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Dias S, Souza RC, Vasconcelos EV, Vasconcelos S, da Silva Oliveira AR, do Vale Martins L, de Oliveira Bustamante F, da Costa VA, Souza G, da Costa AF, Benko-Iseppon AM, Knytl M, Brasileiro-Vidal AC. Cytomolecular diversity among Vigna Savi (Leguminosae) subgenera. PROTOPLASMA 2024; 261:859-875. [PMID: 38467939 DOI: 10.1007/s00709-024-01944-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 03/04/2024] [Indexed: 03/13/2024]
Abstract
The genus Vigna (Leguminosae) comprises about 150 species grouped into five subgenera. The present study aimed to improve the understanding of karyotype diversity and evolution in Vigna, using new and previously published data through different cytogenetic and DNA content approaches. In the Vigna subgenera, we observed a random distribution of rDNA patterns. The 35S rDNA varied in position, from terminal to proximal, and in number, ranging from one (V. aconitifolia, V. subg. Ceratotropis) to seven pairs (V. unguiculata subsp. unguiculata, V. subg. Vigna). On the other hand, the number of 5S rDNA was conserved (one or two pairs), except for V. radiata (V. subg. Ceratotropis), which had three pairs. Genome size was relatively conserved within the genus, ranging from 1C = 0.43 to 0.70 pg in V. oblongifolia and V. unguiculata subsp. unguiculata, respectively, both belonging to V. subg. Vigna. However, we observed a positive correlation between DNA content and the number of 35S rDNA sites. In addition, data from chromosome-specific BAC-FISH suggest that the ancestral 35S rDNA locus is conserved on chromosome 6 within Vigna. Considering the rapid diversification in the number and position of rDNA sites, such conservation is surprising and suggests that additional sites may have spread out from this ancestral locus.
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Affiliation(s)
- Sibelle Dias
- Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco, Recife, PE, Brazil
| | - Rosilda Cintra Souza
- Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco, Recife, PE, Brazil
- Laboratório de Imunopatologia Keizo Asami, Universidade Federal de Pernambuco, Recife, PE, Brazil
| | | | | | | | - Lívia do Vale Martins
- Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco, Recife, PE, Brazil
- Campus Amilcar Ferreira Sobral, Universidade Federal Do Piauí, Floriano, PI, Brazil
| | - Fernanda de Oliveira Bustamante
- Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco, Recife, PE, Brazil
- Universidade Do Estado de Minas Gerais - Unidade Divinópolis, Divinópolis, MG, Brazil
| | - Victor Alves da Costa
- Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco, Recife, PE, Brazil
| | - Gustavo Souza
- Departamento de Botânica, Centro de Biociências, Universidade Federal de Pernambuco, Recife, PE, Brazil
| | | | - Ana Maria Benko-Iseppon
- Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco, Recife, PE, Brazil
| | - Martin Knytl
- Department of Biology, McMaster University, 1280 Main Street West, Hamilton, ON, L8S4K1, Canada
- Department of Cell Biology, Faculty of Science, Charles University, Viničná 7, Prague, 12843, Czech Republic
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Stiehl-Alves EM, Vieira AT, Trevelin C, Cristante Martins A, Souza-Chies TTD, Kaltchuk-Santos E. Can ploidy levels explain the variation of Herbertia lahue (Iridaceae)? Genet Mol Biol 2024; 46:e20230137. [PMID: 39261305 DOI: 10.1590/1678-4685-gmb-2023-0137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 06/15/2024] [Indexed: 09/13/2024] Open
Abstract
Polyploidy is often related with phenotypic variation, as observed in Herbertia lahue, a geophyte species. This study examined the H. lahue polyploid series and departure in cytogenetic, morphometric, and pollen data. Diploids (2n=2x=14) present bimodal karyotype with two long and five short chromosome pairs, while hexaploids (2n=6x=42) and octoploids (2n=8x=56) present a gradual decrease in chromosome size. All cytotypes have CMA+/DAPI- bands co-localized with 18S rDNA sites in the satellite region (no DAPI+ bands in any cytotype). Unlike diploids and octoploids, 5S rDNA interstitial sites in hexaploids are not in a syntenic position with 18S rDNA sites. Genome size is effective as an indirect predictor of the cytotypes since 2C-values increased according to ploidy level. The reduction in the number of the rDNA sites in polyploids associated with their lower 1Cx-values compared to diploids may suggest a genome downsizing process. Morphometric analysis revealed significant differences among cytotypes, and discriminant analysis identified three morphometric groupings corresponding to the cytotypes. The phenotypic variation observed in pollen grains, bulbs, and ovary characters suggested the gigas effect. Concluding, remarkable differentiation was observed at both genomic and phenotypic characters in all the cytotypes analyzed, suggesting a possible ongoing speciation process in H. lahue.
