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Taniguchi E, Satoh K, Ohkubo M, Ue S, Matsuhira H, Kuroda Y, Kubo T, Kitazaki K. Nuclear DNA segments homologous to mitochondrial DNA are obstacles for detecting heteroplasmy in sugar beet (Beta vulgaris L.). PLoS One 2023; 18:e0285430. [PMID: 37552681 PMCID: PMC10409277 DOI: 10.1371/journal.pone.0285430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 04/21/2023] [Indexed: 08/10/2023] Open
Abstract
Heteroplasmy, the coexistence of multiple mitochondrial DNA (mtDNA) sequences in a cell, is well documented in plants. Next-generation sequencing technology (NGS) has made it feasible to sequence entire genomes. Thus, NGS has the potential to detect heteroplasmy; however, the methods and pitfalls in heteroplasmy detection have not been fully investigated and identified. One obstacle for heteroplasmy detection is the sequence homology between mitochondrial-, plastid-, and nuclear DNA, of which the influence of nuclear DNA segments homologous to mtDNA (numt) need to be minimized. To detect heteroplasmy, we first excluded nuclear DNA sequences of sugar beet (Beta vulgaris) line EL10 from the sugar beet mtDNA sequence. NGS reads were obtained from single plants of sugar beet lines NK-195BRmm-O and NK-291BRmm-O and mapped to the unexcluded mtDNA regions. More than 1000 sites exhibited intra-individual polymorphism as detected by genome browsing analysis. We focused on a 309-bp region where 12 intra-individual polymorphic sites were closely linked to each other. Although the existence of DNA molecules having variant alleles at the 12 sites was confirmed by PCR amplification from NK-195BRmm-O and NK-291BRmm-O, these variants were not always called by six variant-calling programs, suggesting that these programs are inappropriate for intra-individual polymorphism detection. When we changed the nuclear DNA reference, a numt absent from EL10 was found to include the 309-bp region. Genetic segregation of an F2 population from NK-195BRmm-O x NK-291BRmm-O supported the numt origin of the variant alleles. Using four references, we found that numt detection exhibited reference dependency, and extreme polymorphism of numts exists among sugar beet lines. One of the identified numts absent from EL10 is also associated with another intra-individual polymorphic site in NK-195mm-O. Our data suggest that polymorphism among numts is unexpectedly high within sugar beets, leading to confusion about the true degree of heteroplasmy.
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Affiliation(s)
- Eigo Taniguchi
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Kosuke Satoh
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Megumi Ohkubo
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Sachiyo Ue
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Hiroaki Matsuhira
- Hokkaido Agricultural Research Center, National Agriculture and Food Research Organization, Memuro, Hokkaido, Japan
| | - Yosuke Kuroda
- Hokkaido Agricultural Research Center, National Agriculture and Food Research Organization, Memuro, Hokkaido, Japan
| | - Tomohiko Kubo
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Kazuyoshi Kitazaki
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido, Japan
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Matsuhira H, Kitazaki K, Matsui K, Kubota K, Kuroda Y, Kubo T. Selection of nuclear genotypes associated with the thermo-sensitivity of Owen-type cytoplasmic male sterility in sugar beet (Beta vulgaris L.). Theor Appl Genet 2022; 135:1457-1466. [PMID: 35147716 DOI: 10.1007/s00122-022-04046-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 01/24/2022] [Indexed: 06/14/2023]
Abstract
Cytoplasmic male sterility in sugar beet becomes thermo-sensitive when combined with specific genotypes, potentially offering a means to environmentally control pollination by this trait. The stability of cytoplasmic male sterility expression in several genetic backgrounds was investigated in sugar beet (Beta vulgaris L.). Nine genetically heterogenous plants from open-pollinated varieties were crossed with a cytoplasmic male sterile line to obtain 266 F1 plants. Based on marker analysis using a multiallelic DNA marker linked to restorer-of-fertility 1 (Rf1), we divided the F1 plants into 15 genotypes. We evaluated the phenotypes of the F1 plants under two environmental conditions: greenhouse rooms with or without daytime heating during the flowering season. Three phenotypic groups appeared: those consistently expressing male sterility, those consistently having restored pollen fertility, and those expressing male sterility in a thermo-sensitive manner. All plants in the consistently male sterile group inherited a specific Rf1 marker type named p4. We tested the potential for thermo-sensitive male sterile plants to serve as seed parents for hybrid seed production, and three genotypes were selected. Open pollination by a pollen parental line with a dominant trait of red-pigmented hypocotyls and leaf veins resulted in seed setting on thermo-sensitive male sterile plants, indicating that their female organs were functional. More than 99.9% of the progeny expressed the red pigmentation trait; hence, highly pure hybrids were obtained. We determined the nucleotide sequences of Rf1 from the three genotypes: One had a novel allele and two had known alleles, of which one was reported to have been selected previously as a non-restoring allele at a single U.S. breeding station but not at other stations in the U.S., or in Europe or Japan, suggesting environmental sensitivity.
