Journal
GENOME BIOLOGY AND EVOLUTION
Volume 10, Issue 9, Pages 2501-2517Publisher
OXFORD UNIV PRESS
DOI: 10.1093/gbe/evy179
Keywords
Caesalpinoideae; mimosoid clade; iterative assembler; PacBio; transgressive; hybrid
Categories
Funding
- National Science Foundation [1238731]
- Swiss National Science Foundation [31003A_135522]
- NMSU Howard Hughes Medical Institute undergraduate research program [52008103]
- NMSU undergraduate National Institutes of Health Maximizing Access to Research Careers (MARC) program [GMO7667-39S1]
- Swiss National Science Foundation (SNF) [31003A_135522] Funding Source: Swiss National Science Foundation (SNF)
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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.
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