PacBio-Based Mitochondrial Genome Assembly of Leucaena trichandra (Leguminosae) and an Intrageneric Assessment of Mitochondrial RNA Editing. (20th August 2018)

• Record Type: Journal Article
• Authors: Kovar, Lynsey; Nageswara-Rao, Madhugiri; Ortega-Rodriguez, Sealtiel; Dugas, Diana V; Straub, Shannon; Cronn, Richard; Strickler, Susan R; Hughes, Colin E; Hanley, Kathryn A; Rodriguez, Deyra N; Langhorst, Bradley W; Dimalanta, Eileen T; Bailey, C Donovan
• Editors: Lavrov, Dennis
• Is Part Of: Genome biology and evolution. Volume 10:Number 9(2018:Sep.)
• Page Start: 2501
• Page End: 2517
• Publication Date: 2018-08-20
• Subjects: Caesalpinoideae -- mimosoid clade -- iterative assembler -- PacBio -- transgressive -- hybrid; Genomics -- Periodicals; Genes -- Periodicals; 572.8605
• DOI: 10.1093/gbe/evy179
• Languages: English
• ISSNs: 1759-6653

Abstract

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.