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Affiliation(s)
- Hiroaki Matsuhira
- Hokkaido Agricultural Research Center, National Agriculture and Food Research Organization, Memuro, Hokkaido, Japan.
| | - Kazuyoshi Kitazaki
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido, Japan.
| | - Katsunori Matsui
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Keisi Kubota
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Yosuke Kuroda
- Hokkaido Agricultural Research Center, National Agriculture and Food Research Organization, Memuro, Hokkaido, Japan
| | - Tomohiko Kubo
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido, Japan
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Arakawa T, Matsunaga M, Matsui K, Itoh K, Kuroda Y, Matsuhira H, Kitazaki K, Kubo T. The molecular basis for allelic differences suggests Restorer-of-fertility 1 is a complex locus in sugar beet (Beta vulgaris L.). BMC Plant Biol 2020; 20:503. [PMID: 33143645 PMCID: PMC7607634 DOI: 10.1186/s12870-020-02721-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 10/26/2020] [Indexed: 05/08/2023]
Abstract
BACKGROUND Cytoplasmic male sterility (CMS) is a widely used trait for hybrid seed production in many crops. Sugar beet CMS is associated with a unique mitochondrial protein named preSATP6 that forms a 250-kDa complex. Restorer-of-fertility 1 (Rf1) is a nuclear gene that suppresses CMS and is, hence, one of the targets of sugar beet breeding. Rf1 has dominant, semi-dominant and recessive alleles, suggesting that it may be a multi-allelic locus; however, the molecular basis for differences in genetic action is obscure. Molecular cloning of Rf1 revealed a gene (orf20) whose protein products produced in transgenics can bind with preSATP6 to generate a novel 200-kDa complex. The complex is also detected in fertility-restored anthers concomitant with a decrease in the amount of the 250-kDa complex. Molecular diversity of the Rf1 locus involves organizational diversity of a gene cluster composed of orf20-like genes (RF-Oma1s). We examined the possibility that members of the clustered RF-Oma1 in this locus could be associated with fertility restoration. RESULTS Six yet uncharacterized RF-Oma1s from dominant and recessive alleles were examined to determine whether they could generate the 200-kDa complex. Analyses of transgenic calli revealed that three RF-Oma1s from a dominant allele could generate the 200-kDa complex, suggesting that clustered RF-Oma1s in the dominant allele can participate in fertility restoration. None of the three copies from two recessive alleles was 200-kDa generative. The absence of this ability was confirmed by analyzing mitochondrial complexes in anthers of plants having these recessive alleles. Together with our previous data, we designed a set of PCR primers specific to the 200-kDa generative RF-Oma1s. The amount of mRNA measured by this primer set inversely correlated with the amount of the 250-kDa complex in anthers and positively correlated with the strength of the Rf1 alleles. CONCLUSIONS Fertility restoration by sugar beet Rf1 can involve multiple RF-Oma1s clustered in the locus, implying that stacking 200-kDa generative copies in the locus strengthens the efficacy, whereas the absence of 200-kDa generative copies in the locus makes the allele recessive irrespective of the copy number. We propose that sugar beet Rf1 is a complex locus.
