Abstract

The sequences and genomic structures of plant mitochondrial (mt) genomes provide unique material for phylogenetic studies. The nature of uniparental inheritance renders an advantage when utilizing mt genomes for determining the parental sources of hybridized taxa. In this study, a concatenated matrix of mt genes was used to infer the phylogenetic relationships of six cultivated Brassica taxa and explore the maternal origins of three allotetraploids. The well-resolved sister relationships between two pairs of diploid and allotetraploid taxa suggest that Brassica carinata (car) possessed a maternal origin from Brassica nigra, while Brassica juncea (jun) was maternally derived from Brassica rapa (cam). Another allotetraploid taxon, Brassica napus (cv. Wester) may have been maternally derived from the common ancestor of B. rapa and Brassica oleracea (ole), and/or have undergone (an) extra hybridization event(s) along its evolutionary history. The characteristics of Brassica mt genomic structures also supported the phylogenetic results. Sinapis arvensis was nested inside the Brassica species, sister to the B. nigra–B. carinata lineage, and possessed an mt genome structure that mostly resembled B. nigra. Collectively, the evidence supported a systematic revision that placed S. arvensis within Brassica. Finally, ancestral mt genomes at each evolutionary node of Brassica were reconstructed, and the detailed and dynamic evolution of Brassica mt genomes was successfully reproduced. The mt genome of B. nigra structurally resembled that of the Brassica ancestor the most, with only one reversion of a block, and the Brassica oleracea underwent the most drastic changes. These findings suggested that repeat-mediated recombinations were largely responsible for the observed structural variations in the evolutionary history of Brassica mt genomes.

Highlights

  • Green plants possess three independent genetic systems that are encoded by the genomes in nuclei, chloroplasts, and mitochondrion

  • Since all of the allotetraploids are supposed to cluster with their maternal parents, it is clear that B. juncea has a maternal origin of B. rapa, and the maternal origin of B. carinata is B. nigra

  • The results derived from Brassica mt genomes largely agree with those of previous studies based on cp or mt genomes (Palmer et al, 1983; Allender and King, 2010; Yang et al, 2016b; Li et al, 2017; Kim et al, 2018) from which the maternal origins of two allotetraploids, B. juncea and B. carinata, were determined

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Summary

Introduction

Green plants possess three independent genetic systems that are encoded by the genomes in nuclei, chloroplasts, and mitochondrion. The nuclear (nu) genome is biparentally inherited between generations, while the chloroplast (cp) and mitochondrial (mt) genomes, referred to as organellar genomes, are uniparentally inherited. Mitochondrial Phylogenomics and Paleogenomics of Brassica organellar genomes are overwhelmingly maternally inherited, except in some gymnosperm lineages where these genomes are paternally inherited, including Pinaceae, Cupressaceae, and Taxodiaceae (Mogensen, 1996; Jansen and Ruhlman, 2012; Worth et al, 2014). The cp genome has a much more conserved structure and cannot be applied for such analyses (Jansen and Ruhlman, 2012)

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