

Assembly and comparative analyses of the mitochondrial genome of Castanospermum australe (Papilionoideae, Leguminosae)

“…Repeats are likely to mediate intramolecular recombination within mitochondrial genomes, leading to their oftencomplex genome structure (Palmer and Shields 1984;Alverson et al 2011b;Cole et al 2018;Kovar et al 2018). Such complexity often precludes confident mitochondrial genome assemblage using short inserts and reads, leading to the availability of few angiosperm mitochondrial genomes, including in Papilionoideae.…”

“…Plant mitochondrial genomes have a high incidence of C-to-U RNA editing (Hiesel et al 1989;Takenaka et al 2008;Alverson et al 2010;Suzuki et al 2013), with~200À800 editing sites in the protein-coding mitochondrial genes of most angiosperms (Mower 2008;Sloan et al 2010;Richardson et al 2013;Guo et al 2016). However, the incidence of RNA editing across lineages of Papilionoideae is largely unknown (Kovar et al 2018;Shi et al 2018). Within C. australe, 487 C to U RNA editing sites were predicted among the 30 protein-coding genes (Table S2, available as Supplementary material to this paper).…”