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Affiliation(s)
- Eudes Maria Stiehl-Alves
- Universidade Federal do Rio Grande do Sul, Instituto de Biociências, Programa de Pós-Graduação em Botânica, Porto Alegre, RS, Brazil
| | - Ariane Tonetto Vieira
- Universidade Federal do Rio Grande do Sul, Instituto de Biociências, Programa de Pós-Graduação em Genética e Biologia Molecular, Porto Alegre, RS, Brazil
| | - Caroline Trevelin
- Universidade Federal do Rio Grande do Sul, Instituto de Biociências, Departamento de Genética, Porto Alegre, RS, Brazil
| | - Alexandre Cristante Martins
- Universidade Federal do Rio Grande do Sul, Instituto de Biociências, Programa de Pós-Graduação em Botânica, Porto Alegre, RS, Brazil
| | - Tatiana Teixeira de Souza-Chies
- Universidade Federal do Rio Grande do Sul, Instituto de Biociências, Programa de Pós-Graduação em Botânica, Porto Alegre, RS, Brazil
| | - Eliane Kaltchuk-Santos
- Universidade Federal do Rio Grande do Sul, Instituto de Biociências, Programa de Pós-Graduação em Botânica, Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul, Instituto de Biociências, Programa de Pós-Graduação em Genética e Biologia Molecular, Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul, Instituto de Biociências, Departamento de Genética, Porto Alegre, RS, Brazil
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Dias Y, Mata-Sucre Y, Thangavel G, Costa L, Báez M, Houben A, Marques A, Pedrosa-Harand A. How diverse a monocentric chromosome can be? Repeatome and centromeric organization of Juncus effusus (Juncaceae). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:1832-1847. [PMID: 38461471 DOI: 10.1111/tpj.16712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 02/19/2024] [Accepted: 02/28/2024] [Indexed: 03/12/2024]
Abstract
Juncus is the largest genus of Juncaceae and was considered holocentric for a long time. Recent findings, however, indicated that 11 species from different clades of the genus have monocentric chromosomes. Thus, the Juncus centromere organization and evolution need to be reassessed. We aimed to investigate the major repetitive DNA sequences of two accessions of Juncus effusus and its centromeric structure by employing whole-genome analyses, fluorescent in situ hybridization, CENH3 immunodetection, and chromatin immunoprecipitation sequencing. We showed that the repetitive fraction of the small J. effusus genome (~270 Mbp/1C) is mainly composed of Class I and Class II transposable elements (TEs) and satellite DNAs. Three identified satellite DNA families were mainly (peri)centromeric, with two being associated with the centromeric protein CENH3, but not strictly centromeric. Two types of centromere organization were discerned in J. effusus: type 1 was characterized by a single CENH3 domain enriched with JefSAT1-155 or JefSAT2-180, whereas type 2 showed multiple CENH3 domains interrupted by other satellites, TEs or genes. Furthermore, while type 1 centromeres showed a higher degree of satellite identity along the array, type 2 centromeres had less homogenized arrays along the multiple CENH3 domains per chromosome. Although the analyses confirmed the monocentric organization of J. effusus chromosomes, our data indicate a more dynamic arrangement of J. effusus centromeres than observed for other plant species, suggesting it may constitute a transient state between mono- and holocentricity.
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Affiliation(s)
- Yhanndra Dias
- Laboratório de Citogenética e Evolução Vegetal, Departamento de Botânica, Centro de Biociências, Universidade Federal de Pernambuco, Recife, Pernambuco, 50670-901, Brazil
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, 06466, Germany
| | - Yennifer Mata-Sucre
- Laboratório de Citogenética e Evolução Vegetal, Departamento de Botânica, Centro de Biociências, Universidade Federal de Pernambuco, Recife, Pernambuco, 50670-901, Brazil
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, Cologne, 50829, Germany
| | - Gokilavani Thangavel
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, Cologne, 50829, Germany
| | - Lucas Costa
- Laboratório de Citogenética e Evolução Vegetal, Departamento de Botânica, Centro de Biociências, Universidade Federal de Pernambuco, Recife, Pernambuco, 50670-901, Brazil
| | - Mariana Báez
- Laboratório de Citogenética e Evolução Vegetal, Departamento de Botânica, Centro de Biociências, Universidade Federal de Pernambuco, Recife, Pernambuco, 50670-901, Brazil
- Plant Breeding Department, University of Bonn, Bonn, Germany
| | - Andreas Houben
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, 06466, Germany
| | - André Marques
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, Cologne, 50829, Germany
| | - Andrea Pedrosa-Harand
- Laboratório de Citogenética e Evolução Vegetal, Departamento de Botânica, Centro de Biociências, Universidade Federal de Pernambuco, Recife, Pernambuco, 50670-901, Brazil
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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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Dias S, de Oliveira Bustamante F, do Vale Martins L, da Costa VA, Montenegro C, Oliveira ARDS, de Lima GS, Braz GT, Jiang J, da Costa AF, Benko-Iseppon AM, Brasileiro-Vidal AC. Translocations and inversions: major chromosomal rearrangements during Vigna (Leguminosae) evolution. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:29. [PMID: 38261028 DOI: 10.1007/s00122-024-04546-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 01/05/2024] [Indexed: 01/24/2024]