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Affiliation(s)
- Takumi Arakawa
- Research Faculty of Agriculture, Hokkaido University, Kita-9, Nishi-9, Kita-ku, Sapporo, 060-8589, Japan
- Gifu Prefectural Research Institute for Agricultural Technology in Hilly and Mountainous Areas, Nakatsugawa, 508-0203, Japan
| | - Muneyuki Matsunaga
- Research Faculty of Agriculture, Hokkaido University, Kita-9, Nishi-9, Kita-ku, Sapporo, 060-8589, Japan
| | - Katsunori Matsui
- Research Faculty of Agriculture, Hokkaido University, Kita-9, Nishi-9, Kita-ku, Sapporo, 060-8589, Japan
| | - Kanna Itoh
- Research Faculty of Agriculture, Hokkaido University, Kita-9, Nishi-9, Kita-ku, Sapporo, 060-8589, Japan
| | - Yosuke Kuroda
- Hokkaido Agricultural Research Center, National Agriculture and Food Research Organization, Shinsei Minami 9-4, Memuro, 082-0081, Japan
| | - Hiroaki Matsuhira
- Hokkaido Agricultural Research Center, National Agriculture and Food Research Organization, Shinsei Minami 9-4, Memuro, 082-0081, Japan
| | - Kazuyoshi Kitazaki
- Research Faculty of Agriculture, Hokkaido University, Kita-9, Nishi-9, Kita-ku, Sapporo, 060-8589, Japan
| | - Tomohiko Kubo
- Research Faculty of Agriculture, Hokkaido University, Kita-9, Nishi-9, Kita-ku, Sapporo, 060-8589, Japan.
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Arakawa T, Sugaya H, Katsuyama T, Honma Y, Matsui K, Matsuhira H, Kuroda Y, Kitazaki K, Kubo T. How did a duplicated gene copy evolve into a restorer-of-fertility gene in a plant? The case of Oma1. R Soc Open Sci 2019; 6:190853. [PMID: 31827833 PMCID: PMC6894571 DOI: 10.1098/rsos.190853] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 10/08/2019] [Indexed: 05/24/2023]
Abstract
Restorer-of-fertility (Rf) is a suppressor of cytoplasmic male sterility (CMS), a mitochondrion-encoded trait that has been reported in many plant species. The occurrence of CMS is considered to be independent in each lineage; hence, the question of how Rf evolved was raised. Sugar beet Rf resembles Oma1, a gene for quality control of the mitochondrial inner membrane. Oma1 homologues comprise a small gene family in the sugar beet genome, unlike Arabidopsis and other eukaryotes. The sugar beet sequence that best matched Arabidopsis atOma1 was named bvOma1; sugar beet Rf (RF1-Oma1) was another member. During anther development, atOma1 mRNA was detected from the tetrad to the microspore stages, whereas bvOma1 mRNA was detected at the microspore stage and RF1-Oma1 mRNA was detected during the meiosis and tetrad stages. A transgenic study revealed that, whereas RF1-Oma1 can bind to a CMS-specific protein and alter the higher-order structure of the CMS-specific protein complex, neither bvOma1 nor atOma1 show such activity. We favour the hypothesis that an ancestral Oma1 gene duplicated to form a small gene family, and that one of the copies evolved and acquired a novel expression pattern and protein function as an Rf, i.e. RF1-Oma1 evolved via neofunctionalization.
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Affiliation(s)
- Takumi Arakawa
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido 060-8589, Japan
| | - Hajime Sugaya
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido 060-8589, Japan
| | - Takaya Katsuyama
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido 060-8589, Japan
| | - Yujiro Honma
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido 060-8589, Japan
- Department of Biotechnology and Environmental Chemistry, Kitami Institute of Technology, Kitami, Hokkaido 090-8507, Japan
| | - Katsunori Matsui
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido 060-8589, Japan
| | - Hiroaki Matsuhira
- Hokkaido Agricultural Research Center, National Agriculture and Food Research Organization, Memuro, Hokkaido 082-0081, Japan
| | - Yosuke Kuroda
- Hokkaido Agricultural Research Center, National Agriculture and Food Research Organization, Memuro, Hokkaido 082-0081, Japan
| | - Kazuyoshi Kitazaki
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido 060-8589, Japan
| | - Tomohiko Kubo
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido 060-8589, Japan
