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He W, Xiang K, Chen C, Wang J, Wu Z. Master graph: an essential integrated assembly model for the plant mitogenome based on a graph-based framework. Brief Bioinform 2023; 24:bbac522. [PMID: 36644898 DOI: 10.1093/bib/bbac522] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 10/03/2022] [Accepted: 11/02/2022] [Indexed: 01/17/2023] Open
Abstract
Unlike the typical single circular structure of most animal mitochondrial genomes (mitogenome), the drastic structural variation of plant mitogenomes is a result of a mixture of molecules of various sizes and structures. Obtaining the full panoramic plant mitogenome is still considered a roadblock in evolutionary biology. In this study, we developed a graph-based sequence assembly toolkit (GSAT) to construct the pan-structural landscape of plant mitogenome with high-quality mitochondrial master graphs (MMGs) for model species including rice (Oryza sativa) and thale cress (Arabidopsis thaliana). The rice and thale cress MMGs have total lengths of 346 562 and 358 041 bp, including 9 and 6 contigs and 12 and 8 links, respectively, and could be further divided into 6 and 3 minimum master circles and 4 and 2 minimum secondary circles separately. The nuclear mitochondrial DNA segments (NUMTs) in thale cress strongly affected the frequency evaluation of the homologous structures in the mitogenome, while the effects of NUMTs in rice were relatively weak. The mitochondrial plastid DNA segments (MTPTs) in both species had no effects on the assessment of the MMGs. All potential recombinant structures were evaluated, and the findings revealed that all, except for nuclear-homologous structures, MMG structures are present at a much higher frequency than non-MMG structures are. Investigations of potential circular and linear molecules further supported multiple dominant structures in the mitogenomes and could be completely summarized in the MMG. Our study provided an efficient and accurate model for assembling and applying graph-based plant mitogenomes to assess their pan-structural variations.
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Affiliation(s)
- Wenchuang He
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Kunli Xiang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Caijin Chen
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
| | - Jie Wang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Zhiqiang Wu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- Kunpeng Institute of Modern Agriculture at Foshan, Chinese Academy of Agricultural Sciences, Foshan 528200, China
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2
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He T, Ding X, Zhang H, Li Y, Chen L, Wang T, Yang L, Nie Z, Song Q, Gai J, Yang S. Comparative analysis of mitochondrial genomes of soybean cytoplasmic male-sterile lines and their maintainer lines. Funct Integr Genomics 2021; 21:43-57. [PMID: 33404916 DOI: 10.1007/s10142-020-00760-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 04/22/2020] [Accepted: 11/11/2020] [Indexed: 11/25/2022]
Abstract
In soybean, only one mitochondrial genome of cultispecies has been completely obtained. To explore the effect of mitochondrial genome on soybean cytoplasmic male sterility (CMS), two CMS lines and three maintainer lines were used for sequencing. Comparative analysis showed that mitochondrial genome of the CMS line was more compact than that of its maintainer line, but genes were highly conserved. Conserved and unique sequence coexisted in the genomes. Mitochondrial genomes contained different sequence lengths and copy numbers of repeats between CMS line and maintainer line. Large and short repeats mediated intramolecular and intermolecular recombination in mitochondria. Unique sequences and genes were also involved in recombination process and constituted a complex network. orf178 and orf261 were identified as CMS-associated candidate genes. They had sequence characteristics of reported CMS genes in other crops and could be transcribed in CMS lines but not in maintainer lines. This report reveals mitochondrial genome of soybean CMS lines and compares complete mitochondrial sequence between CMS lines and their maintainer lines. The information will be helpful in further understanding the characteristics of soybean mitochondrial genome and the mechanism underlying CMS.
