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Muakrong N, Kikuchi S, Fukuhara S, Tanya P, Srinives P. Two jatropha karyotypes constructed from meiotic pachytene chromosomes: Pericentric distribution of heterochromatin and variation in repetitive DNAs. PLoS One 2018; 13:e0208549. [PMID: 30521604 PMCID: PMC6283608 DOI: 10.1371/journal.pone.0208549] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 11/19/2018] [Indexed: 11/19/2022] Open
Abstract
Jatropha (Jatropha curcas) is an oil-bearing plant used for biodiesel production. Construction of its standard karyotype and identification of the euchromatin/heterochromatin distribution associated with gene expression and meiotic recombination are essential to fully characterize its genome. Here, we developed a J. curcas karyotype based on meiotic pachytene chromosomes. In addition, a karyotype of J. integerrima, a useful species for jatropha breeding, was also constructed. Five out of eleven J. curcas chromosomes were metacentric, but only two were metacentric in J. integerrima. Almost all of the heterochromatin was distributed around the pericentric regions. The interstitial and distal regions were euchromatic without heterochromatic knobs, except for small heterochromatin regions associated with the subtelomeric repeat sequence JcSat1. These pericentric heterochromatin distribution patterns, together with chromosome structure data and the results of FISH probing with rDNA and JcSat1, allowed us to classify all chromosomes of both species. The two species had two 35S rDNA loci and one 5S rDNA locus; one 35S rDNA locus in J. integerrima was located on the interstitial region of the short arms. In addition, JcSat1 was found at only the heterochromatic ends of the J. curcas chromosome, not the J. integerrima chromosome. Despite the same chromosome number, the two pachytene chromosome-based karyotypes suggest variation in chromosome structure and distribution of repetitive DNAs in these two species.
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Affiliation(s)
- Narathid Muakrong
- Faculty of Agriculture, Princess of Naradhiwas University, Narathiwat, Thailand
- Laboratory of Genetics and Plant Breeding, Graduate School of Horticulture, Chiba University, Matsudo, Chiba, Japan
- Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Kamphaeng Saen, Nakhon Pathom, Thailand
| | - Shinji Kikuchi
- Laboratory of Genetics and Plant Breeding, Graduate School of Horticulture, Chiba University, Matsudo, Chiba, Japan
- * E-mail: (PS); (SK)
| | - Shuto Fukuhara
- Laboratory of Genetics and Plant Breeding, Graduate School of Horticulture, Chiba University, Matsudo, Chiba, Japan
| | - Patcharin Tanya
- Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Kamphaeng Saen, Nakhon Pathom, Thailand
| | - Peerasak Srinives
- Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Kamphaeng Saen, Nakhon Pathom, Thailand
- Associate Fellow of the Royal Society of Thailand, Sanam Suea Pa, Dusit, Bangkok, Thailand
- * E-mail: (PS); (SK)
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Marinho AC, Vasconcelos S, Vasconcelos EV, Marques DA, Benko-Iseppon AM, Brasileiro-Vidal AC. Karyotype and genome size comparative analyses among six species of the oilseed-bearing genus Jatropha (Euphorbiaceae). Genet Mol Biol 2018; 41:442-449. [PMID: 29767665 PMCID: PMC6082239 DOI: 10.1590/1678-4685-gmb-2017-0120] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 09/19/2017] [Indexed: 01/08/2023] Open
Abstract
Jatropha is an important genus of Euphorbiaceae, with species largely used for various purposes, including the manufacturing of soaps and pharmaceutical products and applications in the bioenergetic industry. Although there have been several studies focusing J. curcas in various aspects, the karyotype features of Jatropha species are poorly known. Therefore, we analyzed six Jatropha species through fluorochrome staining (CMA/DAPI), fluorescent in situ hybridization (FISH) with 5S and 45S rDNA probes and genome size estimation by flow cytometry. Our results revealed several chromosome markers by both CMA/DAPI and FISH for the analyzed species. Five Jatropha species (J. curcas, J. gossypiifolia, J. integerrima, J. multifida and J. podagrica) showed four CMA-positive (CMA+) bands associated with the 5S and 45S rDNA sites (one and two pairs, respectively). However, J. mollissima displayed six CMA+/DAPI- bands co-localized with both 5S and 45S rDNA, which showed a FISH superposition. A gradual variation in the genome sizes was observed (2C = 0.64 to 0.86 pg), although an association between evidenced heterochromatin and genome sizes was not found among species. Except for the unique banding pattern of J. mollissima and the pericentromeric heterochromatin of J. curcas and J. podagrica, our data evidenced relatively conserved karyotypes.