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Kitazaki K, Arakawa T, Matsunaga M, Yui-Kurino R, Matsuhira H, Mikami T, Kubo T. Post-translational mechanisms are associated with fertility restoration of cytoplasmic male sterility in sugar beet (Beta vulgaris). Plant J 2015; 83:290-9. [PMID: 26031622 DOI: 10.1111/tpj.12888] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Revised: 05/08/2015] [Accepted: 05/15/2015] [Indexed: 05/20/2023]
Abstract
Genetic conflict between cytoplasmically inherited elements and nuclear genes arising from their different transmission patterns can be seen in cytoplasmic male sterility (CMS), the mitochondrion-encoded inability to shed functional pollen. CMS is associated with a mitochondrial open reading frame (ORF) that is absent from non-sterility inducing mitochondria (S-orf). Nuclear genes that suppress CMS are called restorer-of-fertility (Rf) genes. Post-transcriptional and translational repression of S-orf mediates the molecular action of Rf that encodes a class of RNA-binding proteins with pentatricopeptide repeat (PPR) motifs. Besides the PPR-type of Rfs, there are also non-PPR Rfs, but the molecular interactions between non-PPR Rf and S-orf have not been described. In this study, we investigated the interaction of bvORF20, a non-PPR Rf from sugar beet (Beta vulgaris), with preSatp6, the S-orf from sugar beet. Anthers expressing bvORF20 contained a protein that interacted with preSATP6 protein. Analysis of anthers and transgenic calli expressing a FLAG-tagged bvORF20 suggested the binding of preSATP6 to bvORF20. To see the effect of bvORF20 on preSATP6, which exists as a 250-kDa protein complex in CMS plants, signal bands of preSATP6 in bvORF20-expressing and non-expressing anthers were compared by immunoblotting combined with Blue Native polyacrylamide gel electrophoresis. The signal intensity of the 250-kDa band decreased significantly, and 200- and 150-kDa bands appeared in bvORF20-expressing anthers. Transgenic callus expressing bvORF20 also generated the 200- and 150-kDa bands. The 200-kDa complex is likely to include both preSATP6 and bvORF20. Post-translational interaction between preSATP6 and bvORF20 appears to alter the higher order structure of preSATP6 that may lead to fertility restoration in sugar beet.
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Affiliation(s)
- Kazuyoshi Kitazaki
- Research Faculty of Agriculture, Hokkaido University, N-9, W-9, Kita-ku, Sapporo, Hokkaido, 060-8589, Japan
| | - Takumi Arakawa
- Research Faculty of Agriculture, Hokkaido University, N-9, W-9, Kita-ku, Sapporo, Hokkaido, 060-8589, Japan
| | - Muneyuki Matsunaga
- Research Faculty of Agriculture, Hokkaido University, N-9, W-9, Kita-ku, Sapporo, Hokkaido, 060-8589, Japan
| | - Rika Yui-Kurino
- Research Faculty of Agriculture, Hokkaido University, N-9, W-9, Kita-ku, Sapporo, Hokkaido, 060-8589, Japan
| | - Hiroaki Matsuhira
- Research Faculty of Agriculture, Hokkaido University, N-9, W-9, Kita-ku, Sapporo, Hokkaido, 060-8589, Japan
| | - Tetsuo Mikami
- Research Faculty of Agriculture, Hokkaido University, N-9, W-9, Kita-ku, Sapporo, Hokkaido, 060-8589, Japan
| | - Tomohiko Kubo
- Research Faculty of Agriculture, Hokkaido University, N-9, W-9, Kita-ku, Sapporo, Hokkaido, 060-8589, Japan
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Abstract
Creating transgenic plants is invaluable for the genetic analysis of sugar beet and will be increasingly important as sugar beet genomic technologies progress. A protocol for Agrobacterium-mediated transformation of sugar beet is described in this chapter. Our protocol is optimized for a sugar beet genotype that performs exceptionally well in tissue culture, including the steps of dedifferentiation, callus proliferation, and regeneration. Because of the infrequent occurrence of such a genotype in sugar beet populations, our protocol includes an in vitro propagation method for germplasm preservation. The starting materials for transgenic experiments are aseptic shoots grown from surface-sterilized seed balls. Callus is induced from leaf explants and subsequently infected with Agrobacterium. Plantlets are regenerated from transgenic callus and vernalized for flowering, if necessary. The efficiency of transformation was quite high; in our laboratory, the culture of only ten leaf explants, on average, generated one transgenic plant.