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Affiliation(s)
- Tingting He
- Soybean Research Institute, National Center for Soybean Improvement, Key Laboratory of Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xianlong Ding
- Soybean Research Institute, National Center for Soybean Improvement, Key Laboratory of Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Hao Zhang
- Soybean Research Institute, National Center for Soybean Improvement, Key Laboratory of Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yanwei Li
- Soybean Research Institute, National Center for Soybean Improvement, Key Laboratory of Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Linfeng Chen
- Soybean Research Institute, National Center for Soybean Improvement, Key Laboratory of Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Tanliu Wang
- Soybean Research Institute, National Center for Soybean Improvement, Key Laboratory of Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Longshu Yang
- Soybean Research Institute, National Center for Soybean Improvement, Key Laboratory of Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhixing Nie
- Soybean Research Institute, National Center for Soybean Improvement, Key Laboratory of Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Qijian Song
- Soybean Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, USDA-ARS, Beltsville, MD, 20705, USA
| | - Junyi Gai
- Soybean Research Institute, National Center for Soybean Improvement, Key Laboratory of Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Shouping Yang
- Soybean Research Institute, National Center for Soybean Improvement, Key Laboratory of Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China.
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3
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Muniandy K, Tan MH, Shehnaz S, Song BK, Ayub Q, Rahman S. Cytosine methylation of rice mitochondrial DNA from grain and leaf tissues. PLANTA 2020; 251:57. [PMID: 32008119 DOI: 10.1007/s00425-020-03349-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 01/22/2020] [Indexed: 06/10/2023]
Abstract
The rice leaf mitochondrial DNA is more methylated compared to the rice grain mitochondrial DNA. The old rice leaf mitochondrial DNA has also a higher methylation level than the young rice leaf mitochondrial DNA. The presence of DNA methylation in rice organelles has not been well characterized. We have previously shown that cytosine methylation of chloroplast DNA is different between leaf and grain, and varies between young and old leaves in rice. However, the variation in cytosine methylation of mitochondrial DNA is still poorly characterized. In this study, we have investigated cytosine methylation of mitochondrial DNA in the rice grain and leaf. Based on CpG, CHG, and CHH methylation analyses, the leaf mitochondrial DNA was found to be more methylated compared to the grain mitochondrial DNA. The methylation of the leaf mitochondrial DNA was also higher in old compared to young leaves. Differences in methylation were observed at different cytosine positions of the mitochondrial DNA between grain and leaf, although there were also positions with a similar level of high methylation in all the tissues examined. The differentially methylated cytosine positions in rice mitochondrial DNA were observed mostly in the intergenic region and in some mitochondrial-specific genes involved in ATP production, transcription, and translation. The functional importance of cytosine methylation in the life cycle of rice mitochondria is still to be determined.
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Affiliation(s)
- Kanagesswari Muniandy
- School of Science, Monash University Malaysia, Jalan Lagoon Selatan, 47500, Bandar Sunway, Selangor Darul Ehsan, Malaysia.
- Genomics Facility, Tropical Medicine and Biology Multidisciplinary Platform, Monash University Malaysia, Jalan Lagoon Selatan, 47500, Bandar Sunway, Selangor Darul Ehsan, Malaysia.
| | - Mun Hua Tan
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, VIC, 3220, Australia
- Deakin Genomics Centre, Deakin University, Geelong, VIC, 3220, Australia
| | - Saiyara Shehnaz
- School of Science, Monash University Malaysia, Jalan Lagoon Selatan, 47500, Bandar Sunway, Selangor Darul Ehsan, Malaysia
- Genomics Facility, Tropical Medicine and Biology Multidisciplinary Platform, Monash University Malaysia, Jalan Lagoon Selatan, 47500, Bandar Sunway, Selangor Darul Ehsan, Malaysia
| | - Beng Kah Song
- School of Science, Monash University Malaysia, Jalan Lagoon Selatan, 47500, Bandar Sunway, Selangor Darul Ehsan, Malaysia
- Genomics Facility, Tropical Medicine and Biology Multidisciplinary Platform, Monash University Malaysia, Jalan Lagoon Selatan, 47500, Bandar Sunway, Selangor Darul Ehsan, Malaysia
| | - Qasim Ayub
- School of Science, Monash University Malaysia, Jalan Lagoon Selatan, 47500, Bandar Sunway, Selangor Darul Ehsan, Malaysia
- Genomics Facility, Tropical Medicine and Biology Multidisciplinary Platform, Monash University Malaysia, Jalan Lagoon Selatan, 47500, Bandar Sunway, Selangor Darul Ehsan, Malaysia
| | - Sadequr Rahman
- School of Science, Monash University Malaysia, Jalan Lagoon Selatan, 47500, Bandar Sunway, Selangor Darul Ehsan, Malaysia.