Abstract
KEY MESSAGE Inversions and translocations are the major chromosomal rearrangements involved in Vigna subgenera evolution, being Vigna vexillata the most divergent species. Centromeric repositioning seems to be frequent within the genus. Oligonucleotide-based fluorescence in situ hybridization (Oligo-FISH) provides a powerful chromosome identification system for inferring plant chromosomal evolution. Aiming to understand macrosynteny, chromosomal diversity, and the evolution of bean species from five Vigna subgenera, we constructed cytogenetic maps for eight taxa using oligo-FISH-based chromosome identification. We used oligopainting probes from chromosomes 2 and 3 of Phaseolus vulgaris L. and two barcode probes designed from V. unguiculata (L.) Walp. genome. Additionally, we analyzed genomic blocks among the Ancestral Phaseoleae Karyotype (APK), two V. unguiculata subspecies (V. subg. Vigna), and V. angularis (Willd.) Ohwi & Ohashi (V. subg. Ceratotropis). We observed macrosynteny for chromosomes 2, 3, 4, 6, 7, 8, 9, and 10 in all investigated taxa except for V. vexillata (L.) A. Rich (V. subg. Plectrotropis), in which only chromosomes 4, 7, and 9 were unambiguously identified. Collinearity breaks involved with chromosomes 2 and 3 were revealed. We identified minor differences in the painting pattern among the subgenera, in addition to multiple intra- and interblock inversions and intrachromosomal translocations. Other rearrangements included a pericentric inversion in chromosome 4 (V. subg. Vigna), a reciprocal translocation between chromosomes 1 and 5 (V. subg. Ceratotropis), a potential deletion in chromosome 11 of V. radiata (L.) Wilczek, as well as multiple intrablock inversions and centromere repositioning via genomic blocks. Our study allowed the visualization of karyotypic patterns in each subgenus, revealing important information for understanding intrageneric karyotypic evolution, and suggesting V. vexillata as the most karyotypically divergent species.
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Affiliation(s)
- Sibelle Dias
- Departamento de Genética, Universidade Federal de Pernambuco, Recife, PE, Brazil
| | - Fernanda de Oliveira Bustamante
- Departamento de Genética, Universidade Federal de Pernambuco, Recife, PE, Brazil
- Universidade do Estado de Minas Gerais, Unidade Divinópolis, Divinópolis, MG, Brazil
| | - Lívia do Vale Martins
- Departamento de Genética, Universidade Federal de Pernambuco, Recife, PE, Brazil
- Universidade Federal do Piauí, Floriano, PI, Brazil
| | | | - Claudio Montenegro
- Departamento de Botânica, Universidade Federal de Pernambuco, Recife, PE, Brazil
| | | | - Geyse Santos de Lima
- Departamento de Genética, Universidade Federal de Pernambuco, Recife, PE, Brazil
| | - Guilherme Tomaz Braz
- Departamento de Biologia, Universidade Estadual de Campinas, Campinas, SP, Brazil
- Department of Plant Biology, Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
| | - Jiming Jiang
- Department of Plant Biology, Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
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Mata-Sucre Y, Matzenauer W, Castro N, Huettel B, Pedrosa-Harand A, Marques A, Souza G. Repeat-based phylogenomics shed light on unclear relationships in the monocentric genus Juncus L. (Juncaceae). Mol Phylogenet Evol 2023; 189:107930. [PMID: 37717642 DOI: 10.1016/j.ympev.2023.107930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 09/12/2023] [Accepted: 09/14/2023] [Indexed: 09/19/2023]
Abstract
The repetitive fraction (repeatome) of eukaryotic genomes is diverse and usually fast evolving, being an important tool for clarify plant systematics. The genus Juncus L. comprises 332 species, karyotypically recognized by having holocentric chromosomes. However, four species were recently described as monocentric, yet our understanding of their genome evolution is largely masked by unclear phylogenetic relationships. Here, we reassess the current Juncus systematics using low-coverage genome skimming data of 33 taxa to construct repeats, nuclear rDNA and plastome-based phylogenetic hypothesis. Furthermore, we characterize the repeatome and chromosomal distribution of Juncus-specific centromeric repeats/CENH3 protein to test the monocentricity reach in the genus. Repeat-base phylogenies revealed topologies congruent with the rDNA tree, but not with the plastome tree. The incongruence between nuclear and plastome chloroplast dataset suggest an ancient hybridization in the divergence of Juncotypus and Tenageia sections 40 Myr ago. The phylogenetic resolution at section level was better fitted with the rDNA/repeat-based approaches, with the recognition of two monophyletic sections (Stygiopsis and Tenageia). We found specific repeatome trends for the main lineages, such as the higher abundances of TEs in the Caespitosi and Iridifolii + Ozophyllum clades. CENH3 immunostaining confirmed the monocentricity of Juncus, which can be a generic synapomorphy for the genus. The heterogeneity of the repeatomes, with high phylogenetic informativeness, identified here may be correlated with their ancient origin (56 Mya) and reveals the potential of comparative genomic analyses for understanding plant systematics and evolution.
