Complete mitochondrial genome sequence and identification of a candidate gene responsible for cytoplasmic male sterility in radish (Raphanus sativus L.) containing DCGMS cytoplasm

Abstract

A novel cytoplasmic male sterility (CMS) conferred by Dongbu cytoplasmic and genic male-sterility (DCGMS) cytoplasm and its restorer-of-fertility gene (Rfd1) was previously reported in radish (Raphanus sativus L.). Its inheritance of fertility restoration and profiles of mitochondrial DNA (mtDNA)-based molecular markers were reported to be different from those of Ogura CMS, the first reported CMS in radish. The complete mitochondrial genome sequence (239,186 bp; GenBank accession No. KC193578) of DCGMS mitotype is reported in this study. Thirty-four protein-coding genes and three ribosomal RNA genes were identified. Comparative analysis of a mitochondrial genome sequence of DCGMS and previously reported complete sequences of normal and Ogura CMS mitotypes revealed various recombined structures of seventeen syntenic sequence blocks. Short-repeat sequences were identified in almost all junctions between syntenic sequence blocks. Phylogenetic analysis of three radish mitotypes showed that DCGMS was more closely related to the normal mitotype than to the Ogura mitotype. A single 1,551-bp unique region was identified in DCGMS mtDNA sequences and a novel chimeric gene, designated orf463, consisting of 128-bp partial sequences of cox1 gene and 1,261-bp unidentified sequences were found in the unique region. No other genes with a chimeric structure, a major feature of most characterized CMS-associated genes in other plant species, were found in rearranged junctions of syntenic sequence blocks. Like other known CMS-associated mitochondrial genes, the predicted gene product of orf463 contained 12 transmembrane domains. Thus, this gene product might be integrated into the mitochondrial membrane. In total, the results indicate that orf463 is likely to be a casual factor for CMS induction in radish containing the DCGMS cytoplasm.

The mitochondrial genome of an asymmetrically cell-fused rapeseed, <i>Brassica napus</i>, containing a radish-derived cytoplasmic male sterility-associated gene

“…The inverted region has a pair of 442bp inverted repeats at its ends (100% identity between the inverted repeat sequences), which are the secondlargest pair of repeats in the genome (the largest repeat is 9,731 bp). Park et al (2013) reported that an Ogura-type CMS radish has multiple master-circle genome structures with a difference of a 79,976-bp inversion with a pair of 311-bp inverted repeats at the ends; however, this inversion is distinct from that reported here.…”

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

“…We also comparatively analyzed the mitochondrial genome of hau CMS with the mitochondrial genomes of nap [AP006444], cam [JF920285], jun [JF920288], ole [JF920286], car [JF920287], polima [FR715249] and ogura [AB694744] in Brassicas [17–20]. A phylogenetic guide tree (Figure 7) and locally collinear blocks (Additional file 6) relating these eight sequenced mitochondrial genomes were calculated by using Neighbor Joining of the Mauve alignment system.…”

“…Since the first plant mitochondrial genome sequencing in Arabidopsis [3], a large number of mitochondrial genomes have been sequenced in angiosperm plants [4–10], especially in those that contain CMS cytoplasm. CMS-associated mitochondrial genome of crop species reported to date include Beta vulgaris [11], Oryza sativa [12–14], Triticumae stivum [15], Zea mays [16], Brassica napus [17, 18], Raphanus sativus [19, 20]. In this study, the mitochondrial genome of hau CMS line, its maintainer line and the normal type line “J163-4” were fully sequenced and assembled into a master circle.…”

Plant Mitochondrial Genome Evolution and Cytoplasmic Male Sterility

“…Novel and chimeric mitochondrial sequences are a frequent result of this recombination (Wise et al, 1987;Kennell and Pring, 1989;Wen and Chase, 1999;Gallagher et al, 2002;Okazaki et al, 2013;Yamagishi and Bhat, 2014;Tang et al, 2017), in which recombination sometimes leads to the creation of transcripts that interfere with normal male gametophyte development (Kitazaki and Kubo, 2010) via the generation of toxic and/or disruptive transmembrane proteins (Korth et al, 1991;Kim et al, 2007;Wan et al, 2007;Zhang et al, 2007;Yang et al, 2009;Gulyas et al, 2010;Jing et al, 2012;Flores-Renteria et al, 2013;Ji et al, 2013;Luo et al, 2013;Okazaki et al, 2013;Park et al, 2013;Hu et al, 2014). Surprisingly, such genes are not only abundant in many fertile plants, such as Arabidopsis thaliana Unseld et al, 1997), Beta vulgaris (Kubo et al, 2000), Oryza sativa (Notsu et al, 2002), Brassica napus (Handa, 2003), Zea mays (Clifton et al, 2004), Triticum aestivum (Ogihara et al, 2005), and Nicotiana tabacum (Sugiyama et al, 2005), but are also constitutively expressed.…”