- Genomics Facility, Tropical Medicine and Biology Multidisciplinary Platform, Monash University Malaysia, Jalan Lagoon Selatan, 47500, Bandar Sunway, Selangor Darul Ehsan, Malaysia.
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4
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Liberatore KL, Dukowic-Schulze S, Miller ME, Chen C, Kianian SF. The role of mitochondria in plant development and stress tolerance. Free Radic Biol Med 2016; 100:238-256. [PMID: 27036362 DOI: 10.1016/j.freeradbiomed.2016.03.033] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Revised: 03/25/2016] [Accepted: 03/28/2016] [Indexed: 01/03/2023]
Abstract
Eukaryotic cells require orchestrated communication between nuclear and organellar genomes, perturbations in which are linked to stress response and disease in both animals and plants. In addition to mitochondria, which are found across eukaryotes, plant cells contain a second organelle, the plastid. Signaling both among the organelles (cytoplasmic) and between the cytoplasm and the nucleus (i.e. nuclear-cytoplasmic interactions (NCI)) is essential for proper cellular function. A deeper understanding of NCI and its impact on development, stress response, and long-term health is needed in both animal and plant systems. Here we focus on the role of plant mitochondria in development and stress response. We compare and contrast features of plant and animal mitochondrial genomes (mtDNA), particularly highlighting the large and highly dynamic nature of plant mtDNA. Plant-based tools are powerful, yet underutilized, resources for enhancing our fundamental understanding of NCI. These tools also have great potential for improving crop production. Across taxa, mitochondria are most abundant in cells that have high energy or nutrient demands as well as at key developmental time points. Although plant mitochondria act as integrators of signals involved in both development and stress response pathways, little is known about plant mtDNA diversity and its impact on these processes. In humans, there are strong correlations between particular mitotypes (and mtDNA mutations) and developmental differences (or disease). We propose that future work in plants should focus on defining mitotypes more carefully and investigating their functional implications as well as improving techniques to facilitate this research.
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Affiliation(s)
- Katie L Liberatore
- United States Department of Agriculture-Agricultural Research Service, Cereal Disease Laboratory, St. Paul, MN 55108, United States; Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108, United States.