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Affiliation(s)
- Yennifer Mata-Sucre
- Laboratório de Citogenética e Evolução Vegetal, Departamento de Botânica, Centro de Biociências, Universidade Federal de Pernambuco. Recife PE 50670-901, Brasil
| | - William Matzenauer
- Laboratório de Morfo-Taxonomia Vegetal, Departamento de Botânica, Centro de Biociências, Universidade Federal de Pernambuco, Recife PE 50670-901, Brasil
| | - Natália Castro
- Laboratório de Citogenética e Evolução Vegetal, Departamento de Botânica, Centro de Biociências, Universidade Federal de Pernambuco. Recife PE 50670-901, Brasil
| | - Bruno Huettel
- Max Planck Genome-Centre Cologne, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Andrea Pedrosa-Harand
- Laboratório de Citogenética e Evolução Vegetal, Departamento de Botânica, Centro de Biociências, Universidade Federal de Pernambuco. Recife PE 50670-901, Brasil
| | - André Marques
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Gustavo Souza
- Laboratório de Citogenética e Evolução Vegetal, Departamento de Botânica, Centro de Biociências, Universidade Federal de Pernambuco. Recife PE 50670-901, Brasil.
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Ferraz ME, Ribeiro T, Sader M, Nascimento T, Pedrosa-Harand A. Comparative analysis of repetitive DNA in dysploid and non-dysploid Phaseolus beans. Chromosome Res 2023; 31:30. [PMID: 37812264 DOI: 10.1007/s10577-023-09739-3] [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: 07/11/2023] [Revised: 08/31/2023] [Accepted: 09/15/2023] [Indexed: 10/10/2023]
Abstract
Structural karyotype changes result from ectopic recombination events frequently associated with repetitive DNA. Although most Phaseolus species present relatively stable karyotypes with 2n = 22 chromosomes, the karyotypes of species of the Leptostachyus group show high rates of structural rearrangements, including a nested chromosome fusion that led to the dysploid chromosome number of the group (2n = 20). We examined the roles of repetitive landscapes in the rearrangements of species of the Leptostachyus group using genome-skimming data to characterize the repeatome in a range of Phaseolus species and compared them to species of that group (P. leptostachyus and P. macvaughii). LTR retrotransposons, especially the Ty3/gypsy lineage Chromovirus, were the most abundant elements in the genomes. Differences in the abundance of Tekay, Retand, and SIRE elements between P. macvaughii and P. leptostachyus were reflected in their total amounts of Ty3/gypsy and Ty1/copia. The satellite DNA fraction was the most divergent among the species, varying both in abundance and distribution, even between P. leptostachyus and P. macvaughii. The rapid turnover of repeats in the Leptostachyus group may be associated with the several rearrangements observed.
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Affiliation(s)
- Maria Eduarda Ferraz
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Biosciences Centre, Federal University of Pernambuco, Recife, PE, Brazil
| | - Tiago Ribeiro
- Integrative Plant Research Lab, Department of Botany and Ecology, Institute of Biosciences, Federal University of Mato Grosso, Cuiabá, MT, Brazil
| | - Mariela Sader
- Multidisciplinary Institute of Plant Biology, National Council for Scientific and Technical Research, National University of Córdoba, Córdoba, Argentina
| | - Thiago Nascimento
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Biosciences Centre, Federal University of Pernambuco, Recife, PE, Brazil
| | - Andrea Pedrosa-Harand
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Biosciences Centre, Federal University of Pernambuco, Recife, PE, Brazil.
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Ramos LC, Báez M, Fuchs J, Houben A, Carvalho R, Pedrosa-Harand A. Differential Repeat Accumulation in the Bimodal Karyotype of Agave L. Genes (Basel) 2023; 14:491. [PMID: 36833420 PMCID: PMC9956584 DOI: 10.3390/genes14020491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Revised: 02/10/2023] [Accepted: 02/10/2023] [Indexed: 02/17/2023] Open
Abstract
The genus Agave presents a bimodal karyotype with x = 30 (5L, large, +25S, small chromosomes). Bimodality within this genus is generally attributed to allopolyploidy in the ancestral form of Agavoideae. However, alternative mechanisms, such as the preferential accumulation of repetitive elements at the macrochromosomes, could also be important. Aiming to understand the role of repetitive DNA within the bimodal karyotype of Agave, genomic DNA from the commercial hybrid 11648 (2n = 2x = 60, 6.31 Gbp) was sequenced at low coverage, and the repetitive fraction was characterized. In silico analysis showed that ~67.6% of the genome is mainly composed of different LTR retrotransposon lineages and one satellite DNA family (AgSAT171). The satellite DNA localized at the centromeric regions of all chromosomes; however, stronger signals were observed for 20 of the macro- and microchromosomes. All transposable elements showed a dispersed distribution, but not uniform across the length of the chromosomes. Different distribution patterns were observed for different TE lineages, with larger accumulation at the macrochromosomes. The data indicate the differential accumulation of LTR retrotransposon lineages at the macrochromosomes, probably contributing to the bimodality. Nevertheless, the differential accumulation of the satDNA in one group of macro- and microchromosomes possibly reflects the hybrid origin of this Agave accession.
