A Lineage-Specific Paralog of Oma1 Evolved into a Gene Family from Which a Suppressor of Male Sterility-Inducing Mitochondria Emerged in Plants

Abstract

Cytoplasmic male sterility (MS) in plants is caused by MS-inducing mitochondria, which have emerged frequently during plant evolution. Nuclear restorer-of-fertility (Rf)genes can suppress their cognate MS-inducing mitochondria. Whereas many Rfs encode a class of RNA-binding protein, the sugar beet (Caryophyllales) Rf encodes a protein resembling Oma1, which is involved in the quality control of mitochondria. In this study, we investigated the molecular evolution of Oma1 homologs in plants. We analyzed 37 plant genomes and concluded that a single copy is the ancestral state in Caryophyllales. Among the sugar beet Oma1 homologs, the orthologous copy is located in a syntenic region that is preserved in Arabidopsis thaliana. The sugar beet Rf is a complex locus consisting of a small Oma1 homolog family (RF-Oma1 family) unique to sugar beet. The gene arrangement in the vicinity of the locus is seen in some but not all Caryophyllalean plants and is absent from Ar. thaliana. This suggests a segmental duplication rather than a whole-genome duplication as the mechanism of RF-Oma1 evolution. Of thirty-seven positively selected codons in RF-Oma1, twenty-six of these sites are located in predicted transmembrane helices. Phylogenetic network analysis indicated that homologous recombination among the RF-Oma1 members played an important role to generate protein activity related to suppression. Together, our data illustrate how an evolutionarily young Rf has emerged from a lineage-specific paralog. Interestingly, several evolutionary features are shared with the RNA-binding protein type Rfs. Hence, the evolution of the sugar beet Rf is representative of Rf evolution in general.

Keywords: restorer-of-fertility; cytoplasmic male sterility; nuclear–mitochondrial interaction; plant mitochondria; positive selection; sugar beet.

Fig. 1.

Phylogeny of the flowering plant Oma1 genes, inferred from their amino acid sequences. Trees were drawn using the neighbor-joining (A) and maximum-likelihood (B) methods. Scale bars indicate evolutionary distances. Superrosids, superasterids, monocots, and basal magnoliophyta are indicated by R, A, M, and BM, respectively, in parentheses. Bootstrap values are shown near the nodes. Abbreviations of scientific names are: Ah, Amaranthus hypochondriacus; Al, Arabidopsis lyrata; At, Arabidopsis thaliana; Br, Brassica rapa; Bv, Beta vulgaris; Ca, Capsicum annuum; Cc, Cynara cardunculus; Cl, Citrullus lanatus; Cm, Cucumis melo; Cp, Carica papaya; Cq, Chenopodium quinoa; Cr, Capsella rubella; Cs, Citrus sinensis; Eg, Eucalyptus grandis; Fv, Fragaria vesca; Gm, Glycine max; Gr, Gossypium raimondii; Ha, Helianthus annuus; Kf, Kalanchoe fedtschenkoi; Ls, Lactuca sativa; Md, Malus domestica; Me, Manihot esculenta; Mp, Marchantia polymorpha; Mt, Medicago truncatula; Os, Oryza sativa; Ppe, Prunus persica; Pt, Populus trichocarpa; Rc, Ricinus communis; Si, Sesamum indicum; Sl, Solanum lycopersicum; So, Spinacia oleracea; St, Solanum tuberosum; Tc, Theobroma cacao; Vv, Vitis vinifera; Zm, Zea mays.

Fig. 2.

Microsynteny of chromosomal regions associated with Oma1 homologs. Annotated genes are shown as horizontal arrows. Genes homologous to the B. vulgaris queries are linked by thin lines. A 50 kbp scale bar is shown on the bottom right. The Oma1 homolog in each segment is shown as a red arrow. Note that the Amaranthus Scaffold_7 has no Oma1 homolog. The chromosomal regions with NCBI accession numbers are: Arabidopsis, A. thaliana (NC_003076, from 20979520 to 21080594); Beta, B. vulgaris (NW_017567367, from 71170 to 557770); Spinacia, S. oleracea (NW_018931419, from 994825 to 1414068); Chenopodium NW_018744460, C. quinoa (NW_018744460, from 1428475 to 1649963); Chenopodium NW_018742987, C. quinoa (NW_018744460, from 2410957 to 2638297); Amaranthus Scaffold_7, Amaranthus hypochondriacus (Scaffold_7, from 22668158 to 23111136); and Amaranthus Scaffold_13, A. hypochondriacus (Scaffold_13, from 4279078 to 4673615).

Fig. 3.

Microsynteny of chromosomal segments associated with the RF-Oma1 genes. Annotated genes within the segments are shown by horizontal arrows. Genes homologous to the B. vulgaris queries are linked by thin lines. A 20 kbp scale bar is shown at the bottom right. The RF-Oma1 gene is shown as a purple arrow. We refer to this copy as orf20_KWS2320. An asterisk denotes the S. oleracea genes LOC110796815, LOC110796811, and LOC110797175 (from left to right) that are annotated as abscisic stress-ripening protein 3-like, long noncoding (lnc) RNA, and lysine-rich arabinogalactan protein 19-like, respectively. A plus sign denotes C. quinoa LOC110725390, which is annotated as an lncRNA but is not related to S. oleracea LOC110796811. The chromosomal regions with NCBI accession numbers are: Beta, B. vulgaris (NC_025814, from 2300755 to 2586046); Spinacia, S. oleracea (NW_018931398, from 1613247 to 1362360); Chenopodium NW_018742205, C. quinoa (NW_018742205, from 265231 to 482238); and Chenopodium NW_018743021, C. quinoa (NW_018743021, from 3318973 to 3346398).

Fig. 4.

Positional relationships between positively selected amino acid residues and transmembrane helices in the RF-Oma1 genes. Vertical and horizontal axes show probability and residue number, respectively. (A) Positively selected codons revealed by Bayes Empirical Bayes analysis. Each vertical line indicates the posterior probability of positive selection on each residue, and is orange if the posterior probability is more than 0.95. (B) Plot showing the probability that each amino acid residue sits within a transmembrane helix (red vertical line), inside the membrane (blue graph line) or outside the membrane (purple graph line).

Fig. 5.

Phylogenetic network of 11 RF-Oma1 genes in B. vulgaris. Genes capable of altering the higher order structure of the cognate MS-inducing mitochondrial protein are highlighted in green or red. A scale bar indicates evolutionary distances. The origins of the RF-Oma1 genes are as follows: orf20_NK-198-1, orf20_NK-198-2, orf20_NK-198-3, and orf20_NK-198-4 are from sugar beet line NK-198; orf20_NK-305-1 and orf20_NK-305-2 are from sugar beet line NK-305; orf20_NK-219-2 and orf20_NK-219-3 are from sugar beet line NK-219mm-O; and orf20_TK-81, orf20_{PI 625522}, and orf20_fukkoku are from sugar beet line TK-81mm-O, sugar beet line PI 615522, and leaf beet accession “Fukkoku-ouba,” respectively (Matsuhira et al. 2012; Ohgami et al. 2016; Arakawa et al. 2018, 2019b).