| | | | - Marisa E Miller
- United States Department of Agriculture-Agricultural Research Service, Cereal Disease Laboratory, St. Paul, MN 55108, United States; Department of Horticultural Science, University of Minnesota, St. Paul, MN 55108, United States
| | - Changbin Chen
- Department of Horticultural Science, University of Minnesota, St. Paul, MN 55108, United States
| | - Shahryar F Kianian
- United States Department of Agriculture-Agricultural Research Service, Cereal Disease Laboratory, St. Paul, MN 55108, United States; Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108, United States
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5
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Chang S, Wang Y, Lu J, Gai J, Li J, Chu P, Guan R, Zhao T. The mitochondrial genome of soybean reveals complex genome structures and gene evolution at intercellular and phylogenetic levels. PLoS One 2013; 8:e56502. [PMID: 23431381 PMCID: PMC3576410 DOI: 10.1371/journal.pone.0056502] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2012] [Accepted: 01/10/2013] [Indexed: 11/19/2022] Open
Abstract
Determining mitochondrial genomes is important for elucidating vital activities of seed plants. Mitochondrial genomes are specific to each plant species because of their variable size, complex structures and patterns of gene losses and gains during evolution. This complexity has made research on the soybean mitochondrial genome difficult compared with its nuclear and chloroplast genomes. The present study helps to solve a 30-year mystery regarding the most complex mitochondrial genome structure, showing that pairwise rearrangements among the many large repeats may produce an enriched molecular pool of 760 circles in seed plants. The soybean mitochondrial genome harbors 58 genes of known function in addition to 52 predicted open reading frames of unknown function. The genome contains sequences of multiple identifiable origins, including 6.8 kb and 7.1 kb DNA fragments that have been transferred from the nuclear and chloroplast genomes, respectively, and some horizontal DNA transfers. The soybean mitochondrial genome has lost 16 genes, including nine protein-coding genes and seven tRNA genes; however, it has acquired five chloroplast-derived genes during evolution. Four tRNA genes, common among the three genomes, are derived from the chloroplast. Sizeable DNA transfers to the nucleus, with pericentromeric regions as hotspots, are observed, including DNA transfers of 125.0 kb and 151.6 kb identified unambiguously from the soybean mitochondrial and chloroplast genomes, respectively. The soybean nuclear genome has acquired five genes from its mitochondrial genome. These results provide biological insights into the mitochondrial genome of seed plants, and are especially helpful for deciphering vital activities in soybean.
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Affiliation(s)
- Shengxin Chang
- National Center for Soybean Improvement, Nanjing, Jiangsu, China
- Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture, Nanjing, Jiangsu, China
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Yankun Wang
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Jiangjie Lu
- National Center for Soybean Improvement, Nanjing, Jiangsu, China
- Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture, Nanjing, Jiangsu, China
| | - Junyi Gai
- National Center for Soybean Improvement, Nanjing, Jiangsu, China
- Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture, Nanjing, Jiangsu, China
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Jijie Li
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Pu Chu
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Rongzhan Guan
- National Center for Soybean Improvement, Nanjing, Jiangsu, China
- Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture, Nanjing, Jiangsu, China
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Tuanjie Zhao
- National Center for Soybean Improvement, Nanjing, Jiangsu, China
- Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture, Nanjing, Jiangsu, China
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, Jiangsu, China
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6
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Bragin AG, Ivanov MK, Dymshits GM. Estimation of stoichiometry of marker sequences of the sugar beet (Beta vulgaris) mitochondrial genome by real-time PCR. DOKLADY BIOLOGICAL SCIENCES : PROCEEDINGS OF THE ACADEMY OF SCIENCES OF THE USSR, BIOLOGICAL SCIENCES SECTIONS 2006; 406:47-51. [PMID: 16572811 DOI: 10.1134/s0012496606010133] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Affiliation(s)
- A G Bragin
- Institute of Cytology and Genetics, Siberian Division, Russian Academy of Sciences, pr. Akademika Lavrent'eva 10, Novosibirsk, 630090 Russia
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7
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Backert S, Lurz R, Börner T. Electron microscopic investigation of mitochondrial DNA from Chenopodium album (L.). Curr Genet 1996; 29:427-36. [PMID: 8625421 DOI: 10.1007/bf02221510] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
DNA molecules from mitochondria of whole plants and a suspension culture of Chenopodium album were prepared, by a gentle method, for analysis by electron microscopy. Mitochondrial (mt) DNA preparations from both sources contained mostly linear molecules of variable sizes (with the majority of molecules ranging from 40 to 160 kb). Open circular molecules with contour lengths corresponding to 0. 3-183 kb represented 23-26% of all mtDNA molecules in the preparations from the suspension culture and 13-15% in the preparations from whole plants. More than 90% of the circular DNA was smaller than 30 kb. Virtually no size classes of the mtDNA molecules could be identified, and circular or linear molecules of the genome size (about 270 kb) were not observed. In contrast, plastid (pt) DNA preparations from the suspension culture contained linear and circular molecules falling into size classes corresponding to monomers, dimers and trimers of the chromosome. About 23% of the ptDNA molecules were circular. DNA preparations from mitochondria contained a higher percentage of more complex molecules (rosette-like structures, catenate-like molecules) than preparations of ptDNA. Sigma-like molecules (putative intermediates of rolling-circle replication) were observed in mtDNA preparations from the suspension culture (18% of the circles), and in much lower amount (1%) in preparations from whole plants. The results are compared with data obtained previously by pulsed-field gel electrophoresis and discussed in relation to the structural organization and replication of the mt genome of higher plants.