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Affiliation(s)
- Lamonier Chaves Ramos
- Laboratory of Plant Cytogenetics, Graduate Program in Agronomy, Genetic Plant Breeding—PPGAMGP, Department of Agronomy, Federal Rural University of Pernambuco, Recife 52171-900, Brazil
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Recife 50670-420, Brazil
| | - Mariana Báez
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Recife 50670-420, Brazil
- Plant Breeding Department, University of Bonn, Katzenburgweg 5, 53115 Bonn, Germany
| | - Joerg Fuchs
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Stadt Seeland, Germany
| | - Andreas Houben
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Stadt Seeland, Germany
| | - Reginaldo Carvalho
- Laboratory of Plant Cytogenetics, Graduate Program in Agronomy, Genetic Plant Breeding—PPGAMGP, Department of Agronomy, Federal Rural University of Pernambuco, Recife 52171-900, Brazil
| | - Andrea Pedrosa-Harand
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Recife 50670-420, Brazil
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Yücel G, Senderowicz M, Kolano B. The Use of Ribosomal DNA for Comparative Cytogenetics. Methods Mol Biol 2023; 2672:265-284. [PMID: 37335483 DOI: 10.1007/978-1-0716-3226-0_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2023]
Abstract
Fluorescence in situ hybridization (FISH) with ribosomal DNA (rDNA) sequences provides excellent chromosome markers for comparative cytogenetic analyses, especially in non-model plant species. The tandem repeat nature of a sequence and the presence of a highly conserved genic region make rDNA sequences relatively easy to isolate and clone. In this chapter, we describe the use of rDNA as markers for comparative cytogenetics studies. Traditionally, cloned probes labeled with Nick-translation have been used to detect rDNA loci. Recently, pre-labeled oligonucleotides are also employed quite frequently to detect both 35S and 5S rDNA loci. Ribosomal DNA sequences, together with other DNA probes in FISH/GISH or with fluorochromes such as CMA3 banding or silver staining, are very useful tools in comparative analyses of plant karyotypes.
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Affiliation(s)
- Gülru Yücel
- Plant Cytogenetics and Molecular Biology Group, Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
- Department of Agricultural Biotechnology, Faculty of Agriculture, Ondokuz Mayıs University, Samsun, Türkiye
| | - Magdalena Senderowicz
- Plant Cytogenetics and Molecular Biology Group, Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
| | - Bożena Kolano
- Plant Cytogenetics and Molecular Biology Group, Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland.
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10
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Fukai E, Yoshikawa M, Shah N, Sandal N, Miyao A, Ono S, Hirakawa H, Akyol TY, Umehara Y, Nonomura KI, Stougaard J, Hirochika H, Hayashi M, Sato S, Andersen SU, Okazaki K. Widespread and transgenerational retrotransposon activation in inter- and intraspecies recombinant inbred populations of Lotus japonicus. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 111:1397-1410. [PMID: 35792830 DOI: 10.1111/tpj.15896] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Accepted: 06/30/2022] [Indexed: 06/15/2023]
Abstract
Transposable elements (TEs) constitute a large proportion of genomes of multicellular eukaryotes, including flowering plants. TEs are normally maintained in a silenced state and their transpositions rarely occur. Hybridization between distant species has been regarded as a 'shock' that stimulates genome reorganization, including TE mobilization. However, whether crosses between genetically close parents that result in viable and fertile offspring can induce TE transpositions has remained unclear. Here, we investigated the activation of long terminal repeat (LTR) retrotransposons in three Lotus japonicus recombinant inbred line (RIL) populations. We found that at least six LTR retrotransposon families were activated and transposed in 78% of the RILs investigated. LORE1a, one of the transposed LTR retrotransposons, showed transgenerational epigenetic activation, indicating the long-term effects of epigenetic instability induced by hybridization. Our study highlights TE activation as an unexpectedly common event in plant reproduction.