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Affiliation(s)
- Anne C.T.A. Marinho
- Universidade Federal de
PernambucoUniversidade Federal de
PernambucoDepartment of GeneticsRecifePEBrazilDepartment of Genetics, Universidade
Federal de Pernambuco, Recife, PE, Brazil
| | - Santelmo Vasconcelos
- Instituto Tecnológico ValeInstituto Tecnológico ValeBelémPABrazilInstituto Tecnológico Vale, Belém, PA,
Brazil
| | - Emanuelle V. Vasconcelos
- Universidade Federal de
PernambucoUniversidade Federal de
PernambucoDepartment of GeneticsRecifePEBrazilDepartment of Genetics, Universidade
Federal de Pernambuco, Recife, PE, Brazil
| | - Daniela A. Marques
- Instituto AgronômicoInstituto AgronômicoCentro de P&D de Recursos Genéticos
VegetaisCampinasSPBrazilCentro de P&D de Recursos Genéticos
Vegetais, Instituto Agronômico, Campinas, SP, Brazil
| | - Ana Maria Benko-Iseppon
- Universidade Federal de
PernambucoUniversidade Federal de
PernambucoDepartment of GeneticsRecifePEBrazilDepartment of Genetics, Universidade
Federal de Pernambuco, Recife, PE, Brazil
| | - Ana Christina Brasileiro-Vidal
- Universidade Federal de
PernambucoUniversidade Federal de
PernambucoDepartment of GeneticsRecifePEBrazilDepartment of Genetics, Universidade
Federal de Pernambuco, Recife, PE, Brazil
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Muakrong N, Kikuchi S, Tanya P, Srinives P. Conservation and Variation of 35S Ribosomal DNA among Five <i>Jatropha</i> Species Revealed by Fluorescence <i>In Situ</i> Hybridization. CYTOLOGIA 2018. [DOI: 10.1508/cytologia.83.57] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Narathid Muakrong
- Laboratory of Genetics and Plant Breeding, Graduate School of Horticulture, Chiba University
- Faculty of Agriculture, Princess Naradhiwas University
| | - Shinji Kikuchi
- Laboratory of Genetics and Plant Breeding, Graduate School of Horticulture, Chiba University
| | - Patcharin Tanya
- Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University
- Center for Advanced Studies for Agriculture and Food, Institute for Advanced Studies, Kasetsart University
| | - Peerasak Srinives
- Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University
- Center for Advanced Studies for Agriculture and Food, Institute for Advanced Studies, Kasetsart University
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Santana KCB, Pinangé DSB, Vasconcelos S, Oliveira AR, Brasileiro-Vidal AC, Alves MV, Benko-Iseppon AM. Unraveling the karyotype structure of the spurges Euphorbia hirta Linnaeus, 1753 and E. hyssopifolia Linnaeus, 1753 (Euphorbiaceae) using genome size estimation and heterochromatin differentiation. COMPARATIVE CYTOGENETICS 2016; 10:657-669. [PMID: 28123686 PMCID: PMC5240516 DOI: 10.3897/compcytogen.v10i4.8193] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Accepted: 04/23/2016] [Indexed: 05/09/2023]
Abstract
Euphorbia Linnaeus, 1753 (Euphorbiaceae) is one of the most diverse and complex genera among the angiosperms, showing a huge diversity in morphologic traits and ecologic patterns. In order to improve the knowledge of the karyotype organization of Euphorbia hirta (2n = 18) and Euphorbia hyssopifolia (2n = 12), cytogenetic studies were performed by means of conventional staining with Giemsa, genome size estimations with flow cytometry, heterochromatin differentiation with chromomycin A3 (CMA) and 4',6-diamidino-2-phenylindole (DAPI) and Giemsa C-banding, fluorescent in situ hybridization (FISH) with 45S and 5S rDNA probes, and impregnation with silver nitrate (AgNO3). Our results revealed small metacentric chromosomes, CMA+/DAPI0 heterochromatin in the pericentromeric regions of all chromosomes and CMA+/DAPI- in the distal part of chromosome arms carriers of nucleolar organizing regions (NORs). The DNA