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MESH Headings
- Artifacts
- Cells, Cultured
- DNA, Chloroplast/isolation & purification
- DNA, Chloroplast/ultrastructure
- DNA, Circular/isolation & purification
- DNA, Circular/ultrastructure
- DNA, Mitochondrial/isolation & purification
- DNA, Mitochondrial/ultrastructure
- DNA, Plant/isolation & purification
- DNA, Plant/ultrastructure
- Electrophoresis, Gel, Pulsed-Field
- Microscopy, Electron
- Plants/genetics
- Plants/ultrastructure
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Affiliation(s)
- S Backert
- Institut für Biologie, Humboldt-Universität zu Berlin, Invalidenstrasse 43, D-10115 Berlin, Germany
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8
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Moeykens CA, Mackenzie SA, Shoemaker RC. Mitochondrial genome diversity in soybean: repeats and rearrangements. PLANT MOLECULAR BIOLOGY 1995; 29:245-54. [PMID: 7579176 DOI: 10.1007/bf00043649] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Mitochondrial (mt) genome organization in soybean was examined at the molecular level. This study builds upon previous reports that four soybean cytoplasmic groups, Bedford, Arksoy, Lincoln, and soja-forage, are differentiated by polymorphisms detected with a 2.3 kb Hind III mtDNA probe [12]. The variation detected results from DNA alterations in a region within and around a 4.8 kb repeat. The Bedford-type cytoplasm is the only cytoplasm that contains copies of a 4.8 kb repeat in four different genomic environments, evidence that it is recombinationally active. The Lincoln- and Arksoy-type cytoplasms each contain two copies of the repeat, as well as unique fragments that appear to result from rare recombination events outside, but near, the repeat. The soja-forage-type cytoplasm contains no complete copies of the repeat, but does contain a unique truncated version of the repeat. Sequence analysis indicates that the truncation is a result of recombination across a 9 bp repeated sequence, CCCCTCCCC. The structural rearrangements that have occurred in the region surrounding the 4.8 kb repeat may provide a means to dissect species relationships and evolution within the subgenus soja.
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Affiliation(s)
- C A Moeykens
- Department of Agronomy, Iowa State University, Ames 50011, USA
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10
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Benslimane AA, Rode A, Quétier F, Hartmann C. Characterization of two minicircular plasmid-like DNAs isolated from date-palm mitochondria. Curr Genet 1994; 26:535-41. [PMID: 7874749 DOI: 10.1007/bf00309946] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
We report here the identification and characterization of two minicircular plasmid-like DNAs isolated from mitochondria of a moroccan date-palm variety. Both molecules were cloned and used as probes in Southern analyses of mitochondrial and total-cellular DNA. Evidence was obtained that these plasmid-like DNAs cross-hybridized but did not show any homology to nuclear, chloroplastic, or main mitochondrial genomes. Sequence analysis revealed that both minicircles, 1,346- and 1,160-bp long, share several stretches of homology, the most important consisting of three identical clusters of lengths 42, 47 and 38 bp. In contrast, no major homology was observed with the other higher-plant plasmid-like DNAs reported so far. Sequence analysis also revealed the presence, in the same strand of one of the minicircles, of two open reading frames potentially encoding proteins 89 and 86 amino acids in length. Interestingly, Northern analyses, using single strands of each minicircle as probes, showed the presence of two transcripts hybridizing only with the strand bearing these two open reading frames. However, computer-assisted comparison of the predicted polypeptide sequences with a protein-sequence library failed to detect any significant homology to known sequences.
