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Hara K, Kikuchi S, Inoue M, Tsusaka T, Sakurai M, Tanabe H, Shirasawa K, Isobe S. B chromosome and its non-Mendelian inheritance in Atractylodes lancea. PLoS One 2024; 19:e0308881. [PMID: 39259755 DOI: 10.1371/journal.pone.0308881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 07/29/2024] [Indexed: 09/13/2024] Open
Abstract
Supernumerary B chromosomes contribute to intraspecific karyotypic variation. B chromosomes have been detected in more than 2000 organisms; they possess unique and diverse features, including non-Mendelian inheritance. Here, we report one or more B chromosomes in the gynodioecious plant Atractylodes lancea. Among 54 A. lancea lines, 0-2 B chromosomes were detected in both hermaphroditic and female plants, with the B chromosomes appearing as DAPI-bright regions within the nuclei. Genomic in situ hybridization revealed that the B chromosomes had no conserved A chromosome DNA sequences, confirmed by fluorescence in situ hybridization probed with independently dissected B chromosomes. In male meiosis, the B chromosome did not pair with an A chromosome and was therefore eliminated; accordingly, only 20.1% and 18.6% of these univalent B chromosomes remained at the end of meiosis for the 1B lines of KY17-148 and KY17-118, respectively. However, we also found that B chromosomes were transmitted from male parents in 40.8%-44.2% and 47.2% of the next generation; although these transmission rates from male parents were not essentially different from Mendelian inheritance (0.5), the transmission of gametes carrying B chromosomes increased through fertilization or seed development. B chromosomes were transmitted from three of four 1B female parents to 64.3%-92.6% of the next generation, suggesting B chromosome accumulation. We propose that the B chromosome of A. lancea has a specific sequence and persists via non-Mendelian inheritance from female parents. Overall, A. lancea, with its unique characteristics, is a promising model for understanding the structure, evolution, and mechanism of non-Mendelian inheritance of B chromosomes.
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Affiliation(s)
- Kazuya Hara
- Graduate School of Horticulture, Chiba University, Chiba, Japan
| | - Shinji Kikuchi
- Graduate School of Horticulture, Chiba University, Chiba, Japan
- Plant Molecular Science Center, Chiba University, Chiba, Japan
- Research Center for Space Agriculture and Horticulture, Chiba University, Chiba, Japan
| | - Misaki Inoue
- Graduate School of Horticulture, Chiba University, Chiba, Japan
| | | | - Miki Sakurai
- Botanical Raw Materials Division, Tsumura & Co., Ibaraki, Japan
| | - Hideyuki Tanabe
- Research Center for Integrative Evolutionary Science, SOKENDAI, Kanagawa, Japan
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Ribeiro T, Vasconcelos E, de Mendonça Filho JR, Sato S, de Argollo Marques D, Brasileiro-Vidal AC. Differential amplification of the subtelomeric satellite DNA JcSAT1 in the genus Jatropha L. (Euphorbiaceae). Genetica 2024; 152:43-49. [PMID: 38349466 DOI: 10.1007/s10709-024-00204-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 02/07/2024] [Indexed: 03/09/2024]
Abstract
Satellite DNAs (satDNAs) are highly repetitive sequences that occur in virtually all eukaryotic genomes and can undergo rapid copy number and nucleotide sequence variation among relatives. After chromosomal mapping of the satDNA JcSAT1, it was found a large accumulation at subtelomeres of Jatropha curcas (subgenus Curcas), but an absence of these monomers in J. integerrima (subgenus Jatropha). This fact suggests a dynamic scenario for this satellite repeat in Jatropha genomes. Here, we used a multitasking approach (sequence analysis, DNA blotting and chromosomal mapping) to investigate the molecular organization and chromosomal abundance and distribution of JcSAT1 in a broader group of species from the subgenus Jatropha (J. gossypiifolia, J. mollissima, J. podagrica, and J. multifida) in addition to J. curcas, with the aiming of understanding the evolution of this satDNA. Based on the analysis of BAC clone sequences of J. curcas, a large array (~ 30 kb) of 80 homogeneous monomers of JcSAT1 was identified in BAC 23J11. The monomer size was conserved (~ 358 bp) and contained a telomeric motif at the 5' end. PCR amplification coupled with a Southern blot revealed the presence of JcSAT1-like sequences in all species examined. However, a large set of genome copies was identified only in J. curcas, where a ladder-like pattern with multimers of different sizes was observed. In situ hybridization of BAC 23J11 confirmed the subtelomeric pattern for J. curcas, but showed no signals on chromosomes of species from the subgenus Jatropha. Our data indicate that JcSAT1 is a highly homogeneous satDNA that originated from a region near the telomeres and spread throughout the chromosomal subtermini, possibly due to frequent ectopic recombination between these regions. The abundance of JcSAT1 in the genome of J. curcas suggests that an amplification event occurred either at the base of the subgenus Curcas or at least in this species, although the repeat is shared by all species of the genus studied so far.