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Affiliation(s)
- Eigo Fukai
- Graduate School of Science and Technology, Niigata University, Ikarashi-ninocho, 950-2181, Niigata, Japan
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, 1-2, Oowashi, Tsukuba, Ibaraki, 305-8634, Japan
- Department of Molecular Biology and Genetics, Aarhus University, 8000, Aarhus, Denmark
- Plant Cytogenetics, Department of Gene Function and Phenomics, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka, 411-8540, Japan
- Department of Technology Development, Kazusa DNA Research Institute, Kisarazu, Chiba, 292-0818, Japan
| | - Manabu Yoshikawa
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, 1-2, Oowashi, Tsukuba, Ibaraki, 305-8634, Japan
| | - Niraj Shah
- Department of Molecular Biology and Genetics, Aarhus University, 8000, Aarhus, Denmark
| | - Niels Sandal
- Department of Molecular Biology and Genetics, Aarhus University, 8000, Aarhus, Denmark
| | - Akio Miyao
- Institute of Crop Science, National Agriculture and Food Research Organization, 2-1-2, Kannondai, Tsukuba, Ibaraki, 305-8518, Japan
| | - Seijiro Ono
- Plant Cytogenetics, Department of Gene Function and Phenomics, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka, 411-8540, Japan
| | - Hideki Hirakawa
- Department of Technology Development, Kazusa DNA Research Institute, Kisarazu, Chiba, 292-0818, Japan
| | - Turgut Yigit Akyol
- Department of Molecular Biology and Genetics, Aarhus University, 8000, Aarhus, Denmark
| | - Yosuke Umehara
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, 1-2, Oowashi, Tsukuba, Ibaraki, 305-8634, Japan
| | - Ken-Ichi Nonomura
- Department of Technology Development, Kazusa DNA Research Institute, Kisarazu, Chiba, 292-0818, Japan
| | - Jens Stougaard
- Department of Molecular Biology and Genetics, Aarhus University, 8000, Aarhus, Denmark
| | - Hirohiko Hirochika
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, 1-2, Oowashi, Tsukuba, Ibaraki, 305-8634, Japan
| | - Makoto Hayashi
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, 1-2, Oowashi, Tsukuba, Ibaraki, 305-8634, Japan
- Center for Sustainable Resource Science, RIKEN, Yokohama, Kanagawa, 230-0045, Japan
| | - Shusei Sato
- Department of Technology Development, Kazusa DNA Research Institute, Kisarazu, Chiba, 292-0818, Japan
- Graduate School of Life Sciences, Tohoku University, Katahira, Aoba-ku, Sendai, Miyagi, 980-8577, Japan
| | | | - Keiichi Okazaki
- Graduate School of Science and Technology, Niigata University, Ikarashi-ninocho, 950-2181, Niigata, Japan
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11
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Hofstatter PG, Thangavel G, Lux T, Neumann P, Vondrak T, Novak P, Zhang M, Costa L, Castellani M, Scott A, Toegelová H, Fuchs J, Mata-Sucre Y, Dias Y, Vanzela AL, Huettel B, Almeida CC, Šimková H, Souza G, Pedrosa-Harand A, Macas J, Mayer KF, Houben A, Marques A. Repeat-based holocentromeres influence genome architecture and karyotype evolution. Cell 2022; 185:3153-3168.e18. [DOI: 10.1016/j.cell.2022.06.045] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 05/24/2022] [Accepted: 06/24/2022] [Indexed: 01/30/2023]
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12
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Ibiapino A, Báez M, García MA, Costea M, Stefanović S, Pedrosa-Harand A. Karyotype asymmetry in Cuscuta L. subgenus Pachystigma reflects its repeat DNA composition. Chromosome Res 2022; 30:91-107. [PMID: 35089455 DOI: 10.1007/s10577-021-09683-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 12/24/2021] [Accepted: 12/27/2021] [Indexed: 12/25/2022]
Abstract
Cuscuta is a cytogenetically diverse genus, with karyotypes varying 18-fold in chromosome number and 127-fold in genome size. Each of its four subgenera also presents particular chromosomal features, such as bimodal karyotypes in Pachystigma. We used low coverage sequencing of the Cuscuta nitida genome (subgenus Pachystigma), as well as chromosome banding and molecular cytogenetics of three subgenus representatives, to understand the origin of bimodal karyotypes. All three species, C. nitida, C. africana (2n = 28) and C. angulata (2n = 30), showed heterochromatic bands mainly in the largest chromosome pairs. Eighteen satellite DNAs were identified in C. nitida genome, two showing similarity to mobile elements. The most abundant were present at the largest pairs, as well as the highly abundant ribosomal DNAs. The most abundant Ty1/Copia and Ty3/Gypsy elements were also highly enriched in the largest pairs, except for the Ty3/Gypsy CRM, which also labelled the pericentromeric regions of the smallest chromosomes. This accumulation of repetitive DNA in the larger pairs indicates that these sequences are largely responsible for the formation of bimodal karyotypes in the subgenus Pachystigma. The repetitive DNA fraction is directly linked to karyotype evolution in Cuscuta.
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Affiliation(s)
- Amalia Ibiapino
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Recife, Brazil
| | - Mariana Báez
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Recife, Brazil.,Plant Breeding Department, University of Bonn, Bonn, Germany
| | | | - Mihai Costea
- Department of Biology, Wilfrid Laurier University, Waterloo, Ontario, Canada
| | - Saša Stefanović
- Department of Biology, University of Toronto Mississauga, Mississauga, Ontario, Canada
| | - Andrea Pedrosa-Harand
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Recife, Brazil.