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MESH Headings
- Base Sequence
- Blotting, Northern
- Blotting, Southern
- Cloning, Molecular
- DNA, Mitochondrial/chemistry
- DNA, Mitochondrial/isolation & purification
- DNA, Plant/biosynthesis
- DNA, Plant/chemistry
- DNA, Plant/isolation & purification
- Fruit/genetics
- Molecular Sequence Data
- Open Reading Frames
- Plasmids/chemistry
- Plasmids/isolation & purification
- RNA, Plant/analysis
- RNA, Plant/biosynthesis
- Restriction Mapping
- Sequence Homology, Nucleic Acid
- Transcription, Genetic
- Trees/genetics
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Affiliation(s)
- A A Benslimane
- Département de Biologie, Faculté des Sciences Semlalia, Université Cadi Ayyad, Marrakech, Maroc
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11
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Chanut FA, Grabau EA, Gesteland RF. Complex organization of the soybean mitochondrial genome: recombination repeats and multiple transcripts at the atpA loci. Curr Genet 1993; 23:234-47. [PMID: 8435853 DOI: 10.1007/bf00351502] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Identification of the soybean mitochondrial atpA open reading frame (atpA ORF) was based on sequence similarity with atpA genes in other plant mitochondria and partial protein sequencing. The atpA reading frame ends with four tandem UGA codons which overlap four tandem AUG codons initiating an unidentified reading frame, orf214. The atpA-orf214 region is found in multiple sequence contexts in soybean mitochondrial DNA (mtDNA), which can be attributed to the presence of two recombination repeats. A 1-kb repeat spans 600 nucleotides (nt) of atpA N-terminal coding region and 400 nt of upstream sequence. Its four configurations correspond to two full-length atpA-orf214 genes and two truncated pseudogenes. A 2-kb repeat lies 3 kb downstream from the 1-kb repeat. Restriction maps of cosmid clones suggest that a 10-kb segment containing both repeats is itself duplicated in the mt genome. With two recombination repeats present in a total of three copies per genome, soybean mtDNA is expected to consist of a complex population of subgenomic molecules. Transcription of the atpA loci was analysed by Northern blotting and S1 nuclease protection. The atpA genes express multiple transcripts with one major 3' end and heterogeneous 5' sequences extending several kb upstream of the atpA coding region. The atpA gene and orf214 are co-transcribed on all major transcripts. The pseudogenes do not express stable RNAs.
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Affiliation(s)
- F A Chanut
- Howard Hughes Medical Institute, Eccles Institute of Human Genetics, University of Utah, Salt Lake City 84112
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12
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Kirnos MD, Alexandrushkina NI, Zagorskaya GYa, Kireev II, Vanyushin BF. Superproduction of heavy minicircular mitochondrial DNA in aging wheat coleoptiles. FEBS Lett 1992; 298:109-12. [PMID: 1544430 DOI: 10.1016/0014-5793(92)80033-d] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
On incubation of 7-day-old wheat seedlings in the presence of [3H]thymidine, the radioactivity incorporated into coleoptile DNA is found to be localized mainly (greater than 95%) in the fraction of heavy mitochondrial DNA (H-mt DNA; rho = 1.716 gm/cm3). Upon long (48-72 h) incubation of cut-off seedlings in water, the amount of this DNA shows a dramatic increase and corresponds to about 10% of the total coleoptile DNA. H-mtDNA is represented by open circular molecules with a contour length varying from 0.12 to 0.6 microns. The functional role of this DNA is still unknown.