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Affiliation(s)
- Tiago Ribeiro
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco (UFPE), Recife, PE, 50670-423, Brazil.
- Current address: Integrative Plant Research Laboratory, Department of Botany and Ecology, Federal University of Mato Grosso (UFMT), Cuiabá, MT, 78060-900, Brazil.
| | - Emanuelle Vasconcelos
- Laboratory of Plant Genetics and Biotechnology, Department of Genetics, Federal University of Pernambuco (UFPE), Recife, PE, 50670-423, Brazil
| | - José Roseno de Mendonça Filho
- Laboratory of Plant Genetics and Biotechnology, Department of Genetics, Federal University of Pernambuco (UFPE), Recife, PE, 50670-423, Brazil
| | - Shusei Sato
- Graduate School of Life Sciences, Tohoku University, Aoba-ku, Sendai, 980-8577, Japan
| | | | - Ana Christina Brasileiro-Vidal
- Laboratory of Plant Genetics and Biotechnology, Department of Genetics, Federal University of Pernambuco (UFPE), Recife, PE, 50670-423, Brazil.
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Makai D, Mihók E, Polgári D, Cseh A, Lenykó-Thegze A, Sepsi A, Sági L. Rapid in-solution preparation of somatic and meiotic plant cell nuclei for high-quality 3D immunoFISH and immunoFISH-GISH. PLANT METHODS 2023; 19:80. [PMID: 37553677 PMCID: PMC10408160 DOI: 10.1186/s13007-023-01061-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Accepted: 07/22/2023] [Indexed: 08/10/2023]
Abstract
BACKGROUND Though multicolour labelling methods allow the routine detection of a wide range of fluorescent (immuno)probe types in molecular cytogenetics, combined applications for the simultaneous in situ detection of proteins and nucleic acids are still sporadic in plant cell biology. A major bottleneck has been the availability of high-quality plant nuclei with a balance between preservation of 3D ultrastructure and maintaining immunoreactivity. The aim of this study was to develop a quick and reliable procedure to prepare plant nuclei suitable for various combinations of immunolabelling and fluorescence in situ hybridisation methods (immunoFISH-GISH). RESULTS The mechanical removal of the cell wall and cytoplasm, instead of enzymatic degradation, resulted in a gentle, yet effective, cell permeabilisation. Rather than manually releasing the nuclei from the fixed tissues, the procedure involves in-solution cell handling throughout the fixation and the preparation steps as ended with pipetting the pure nuclei suspension onto microscope slides. The optimisation of several critical steps is described in detail. Finally, the procedure is shown to be compatible with immunolabelling, FISH and GISH as well as their simultaneous combinations. CONCLUSION A simple plant cell nuclei preparation procedure was developed for combined immunolabelling-in situ hybridisation methods. The main and critical elements of the procedure are: a short period of fixation, incorporation of detergents to facilitate the fixation of tissues and the penetration of probes, tissue grinding to eliminate unwanted cell components, and an optimal buffer to handle nuclei. The procedure is time efficient and is easily transferable without prior expertise.
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Affiliation(s)
- Diána Makai
- Centre for Agricultural Research, Eötvös Loránd Research Network, Martonvásár, 2462, Hungary
- Doctoral School of Plant Sciences, Hungarian University of Agriculture and Life Sciences, Gödöllő, 2100, Hungary
| | - Edit Mihók
- Centre for Agricultural Research, Eötvös Loránd Research Network, Martonvásár, 2462, Hungary
- Doctoral School of Plant Sciences, Hungarian University of Agriculture and Life Sciences, Gödöllő, 2100, Hungary
| | - Dávid Polgári
- Centre for Agricultural Research, Eötvös Loránd Research Network, Martonvásár, 2462, Hungary
- Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences, Gödöllő, 2100, Hungary
| | - András Cseh
- Centre for Agricultural Research, Eötvös Loránd Research Network, Martonvásár, 2462, Hungary
| | - Andrea Lenykó-Thegze
- Centre for Agricultural Research, Eötvös Loránd Research Network, Martonvásár, 2462, Hungary
- Doctoral School of Biology, Eötvös Loránd University, Budapest, 1117, Hungary
| | - Adél Sepsi
- Centre for Agricultural Research, Eötvös Loránd Research Network, Martonvásár, 2462, Hungary.
| | - László Sági
- Agribiotechnology and Precision Breeding for Food Security National Laboratory, Plant Biotechnology Section, Centre for Agricultural Research, Martonvásár, 2462, Hungary.