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13
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Gao D, Nascimento EFMB, Leal-Bertioli SCM, Abernathy B, Jackson SA, Araujo ACG, Bertioli DJ. TAR30, a homolog of the canonical plant TTTAGGG telomeric repeat, is enriched in the proximal chromosome regions of peanut (Arachis hypogaea L.). Chromosome Res 2022; 30:77-90. [DOI: 10.1007/s10577-022-09684-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 01/07/2022] [Accepted: 01/11/2022] [Indexed: 11/03/2022]
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14
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Ibiapino A, García MA, Amorim B, Baez M, Costea M, Stefanović S, Pedrosa-Harand A. The Evolution of Cytogenetic Traits in Cuscuta (Convolvulaceae), the Genus With the Most Diverse Chromosomes in Angiosperms. FRONTIERS IN PLANT SCIENCE 2022; 13:842260. [PMID: 35432411 PMCID: PMC9011109 DOI: 10.3389/fpls.2022.842260] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 03/03/2022] [Indexed: 05/17/2023]
Abstract
Karyotypes are characterized by traits such as chromosome number, which can change through whole-genome duplication and dysploidy. In the parasitic plant genus Cuscuta (Convolvulaceae), chromosome numbers vary more than 18-fold. In addition, species of this group show the highest diversity in terms of genome size among angiosperms, as well as a wide variation in the number and distribution of 5S and 35S ribosomal DNA (rDNA) sites. To understand its karyotypic evolution, ancestral character state reconstructions were performed for chromosome number, genome size, and position of 5S and 35S rDNA sites. Previous cytogenetic data were reviewed and complemented with original chromosome counts, genome size estimates, and rDNA distribution assessed via fluorescence in situ hybridization (FISH), for two, seven, and 10 species, respectively. Starting from an ancestral chromosome number of x = 15, duplications were inferred as the prevalent evolutionary process. However, in holocentric clade (subgenus Cuscuta), dysploidy was identified as the main evolutionary mechanism, typical of holocentric karyotypes. The ancestral genome size of Cuscuta was inferred as approximately 1C = 12 Gbp, with an average genome size of 1C = 2.8 Gbp. This indicates an expansion of the genome size relative to other Convolvulaceae, which may be linked to the parasitic lifestyle of Cuscuta. Finally, the position of rDNA sites varied mostly in species with multiple sites in the same karyotype. This feature may be related to the amplification of rDNA sites in association to other repeats present in the heterochromatin. The data suggest that different mechanisms acted in different subgenera, generating the exceptional diversity of karyotypes in Cuscuta.
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Affiliation(s)
- Amalia Ibiapino
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Recife, Brazil
| | | | - Bruno Amorim
- Postgraduate Program of Biotechnology and Natural Resources of the Amazonia (PPGMBT), State University of Amazonas, Manaus, Brazil
| | - Mariana Baez
- Plant Breeding Department, University of Bonn, Bonn, Germany
| | - Mihai Costea
- Department of Biology, University of Wilfrid Laurier, Waterloo, ON, Canada
| | - Saša Stefanović
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, Canada
| | - Andrea Pedrosa-Harand
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Recife, Brazil
- *Correspondence: Miguel A. García,
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15
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Maravilla AJ, Rosato M, Álvarez I, Nieto Feliner G, Rosselló JA. Interstitial Arabidopsis-Type Telomeric Repeats in Asteraceae. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10122794. [PMID: 34961265 PMCID: PMC8705333 DOI: 10.3390/plants10122794] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 12/09/2021] [Accepted: 12/13/2021] [Indexed: 05/13/2023]
Abstract
Tandem repeats of telomeric-like motifs at intra-chromosomal regions, known as interstitial telomeric repeats (ITR), have drawn attention as potential markers of structural changes, which might convey information about evolutionary relationships if preserved through time. Building on our previous work that reported outstanding ITR polymorphisms in the genus Anacyclus, we undertook a survey across 132 Asteraceae species, focusing on the six most speciose subfamilies and considering all the ITR data published to date. The goal was to assess whether the presence, site number, and chromosomal location of ITRs convey any phylogenetic signal. We conducted fluorescent in situ hybridization (FISH) using an Arabidopsis-type telomeric sequence as a probe on karyotypes obtained from mitotic chromosomes. FISH signals of ITR sites were detected in species of subfamilies Asteroideae, Carduoideae, Cichorioideae, Gymnarhenoideae, and Mutisioideae, but not in Barnadesioideae. Although six small subfamilies have not yet been sampled, altogether, our results suggest that the dynamics of ITR formation in Asteraceae cannot accurately trace the complex karyological evolution that occurred since the early diversification of this family. Thus, ITRs do not convey a reliable signal at deep or shallow phylogenetic levels and cannot help to delimitate taxonomic categories, a conclusion that might also hold for other important families such as Fabaceae.