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Affiliation(s)
- M D Kirnos
- A.N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, USSR
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13
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Hanson MR, Folkerts O. Structure and Function of the Higher Plant Mitochondrial Genome. INTERNATIONAL REVIEW OF CYTOLOGY 1992. [DOI: 10.1016/s0074-7696(08)62065-3] [Citation(s) in RCA: 57] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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15
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Macfarlane JL, Wahleithner JA, Wolstenholme DR. A broad bean mitochondrial atp6 gene with an unusually simple, non-conserved 5' region. Curr Genet 1990; 18:87-91. [PMID: 2245478 DOI: 10.1007/bf00321121] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
A nucleotide sequence of broad bean mitochondrial DNA (mtDNA) that contains an atp6 gene of 876 ntp is presented. Relative to other plant atp6 genes, this broad bean gene comprises a 90 ntp non-conserved 5' region, a 759 ntp highly conserved central region and a 27 ntp non-conserved 3' region. The non-conserved, 5' region of the broad bean atp6 gene differs from the corresponding regions of most other plant atp6 genes in that it contains only one potential translation initiation codon and, following this codon, a 63 ntp segment that predicts an amino acid sequence with a predominance of alternating leucines.
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Affiliation(s)
- J L Macfarlane
- Department of Biology, University of Utah, Salt Lake City 84112
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16
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Macfarlane JL, Wahleithner JA, Wolstenholme DR. A gene for cytochrome c oxidase subunit III (COXIII) in broad bean mitochondrial DNA: structural features and sequence evolution. Curr Genet 1990; 17:33-40. [PMID: 2155709 DOI: 10.1007/bf00313246] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
A nucleotide sequence of broad bean mitochondrial DNA (mtDNA) that contains the coxIII gene is presented, and compared to corresponding sequences of Oenothera and corn mtDNAs. Upstream from the broad bean coxIII gene are three potential secondary structures: a single stem and loop (hairpin) that is conserved in the Oenothera and corn sequences; a second single stem and loop; and a double stem and loop. The rate of evolution of the coxIII gene has been slower in plants than in mammals. Constraints on the fixation of at least some kinds of mutations in silent (synonymous) third position nucleotides, as well as of mutations that cause amino acid replacements, seem to have contributed to this slower rate.
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Affiliation(s)
- J L Macfarlane
- Department of Biology, University of Utah, Salt Lake City 84112
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17
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Wang B, Cheng W, Li YN, Li DD. Some physicochemical properties of rice mitochondrial DNA. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 1989; 77:581-586. [PMID: 24232728 DOI: 10.1007/bf00274284] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/1988] [Accepted: 01/04/1989] [Indexed: 06/02/2023]
Abstract
Certain physicochemical properties of rice mitochondrial DNA (mtDNA) were determined. Certain low-molecular-weight mtDNA bands were found in addition to the major mtDNA band. Rice mtDNA appeared in the electron microscope as a collection of linear molecules with heterogeneous length in the range of 1-156 kb. The major distribution area was 60-105 kb. A small fraction (less than 5%) of rice mtDNA was found in the form of a circular molecule. Some molecules had the appearance of being supercoiled. Replication fork structures were found in both circular and linear mtDNA molecules. In one rice species, Jin Nante, 15 different circular molecules were found. Rice mtDNA was digested with different restriction enzymes. The total molecular weight of rice mtDNA was calculated to be about 300 kb according to the data of restriction enzyme digestion and electron microscopy.
