Comparative analysis of mitochondrial genomes between the hau cytoplasmic male sterility (CMS) line and its iso-nuclear maintainer line in Brassica juncea to reveal the origin of the CMS-associated gene orf288

Abstract

BackgroundCytoplasmic male sterility (CMS) is not only important for exploiting heterosis in crop plants, but also as a model for investigating nuclear-cytoplasmic interaction. CMS may be caused by mutations, rearrangement or recombination in the mitochondrial genome. Understanding the mitochondrial genome is often the first and key step in unraveling the molecular and genetic basis of CMS in plants. Comparative analysis of the mitochondrial genome of the hau CMS line and its maintainer line in B. juneca (Brassica juncea) may help show the origin of the CMS-associated gene orf288.ResultsThrough next-generation sequencing, the B. juncea hau CMS mitochondrial genome was assembled into a single, circular-mapping molecule that is 247,903 bp in size and 45.08% in GC content. In addition to the CMS associated gene orf288, the genome contains 35 protein-encoding genes, 3 rRNAs, 25 tRNA genes and 29 ORFs of unknown function. The mitochondrial genome sizes of the maintainer line and another normal type line “J163-4” are both 219,863 bp and with GC content at 45.23%. The maintainer line has 36 genes with protein products, 3 rRNAs, 22 tRNA genes and 31 unidentified ORFs. Comparative analysis the mitochondrial genomes of the hau CMS line and its maintainer line allowed us to develop specific markers to separate the two lines at the seedling stage. We also confirmed that different mitotypes coexist substoichiometrically in hau CMS lines and its maintainer lines in B. juncea. The number of repeats larger than 100 bp in the hau CMS line (16 repeats) are nearly twice of those found in the maintainer line (9 repeats). Phylogenetic analysis of the CMS-associated gene orf288 and four other homologous sequences in Brassicaceae show that orf288 was clearly different from orf263 in Brassica tournefortii despite of strong similarity.ConclusionThe hau CMS mitochondrial genome was highly rearranged when compared with its iso-nuclear maintainer line mitochondrial genome. This study may be useful for studying the mechanism of natural CMS in B. juncea, performing comparative analysis on sequenced mitochondrial genomes in Brassicas, and uncovering the origin of the hau CMS mitotype and structural and evolutionary differences between different mitotypes.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-322) contains supplementary material, which is available to authorized users.

A Comparative Analysis of the atp8 Gene Between a Cytoplasmic Male Sterile Line and Its Maintainer and Further Development of a Molecular Marker Specific to Male Sterile Cytoplasm in Kenaf (Hibiscus cannabinus L.)

“…The biochemical mechanism of CMS had been studied in many plants (Peng et al 2009;Heng et al 2014;Jo et al 2014). Some studies had been performed to analyze the differences of organizational and structure in mtDNA genome between cytoplasmic male sterile line and male fertile lines with RFLP (Chen and Zhou 2011a, b) in kenaf.…”

Plant Mitochondrial Genome Evolution and Cytoplasmic Male Sterility

“…A similar configuration has been observed in Brassica oleracea, which displays a tripartite structure consisting of a 220 kb master circle that is also split into two subgenomic circles (170 and 50 kb each) via homologous recombination of repeated sequences (Grewe et al, 2014). Observations in the hau CMS line of Brassica and its maintainer line in B. juncea suggest not only a multipartite structure, but also the substoichiometric coexistence of different mitotypes (Heng et al, 2014). Multichromosomal mitochondrial genomes have been identified in four independent angiosperm lineages (Alverson et al, 2011a;Sloan et al, 2012a;Rice et al, 2013;Sanchez-Puerta et al, 2017).…”

“…In Brassica juncea, for example, comparison between the hau CMS line and its maintainer line revealed that repeats in the CMS line were typically twice the size as those in the maintainer line (for repeats >100 bp). Furthermore, the presence of three large repeats downstream from the hau CMSassociated gene orf288 has been implicated in the formation of this chimera (Heng et al, 2014). Comparative analysis between the mitogenomes of CMS and male-fertile lines of pepper (Capsicum annuum L.) showed that CMS candidate genes orf507 and catp6-2 were proximal to edges of highly rearranged CMS-specific DNA regions, whose evolution may be the result of nearby intermediate or large-sized repeats (Jo et al, 2014).…”

Detection of differentially methylated regions of irradiated fig tree selections

“…Since the first mitochondrial genome was sequenced in Arabidopsis (Unseld et al, 1997), a huge number of mitochondrial genomes have been sequenced in angiosperms, such as beetroot (Kubo et al, 2000), rice (Notsu et al, 2002), rapeseed (Handa, 2003), corn (Clifton et al, 2004), wheat (Ogihara et al, 2005), Indian mustard (Heng et al, 2014) and arugula (Wang et al, 2014).…”