content measurements revealed small genomes for both species: Euphorbia hirta with 2C = 0.77 pg and Euphorbia hyssopifolia with 2C = 1.41 pg. After FISH procedures, Euphorbia hirta, and Euphorbia hyssopifolia presented three and four pairs of terminal 45S rDNA sites, respectively, colocalizing with CMA+ heterochromatic blocks, besides only one interstitial pair of 5S rDNA signals. Additionally, the maximum number of active NORs agreed with the total number of observed 45S rDNA sites. This work represents the first analysis using FISH in the subfamily Euphorbioideae, revealing a significant number of chromosomal markers, which may be very helpful to understand evolutionary patterns among Euphorbia species.
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Affiliation(s)
- Karla C. B. Santana
- Departamento de Genética, Centro de Ciências Biológicas, Universidade Federal de Pernambuco, Av. da Engenharia s/n, CEP 50740-600 Recife, PE, Brazil
| | - Diego S. B. Pinangé
- Departamento de Genética, Centro de Ciências Biológicas, Universidade Federal de Pernambuco, Av. da Engenharia s/n, CEP 50740-600 Recife, PE, Brazil
- Departamento de Botânica, Centro de Ciências Biológicas, Universidade Federal de Pernambuco, Rua Prof. Nelson Chaves s/n, CEP 50670-901 Recife, PE, Brazil
| | - Santelmo Vasconcelos
- Departamento de Genética, Centro de Ciências Biológicas, Universidade Federal de Pernambuco, Av. da Engenharia s/n, CEP 50740-600 Recife, PE, Brazil
- Department of Sustainable Development, Vale Institute of Technology, Rua Boaventura da Silva, 955, Umarizal, CEP 66055-090, Belém, PA, Brazil
| | - Ana R. Oliveira
- Departamento de Genética, Centro de Ciências Biológicas, Universidade Federal de Pernambuco, Av. da Engenharia s/n, CEP 50740-600 Recife, PE, Brazil
| | - Ana C. Brasileiro-Vidal
- Departamento de Genética, Centro de Ciências Biológicas, Universidade Federal de Pernambuco, Av. da Engenharia s/n, CEP 50740-600 Recife, PE, Brazil
| | - Marccus V. Alves
- Departamento de Botânica, Centro de Ciências Biológicas, Universidade Federal de Pernambuco, Rua Prof. Nelson Chaves s/n, CEP 50670-901 Recife, PE, Brazil
| | - Ana M. Benko-Iseppon
- Departamento de Genética, Centro de Ciências Biológicas, Universidade Federal de Pernambuco, Av. da Engenharia s/n, CEP 50740-600 Recife, PE, Brazil
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Alipour A, Tsuchimoto S, Sakai H, Ohmido N, Fukui K. Structural characterization of copia-type retrotransposons leads to insights into the marker development in a biofuel crop, Jatropha curcas L. BIOTECHNOLOGY FOR BIOFUELS 2013; 6:129. [PMID: 24020916 PMCID: PMC3852365 DOI: 10.1186/1754-6834-6-129] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Accepted: 09/02/2013] [Indexed: 05/14/2023]
Abstract
BACKGROUND Recently, Jatropha curcas L. has attracted worldwide attention for its potential as a source of biodiesel. However, most DNA markers have demonstrated high levels of genetic similarity among and within jatropha populations around the globe. Despite promising features of copia-type retrotransposons as ideal genetic tools for gene tagging, mutagenesis, and marker-assisted selection, they have not been characterized in the jatropha genome yet. Here, we examined the diversity, evolution, and genome-wide organization of copia-type retrotransposons in the Asian, African, and Mesoamerican accessions of jatropha, then introduced a retrotransposon-based marker for this biofuel crop. RESULTS In total, 157 PCR fragments that were amplified using the degenerate primers for the reverse transcriptase (RT) domain of copia-type retroelements were sequenced and aligned to construct the neighbor-joining tree. Phylogenetic analysis demonstrated that isolated copia RT sequences were classified into