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Affiliation(s)
- B Wang
- Institute of Genetics, Academia Sinica, Beijing, People's Republic of China
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18
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Shirzadegan M, Christey M, Earle ED, Palmer JD. Rearrangement, amplification, and assortment of mitochondrial DNA molecules in cultured cells of Brassica campestris. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 1989; 77:17-25. [PMID: 24232468 DOI: 10.1007/bf00292310] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/1988] [Accepted: 06/29/1988] [Indexed: 05/28/2023]
Abstract
We compared Brassica campestris mitochondrial and chloroplast DNAs from whole plants and from a 2-year-old cell culture. No differences were observed in the chloroplast DNAs (cpDNAs), whereas the culture mitochondrial DNA (mtDNA) was extensively altered. Hybridization analysis revealed that the alterations are due entirely to rearrangement. At least two inversions and one large duplication are found in the culture mtDNA. The duplication element is shown to have the usual properties of a plant mtDNA high frequency "recombination repeat". The culture mtDNA exists as a complex heterogeneous population of rearranged and unrearranged molecules. Some of the culture-associated rearranged molecules are present in low levels in native plant tissue and appear to have sorted out and amplified in the culture. Other mtDNA rearrangements may have occurred de novo. In addition to alterations of the main mitochondrial genome, an 11.3 kb linear mtDNA plasmid present in whole plants is absent from the culture. Contrary to findings in cultured cells of other plants, small circular mtDNA molecules were not detected in the B. campestris cell culture.
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Affiliation(s)
- M Shirzadegan
- Department of Biology, University of Michigan, 48109, Ann Arbor, MI, USA
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19
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Kadowaki K, Yazaki K, Osumi T, Harada K, Katsuta M, Nakagahra M. Distribution of mitochondrial plasmid-like DNA in cultivated rice (Oryza sativa L.) and its relationship with varietal groups. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 1988; 76:809-814. [PMID: 24232388 DOI: 10.1007/bf00273665] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/1988] [Accepted: 06/27/1988] [Indexed: 06/02/2023]
Abstract
Mitochondrial (mt) plasmid-like DNA was found in most of more than 100 rice cultivars (Oryza sativa L.) by the use of 0.7% agarose gel electrophoresis (AGE). The DNA varied in molecular weight and number. By electron microscopy, small circular DNAs of different sizes could be detected in addition to the DNAs of high molecular weight, even in cultivars in which mt plasmid-like DNA was not detected by AGE. The detection of the mt plasmid-like DNAs by AGE did not depend on their presence or absence, but on their high stoichiometry. The relationship between cytoplasms with mt plasmid-like DNAs and varietal (for example, Indica rice) groups was close. The geographical distribution of cytoplasms is discussed.
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Affiliation(s)
- K Kadowaki
- National Institute of Agrobiological Resources, Kannondai, 305, Tsukuba City, Ibaraki, Japan
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20
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Biased organelle transmission in somatic hybrids ofLycopersicon esculentum andSolanum lycopersicoides. Curr Genet 1988. [DOI: 10.1007/bf00569342] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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21
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Wahleithner JA, Wolstenholme DR. Origin and direction of replication in mitochondrial plasmid DNAs of broad bean, Vicia faba. Curr Genet 1988; 14:163-70. [PMID: 2846190 DOI: 10.1007/bf00569340] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Broad bean (Vicia faba) mitochondrial DNA (mtDNA) includes three circular plasmids: mt-plasmid 1 (1,704 ntp), mt-plasmid 2 (1,695 ntp) and mt-plasmid 3 (1,476 ntp). Partially replicated circular forms of these mt-plasmids have been observed in electron microscope preparations. Restriction enzymes that cleave either mt-plasmid 2 (but not mt-plasmids 1 and 3) or mt-plasmid 3 (but not mt-plasmids 1 and 2) were used to generate linear forms of partially replicated mt-plasmid 2 and mt-plasmid 3 molecules. Analyses of these linearized replicative intermediates, observed by electron microscopy, indicated that in both mt-plasmid 2 and mt-plasmid 3 replication originates at a specific location and proceeds in the same, single direction around the molecules. The replication origins of mt-plasmid 2 and mt-plasmid 3 map close to sequences that can fold into hairpin structures.
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Affiliation(s)
- J A Wahleithner
- Department of Biology, University of Utah, Salt Lake City 84112
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