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Affiliation(s)
- Hiroyo Kagami
- Research Faculty of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan
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Matsuhira H, Tamura KI, Tamagake H, Sato Y, Anzai H, Yoshida M. High production of plant type levan in sugar beet transformed with timothy (Phleum pratense) 6-SFT genes. J Biotechnol 2014; 192 Pt A:215-22. [DOI: 10.1016/j.jbiotec.2014.09.025] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Revised: 09/26/2014] [Accepted: 09/30/2014] [Indexed: 10/24/2022]
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Moritani M, Taguchi K, Kitazaki K, Matsuhira H, Katsuyama T, Mikami T, Kubo T. Identification of the predominant nonrestoring allele for Owen-type cytoplasmic male sterility in sugar beet ( Beta vulgaris L.): development of molecular markers for the maintainer genotype. Mol Breed 2013; 32:91-100. [PMID: 23794939 PMCID: PMC3684711 DOI: 10.1007/s11032-013-9854-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2012] [Accepted: 03/06/2013] [Indexed: 05/22/2023]
Abstract
Hybrid seed production in sugar beet relies on cytoplasmic male sterility (CMS). As time-consuming and laborious test crosses with a CMS tester are necessary to identify maintainer lines, development of a marker-assisted selection method for the rf gene (the nonrestoring allele of restorer-of-fertility locus) is highly desirable for sugar-beet breeding. To develop such a method, we investigated genetic variation at the Rf1 locus, one of two Rf loci known in sugar beet. After HindIII-digestion, genomic DNAs from beet plants known to have a restoring Rf1 allele yielded a range of hybridization patterns on agarose gels, indicating that Rf1 is a multi-allelic locus. However, the hybridization patterns of 22 of 23 maintainer lines were indistinguishable. The nucleotide sequences of the rf1 coding regions of these 22 maintainer lines were found to be identical, confirming that the lines had the same rf1 allele. Two PCR markers were developed that targeted a downstream intergenic sequence and an intron of Rf1. The electrophoretic patterns of both markers indicated multiple Rf1 alleles, one of which, named the dd(L) type, was associated with the maintainer genotype. To test the validity of marker-assisted selection, 147 sugar beet plants were genotyped using these markers. Additionally, the 147 sugar beet plants were crossed with CMS plants to determine whether they possessed the maintainer genotype. Analysis of 5038 F1 offspring showed that 53 % of the dd(L) plants, but none of the plants with other alleles, had the maintainer genotype. Thus, selection for the dd(L) type considerably enriched the proportion of plants with the maintainer genotype.
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Affiliation(s)
- Mari Moritani
- Research Faculty of Agriculture, Hokkaido University, N-9, W-9, Kita-ku, Sapporo, 060-8589 Japan
| | - Kazunori Taguchi
- Memuro Upland Farming Research Station, Hokkaido Agricultural Research Center (HARC), National Agriculture and Food Research Organization (NARO), Memuro, Hokkaido 082-0081 Japan
| | - Kazuyoshi Kitazaki
- Research Faculty of Agriculture, Hokkaido University, N-9, W-9, Kita-ku, Sapporo, 060-8589 Japan
- Present Address: Central Research Institute of Electric Power Industry, Abiko, Chiba 270-1194 Japan
| | - Hiroaki Matsuhira
- Research Faculty of Agriculture, Hokkaido University, N-9, W-9, Kita-ku, Sapporo, 060-8589 Japan
- Present Address: HARC-NARO, Sapporo, Hokkaido 062-8555 Japan
| | - Takaya Katsuyama
- Research Faculty of Agriculture, Hokkaido University, N-9, W-9, Kita-ku, Sapporo, 060-8589 Japan
| | - Tetsuo Mikami
- Research Faculty of Agriculture, Hokkaido University, N-9, W-9, Kita-ku, Sapporo, 060-8589 Japan
| | - Tomohiko Kubo
- Research Faculty of Agriculture, Hokkaido University, N-9, W-9, Kita-ku, Sapporo, 060-8589 Japan
