Prospects on the evolutionary mitogenomics of plants: A case study on the olive family (Oleaceae)

Abstract

The mitogenome is rarely used to reconstruct the evolutionary history of plants, contrary to nuclear and plastid markers. Here, we evaluate the usefulness of mitochondrial DNA for molecular evolutionary studies in Oleaceae, in which cases of cytoplasmic male sterility (CMS) and of potentially contrasted organelle inheritance are known. We compare the diversity and the evolution of mitochondrial and chloroplast genomes by focusing on the olive complex and related genera. Using high-throughput techniques, we reconstructed complete mitogenomes (ca. 0.7 Mb) and plastomes (ca. 156 kb) for six olive accessions and one Chionanthus. A highly variable organization of mitogenomes was observed at the species level. In olive, two specific chimeric genes were identified in the mitogenome of lineage E3 and may be involved in CMS. Plastid-derived regions (mtpt) were observed in all reconstructed mitogenomes. Through phylogenetic reconstruction, we demonstrate that multiple integrations of mtpt regions have occurred in Oleaceae, but mtpt regions shared by all members of the olive complex derive from a common ancestor. We then assembled 52 conserved mitochondrial gene regions and complete plastomes of ten additional accessions belonging to tribes Oleeae, Fontanesieae and Forsythieae. Phylogenetic congruence between topologies based on mitochondrial regions and plastomes suggests a strong disequilibrium linkage between both organellar genomes. Finally, while phylogenetic reconstruction based on plastomes fails to resolve the evolutionary history of maternal olive lineages in the Mediterranean area, their phylogenetic relationships were successfully resolved with complete mitogenomes. Overall, our study demonstrates the great potential of using mitochondrial DNA in plant phylogeographic and metagenomic studies.

Genomic evidence for recurrent genetic admixture during domestication mediterranean olive trees (Olea europaea)

“…In addition, we assembled the plastid and mitochondrial genomes of the cultivar Farga, which were not provided as separate assemblies in the previous release (22) (see materials and methods). The final assembly of the plastid genome comprised 155,658 base pairs (bp) (Additional file 2: Table S3), in agreement with previously reported olive plastid sequences, which range from 155,531 to 155,896 bp (16,38,39). We annotated 130 genes out of the 130-file 2: Table S3) (16,38), of which 85 are protein coding genes, 37 are transfer RNAs, and eight are ribosomal RNAs.…”

“…We annotated 130 genes out of the 130-file 2: Table S3) (16,38), of which 85 are protein coding genes, 37 are transfer RNAs, and eight are ribosomal RNAs. The final assembly of the mitochondrial genome has a size of 755,572 bp (Additional file 2: Table S3), which is similar to that of previously sequenced wild olive mitochondrial genomes (710,737 -769,995 bp) (39). The coding regions in the olive mitochondrion comprise 46 protein-coding genes, 3 ribosomal RNA genes, and 26 transfer RNA genes (Additional file 1: Fig.…”

Siberian larch (Larix sibirica Ledeb.) mitochondrial genome assembled using both short and long nucleotide sequence reads is currently the largest known mitogenome

“…The utility of mitogenome sequences as a source of genetic markers has been extensively documented and is thus unquestionable [28,29]. Many mitochondrial genes such as atp1, cob, cox1, cox2, and cox3 are widely used to resolve phylogenetic relationships between lineages, conduct biodiversity analyses and construct phylogeographic and evolutionary history of species.…”

Assembly of a Complete Mitogenome of Chrysanthemum nankingense Using Oxford Nanopore Long Reads and the Diversity and Evolution of Asteraceae Mitogenomes

“…Compared with plastomes and nuclear genes, mitogenomes are seldom used to reconstruct phylogenies partly due to the slowness in nucleotide substitution rate and the difficulty in complete assembly and direct alignment [ 3 , 62 ]. Here, we identified the LCBs of the mitochondrial contigs from 28 Asteraceae species and one outgroup based on the assembly method mentioned above and performed LCB alignment, which provided an approach for aligning the dynamic mitogenomes.…”

“…Accessed on 21 October 2018). The genomic information from the mitogenomes of higher plants has been extensively used for the investigation of genomic evolution related to the gain/loss of genetic materials [ 2 ], phylogenetic relationships [ 3 ], nucleo-cytoplasmic interactions (e.g., cytoplasmic male sterility) [ 4 ], RNA editing [ 5 ], and genomic recombination and structural rearrangements [ 6 ]. However, the information of the diversity and evolution of mitogenomes within large angiosperm lineages remains limited.…”