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Zhao Y, Liu G, Wang Z, Ning Y, Ni R, Xi M. Oligo-FISH of Populus simonii Pachytene Chromosomes Improves Karyotyping and Genome Assembly. Int J Mol Sci 2023; 24:9950. [PMID: 37373099 DOI: 10.3390/ijms24129950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 05/31/2023] [Accepted: 06/06/2023] [Indexed: 06/29/2023] Open
Abstract
Poplar was one of the first woody species whose individual chromosomes could be identified using chromosome specific painting probes. Nevertheless, high-resolution karyotype construction remains a challenge. Here, we developed a karyotype based on the meiotic pachytene chromosome of Populus simonii which is a Chinese native species with many excellent traits. This karyotype was anchored by oligonucleotide (oligo)-based chromosome specific painting probes, a centromere-specific repeat (Ps34), ribosomal DNA, and telomeric DNA. We updated the known karyotype formula for P. simonii to 2n = 2x = 38 = 26m + 8st + 4t and the karyotype was 2C. The fluorescence in situ hybridization (FISH) results revealed some errors in the current P. simonii genome assembly. The 45S rDNA loci were located at the end of the short arm of chromosomes 8 and 14 by FISH. However, they were assembled on pseudochromosomes 8 and 15. In addition, the Ps34 loci were distributed in every centromere of the P. simonii chromosome in the FISH results, but they were only found to be present in pseudochromosomes 1, 3, 6, 10, 16, 17, 18, and 19. Our results reveal that pachytene chromosomes oligo-FISH is a powerful tool for constructing high-resolution karyotypes and improving the quality of genome assembly.
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Affiliation(s)
- Yilian Zhao
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing 210037, China
| | - Guangxin Liu
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing 210037, China
| | - Ziyue Wang
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing 210037, China
| | - Yihang Ning
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing 210037, China
| | - Runxin Ni
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing 210037, China
| | - Mengli Xi
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing 210037, China
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Sugiyama M, Norizuki M, Kikuchi S, Yasui Y, Matsui K. Development and chromosomal characterization of interspecific hybrids between common buckwheat ( Fagopyrum esculentum) and a related perennial species ( F. cymosum). BREEDING SCIENCE 2023; 73:230-236. [PMID: 37404347 PMCID: PMC10316306 DOI: 10.1270/jsbbs.22063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 01/17/2023] [Indexed: 07/06/2023]
Abstract
Common buckwheat (Fagopyrum esculentum) is an annual self-incompatible plant that is widely grown. The genus Fagopyrum comprises more than 20 species, including F. cymosum, a perennial that, unlike common buckwheat, is highly resistant to excess water. In this study, we developed interspecific hybrids between F. esculentum and F. cymosum via embryo rescue, to improve undesirable traits of common buckwheat, such as low tolerance to excess water. The interspecific hybrids were confirmed by genomic in situ hybridization (GISH). We also developed DNA markers to confirm the identity of the hybrids and if genes derived from each genome were inherited by the next generation. Observations of pollen indicated that the interspecific hybrids were essentially sterile. Unpaired chromosomes and abnormal segregation during meiosis were likely responsible for the pollen sterility of the hybrids. These findings could facilitate buckwheat breeding to produce lines that can withstand harsh environments with wild or related species in the genus Fagopyrum.
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Affiliation(s)
- Mari Sugiyama
- Shimane Agricultural Technology Center, 2440 Ashiwata-cho, Izumo, Shimane 693-0035, Japan
| | - Miyu Norizuki
- Graduate School of Horticulture, Chiba University, 648 Matsudo, Matsudo-shi, Chiba 271-8510, Japan
| | - Shinji Kikuchi
- Graduate School of Horticulture, Chiba University, 648 Matsudo, Matsudo-shi, Chiba 271-8510, Japan
| | - Yasuo Yasui
- Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Sakyou-ku, Kyoto 606-8502, Japan
| | - Katsuhiro Matsui
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
- Institute of Life and Environmental Sciences, University of Tsukuba, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
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