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Kitazaki K, Kubo T, Kagami H, Matsumoto T, Fujita A, Matsuhira H, Matsunaga M, Mikami T. A horizontally transferred tRNA(Cys) gene in the sugar beet mitochondrial genome: evidence that the gene is present in diverse angiosperms and its transcript is aminoacylated. Plant J 2011; 68:262-72. [PMID: 21699590 DOI: 10.1111/j.1365-313x.2011.04684.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Of the two tRNA(Cys) (GCA) genes, trnC1-GCA and trnC2-GCA, previously identified in mitochondrial genome of sugar beet, the former is a native gene and probably a pseudo-copy, whereas the latter, of unknown origin, is transcribed into a tRNA [tRNA(Cys2) (GCA)]. In this study, the trnC2-GCA sequence was mined from various public databases. To evaluate whether or not the trnC2-GCA sequence is located in the mitochondrial genome, the relative copy number of its sequence to nuclear gene was assessed in a number of angiosperm species, using a quantitative real-time PCR assay. The trnC2-GCA sequence was found to exist sporadically in the mitochondrial genomes of a wide range of angiosperms. The mitochondrial tRNA(Cys2) (GCA) species from sugar beet (Beta vulgaris), spinach (Spinacea oleracea) and cucumber (Cucumis sativus) were found to be aminoacylated, indicating that they may participate in translation. We also identified a sugar beet nuclear gene that encodes cysteinyl-tRNA synthetase, which is dual-targeted to mitochondria and plastids, and may aminoacylate tRNA(Cys2) (GCA). What is of particular interest is that trnC1-GCA and trnC2-GCA co-exist in the mitochondrial genomes of eight diverse angiosperms, including spinach, and that the spinach tRNA(Cys1) (GCA) is also aminoacylated. Taken together, our observations lead us to surmise that trnC2-GCA may have been horizontally transferred to a common ancestor of eudicots, followed by co-existence and dual expression of trnC1-GCA and trnC2-GCA in mitochondria with occasional loss or inactivation of either trnC-GCA gene during evolution.
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MESH Headings
- Amino Acyl-tRNA Synthetases/genetics
- Amino Acyl-tRNA Synthetases/metabolism
- Aminoacylation/genetics
- Beta vulgaris/enzymology
- Beta vulgaris/genetics
- Beta vulgaris/metabolism
- Biological Evolution
- DNA, Complementary/genetics
- DNA, Mitochondrial/genetics
- DNA, Plant/genetics
- Databases, Nucleic Acid
- Gene Dosage
- Gene Transfer, Horizontal
- Genome, Mitochondrial/genetics
- Magnoliopsida/enzymology
- Magnoliopsida/genetics
- Magnoliopsida/metabolism
- Mitochondria/genetics
- Mitochondria/metabolism
- Nucleic Acid Conformation
- Plant Proteins/genetics
- Plant Proteins/metabolism
- RNA, Plant/genetics
- RNA, Transfer, Cys/genetics
- RNA, Transfer, Cys/metabolism
- Sequence Analysis, DNA
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Affiliation(s)
- Kazuyoshi Kitazaki
- Laboratory of Genetic Engineering, Research Faculty of Agriculture, Hokkaido University, 060-8589 N-9, W-9, Kita-ku Sapporo, Japan
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Hagihara E, Matsuhira H, Ueda M, Mikami T, Kubo T. Sugar beet BAC library construction and assembly of a contig spanning Rf1, a restorer-of-fertility gene for Owen cytoplasmic male sterility. Mol Genet Genomics 2005; 274:316-23. [PMID: 16080000 DOI: 10.1007/s00438-005-0024-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2005] [Accepted: 05/18/2005] [Indexed: 10/25/2022]
Abstract
Rf1 is a nuclear gene that controls fertility restoration in cases of cytoplasmic male sterility caused by the Owen cytoplasm in sugar beet. In order to isolate the gene by positional cloning, a BAC library was constructed from a restorer line, NK198, with the genotype Rf1Rf1. The library contained 32,180 clones with an average insert size of 97.8 kb, providing 3.4 genome equivalents. Five AFLP markers closely linked to Rf1 were used to screen the library. As a result, we identified eight different BAC clones that were clustered into two contigs. The gap between the two contigs was filled by chromosome walking. To map the Rf1 region in more detail, we developed five cleaved amplified polymorphic sequence (CAPS) markers from the BAC DNAs identified, and carried out genotyping of 509 plants in the mapping population with the Rf1-flanking AFLP and CAPS markers. Thirteen plants in which recombination events had occurred in the vicinity of the Rf1 locus were identified and used to map the molecular markers relative to each other and to Rf1. In this way, we were able to restrict the possible location of the Rf1 gene to a minimum of six BAC clones spanning an interval of approximately 250 kb.
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Affiliation(s)
- Eiki Hagihara
- Graduate School of Agriculture, Hokkaido University, Kita-ku, Sapporo, Japan
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