ten families, which were then grouped into three lineages. An in-depth study of the jatropha genome for the RT sequences of each family led to the characterization of full consensus sequences of the jatropha copia-type families. Estimated copy numbers of target sequences were largely different among families, as was presence of genes within 5 kb flanking regions for each family. Five copia-type families were as appealing candidates for the development of DNA marker systems. A candidate marker from family Jc7 was particularly capable of detecting genetic variation among different jatropha accessions. Fluorescence in situ hybridization (FISH) to metaphase chromosomes reveals that copia-type retrotransposons are scattered across chromosomes mainly located in the distal part regions. CONCLUSION This is the first report on genome-wide analysis and the cytogenetic mapping of copia-type retrotransposons of jatropha, leading to the discovery of families bearing high potential as DNA markers. Distinct dynamics of individual copia-type families, feasibility of a retrotransposon-based insertion polymorphism marker system in examining genetic variability, and approaches for the development of breeding strategies in jatropha using copia-type retrotransposons are discussed.
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Affiliation(s)
- Atefeh Alipour
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan
| | - Suguru Tsuchimoto
- Plant Bioengineering for Bioenergy Laboratory, Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan
| | - Hiroe Sakai
- Plant Bioengineering for Bioenergy Laboratory, Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan
| | - Nobuko Ohmido
- Graduate School of Human Development and Environment, Kobe University, Kobe, Hyogo 657-8501, Japan
| | - Kiichi Fukui
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan
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Vasconcelos S, Souza AAD, Gusmão CLS, Milani M, Benko-Iseppon AM, Brasileiro-Vidal AC. Heterochromatin and rDNA 5S and 45S sites as reliable cytogenetic markers for castor bean (Ricinus communis, Euphorbiaceae). Micron 2010; 41:746-53. [PMID: 20615717 DOI: 10.1016/j.micron.2010.06.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2010] [Revised: 06/10/2010] [Accepted: 06/14/2010] [Indexed: 11/24/2022]
Abstract
The increasing need for renewable energy resources has led to higher demands for biofuel, a scenario where the castor bean (Ricinus communis L.) seed oil represents a promising source of raw material. Despite that, information regarding the genome organization of R. communis is still scarce, impairing the application of modern biotechnological and breeding procedures. The present work brings the first evaluation of the mitotic chromosomes of this species, including 10 potentially interesting accessions for cultivation in semi-arid environments aiming at the biofuel production. The approach included standard staining, fluorochrome staining (CMA/DAPI), fluorescent in situ hybridization (FISH) with rDNA 5S and 45S, as well as silver impregnation. All accessions were diploid with 2n=2x=20, displaying mainly metacentric chromosomes, with CMA-positive bands (GC-rich) in all pairs of the complement. After silver impregnation, one to 14 nucleoli were observed, while the FISH with rDNA 45S revealed two large sites and a variety of minor dots, and the DNAr 5S hybridized in a single pair. The observed features were discussed and compared with literature data regarding pachytene bivalents.
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Affiliation(s)
- Santelmo Vasconcelos
- Department of Genetics, Federal University of Pernambuco, Av. Prof. Moraes Rego s/n, Recife, PE, Brazil
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