A possible breakage of linkage disequilibrium between mitochondrial and chloroplast genomes during Emmer and Dinkel wheat evolution

Abstract

In wheat (Triticum) and Aegilops, chloroplast and mitochondrial genomes have been studied for over three decades to clarify the phylogenetic relationships among species, and most of the maternal lineages of polyploid species have been clarified. Mitochondrial genomes of Emmer (tetraploid with nuclear genome AABB) and Dinkel (hexaploid with AABBDD) wheat are classified into two different types, VIIa and VIIb, by the presence-absence of the third largest HindIII fragment (named H3) in the mitochondrial DNA. Although the mitochondrial genome in the genera often provides useful information to clarify the phylogenetic relationship among closely related species, the phylogenetic significance of this dimorphism has yet not been clarified. In this study, to facilitate analysis using a large number of accessions, a sequence characterized amplified region (SCAR) marker that distinguishes the type VIIb mitochondrial genome from type VIIa was first developed. Mitochondrial genome type was determined for each of 30 accessions of wild and cultivated Emmer wheat and 25 accessions of Dinkel wheat. The mitochondrial genome type for each accession was compared with the plastogroup that had been determined using chloroplast microsatellite markers. Unexpectedly, the distribution of mitochondrial genome type was not in accordance with that of the plastogroups, suggesting occasional paternal leakage of either the mitochondrial or chloroplast genome during speciation and differentiation of Emmer and Dinkel wheat. An alternative possibility that substoichiometric shifting is involved in the observed dimorphism of the mitochondrial genome is also discussed.

Complete mitochondrial genomes of three Mangifera species, their genomic structure and gene transfer from chloroplast genomes

“…There were several inconsistencies between the chloroplast and mitochondrial phylogenetic trees regarding the phylogenetic topology [ 32 ]. Differential inheritance of organelles in the same cytoplasm can disrupt the linkage disequilibrium between mitochondrion and chloroplast [ 53 , 54 ], and if this occurs, phylogenetic reconstruction of the two organelle genomes could conflict. In addition, limited sampling, incomplete lineage classification, and differences in the evolutionary rates could account for the conflicting phylogenetic reconstruction of the two organelle genomes [ 55 ].…”

Large-scale phylogenomics reveals ancient introgression in Asian Hepatica and new insights into the origin of the insular endemic Hepatica maxima

“…5), indicating that Asian Hepatica may have experienced complicated evolutionary events. For example, the conflict between two organellar genomes suggests differential inheritance of organelles in the Asian Hepatica lineages, which resulted in the disruption of linkage disequilibrium (LD) between plastids and mitochondria 41 . The presence of CMS in gynodioecious systems can select for the paternal leakage of their mitochondrial genomes 21 .…”

Phylogenetic relationships in Leymus (Triticeae; Poaceae): Evidence from chloroplast trnH‐psbA and mitochondrial coxII intron sequences

“…There are two possible explanations for the occurrence of genealogical conflict. First, although mitochondrial DNA was considered to be inherited paternally in some alloplasmic Triticeae plants (Tsukamoto et al, ), it has been pointed out that the maternal mitochondrial genome had never been replaced completely by a paternal one, even under artificial conditions such as repeated backcrosses between Triticeae plants (Tsujimura et al, ). If parental mitochondrial inheritance occurred in Leymus , the Ns lineages indicated as maternal chloroplast donors should be the parental mitochondrial in Eurasian Leymus (except L. komarovii and L. coreanus ), and the Xm lineages (closely related to Agropyron , Pseudoroegneria , and Eremopyrum ) should be suggested as parental mitochondrial in American Leymus species, L. komarovii and L. coreanus .…”