Comparative analyses of three complete Primula mitogenomes with insights into mitogenome size variation in Ericales

Abstract

AbstractBackgroundAlthough knowledge of the sizes, contents, and forms of plant mitochondrial genomes (mitogenomes) is increasing, little is known about the mechanisms underlying their structural diversity. Evolutionary information on the mitogenomes ofPrimula, an important ornamental taxon, is more limited than the information on their nuclear and plastid counterparts, which has hindered the comprehensive understanding ofPrimulamitogenomic diversity and evolution. The present study reported and compared threePrimulamitogenomes and discussed the size expansion of mitogenomes in Ericales.ResultsMitogenome master circles were sequenced and successfully assembled for threePrimulataxa and were compared with publicly available Ericales mitogenomes. The three mitogenomes contained similar gene contents and varied primarily in their structures. ThePrimulamitogenomes possessed relatively high nucleotide diversity among all examined plant lineages. In addition, high nucleotide diversity was found amongPrimulaspecies between the Mediterranean and Himalaya-Hengduan Mountains. Most predicted RNA editing sites appeared in the second amino acid codon, increasing the hydrophobic character of the protein. An early stop inatp6caused by RNA editing was conserved across all examined Ericales species. The interfamilial relationships within Ericales and interspecific relationships withinPrimulacould be well resolved based on mitochondrial data. Transfer of the two longest mitochondrial plastid sequences (MTPTs) occurred before the divergence ofPrimulaand its close relatives, and multiple independent transfers could also occur in a single MTPT sequence. Foreign sequence [MTPTs and mitochondrial nuclear DNA sequences (NUMTs)] uptake and repeats were to some extent associated with changes in Ericales mitogenome size, although none of these relationships were significant overall.ConclusionsThe present study revealed relatively conserved gene contents, gene clusters, RNA editing, and MTPTs but considerable structural variation inPrimulamitogenomes. Relatively high nucleotide diversity was found in thePrimulamitogenomes. In addition, mitogenomic genes, collinear gene clusters, and locally collinear blocks (LCBs) all showed phylogenetic signals. The evolutionary history of MTPTs inPrimulawas complicated, even in a single MTPT sequence. Various reasons for the size variation observed in Ericales mitogenomes were found.