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Affiliation(s)
- Alexis J. Maravilla
- Jardín Botánico, Instituto Cavanilles de Biodiversidad y Biología Evolutiva, Universitat de València, c/Quart 80, E-46008 Valencia, Spain; (A.J.M.); (M.R.)
| | - Marcela Rosato
- Jardín Botánico, Instituto Cavanilles de Biodiversidad y Biología Evolutiva, Universitat de València, c/Quart 80, E-46008 Valencia, Spain; (A.J.M.); (M.R.)
| | - Inés Álvarez
- Real Jardín Botánico (RJB), Consejo Superior de Investigaciones Científicas (CSIC), Plaza de Murillo 2, E-28014 Madrid, Spain; (I.Á.); (G.N.F.)
| | - Gonzalo Nieto Feliner
- Real Jardín Botánico (RJB), Consejo Superior de Investigaciones Científicas (CSIC), Plaza de Murillo 2, E-28014 Madrid, Spain; (I.Á.); (G.N.F.)
| | - Josep A. Rosselló
- Jardín Botánico, Instituto Cavanilles de Biodiversidad y Biología Evolutiva, Universitat de València, c/Quart 80, E-46008 Valencia, Spain; (A.J.M.); (M.R.)
- Correspondence: ; Tel.: +34-963-156-800
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16
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Maravilla AJ, Rosato M, Rosselló JA. Interstitial Telomeric-like Repeats (ITR) in Seed Plants as Assessed by Molecular Cytogenetic Techniques: A Review. PLANTS (BASEL, SWITZERLAND) 2021; 10:2541. [PMID: 34834904 PMCID: PMC8621592 DOI: 10.3390/plants10112541] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 11/11/2021] [Accepted: 11/16/2021] [Indexed: 05/12/2023]
Abstract
The discovery of telomeric repeats in interstitial regions of plant chromosomes (ITRs) through molecular cytogenetic techniques was achieved several decades ago. However, the information is scattered and has not been critically evaluated from an evolutionary perspective. Based on the analysis of currently available data, it is shown that ITRs are widespread in major evolutionary lineages sampled. However, their presence has been detected in only 45.6% of the analysed families, 26.7% of the sampled genera, and in 23.8% of the studied species. The number of ITR sites greatly varies among congeneric species and higher taxonomic units, and range from one to 72 signals. ITR signals mostly occurs as homozygous loci in most species, however, odd numbers of ITR sites reflecting a hemizygous state have been reported in both gymnosperm and angiosperm groups. Overall, the presence of ITRs appears to be poor predictors of phylogenetic and taxonomic relatedness at most hierarchical levels. The presence of ITRs and the number of sites are not significantly associated to the number of chromosomes. The longitudinal distribution of ITR sites along the chromosome arms indicates that more than half of the ITR presences are between proximal and terminal locations (49.5%), followed by proximal (29.0%) and centromeric (21.5%) arm regions. Intraspecific variation concerning ITR site number, chromosomal locations, and the differential presence on homologous chromosome pairs has been reported in unrelated groups, even at the population level. This hypervariability and dynamism may have likely been overlooked in many lineages due to the very low sample sizes often used in cytogenetic studies.
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Affiliation(s)
| | | | - Josep A. Rosselló
- Jardín Botánico, ICBiBE, Universitat de València, c/Quart 80, E-46008 València, Spain; (A.J.M.); (M.R.)
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17
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Lukjanová E, Řepková J. Chromosome and Genome Diversity in the Genus Trifolium (Fabaceae). PLANTS (BASEL, SWITZERLAND) 2021; 10:2518. [PMID: 34834880 PMCID: PMC8621578 DOI: 10.3390/plants10112518] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 11/11/2021] [Accepted: 11/16/2021] [Indexed: 06/13/2023]
Abstract
Trifolium L. is an economically important genus that is characterized by variable karyotypes relating to its ploidy level and basic chromosome numbers. The advent of genomic resources combined with molecular cytogenetics provides an opportunity to develop our understanding of plant genomes in general. Here, we summarize the current state of knowledge on Trifolium genomes and chromosomes and review methodologies using molecular markers that have contributed to Trifolium research. We discuss possible future applications of cytogenetic methods in research on the Trifolium genome and chromosomes.
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Affiliation(s)
| | - Jana Řepková
- Department of Experimental Biology, Faculty of Sciences, Masaryk University, 611 37 Brno, Czech Republic;
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18
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Zhang T, Liu G, Zhao H, Braz GT, Jiang J. Chorus2: design of genome-scale oligonucleotide-based probes for fluorescence in situ hybridization. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:1967-1978. [PMID: 33960617 PMCID: PMC8486243 DOI: 10.1111/pbi.13610] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 04/11/2021] [Accepted: 04/19/2021] [Indexed: 05/04/2023]
Abstract
Oligonucleotide (oligo)-fluorescence in situ hybridization (FISH) has rapidly becoming the new generation of FISH technique in plant molecular cytogenetics research. Genome-scale identification of single-copy oligos is the foundation of successful oligo-FISH experiments. Here, we introduce Chorus2, a software that is developed specifically for oligo selection. We demonstrate that Chorus2 is highly effective to remove all repetitive elements in selection of single-copy oligos, which is critical for the development of successful FISH probes. Chorus2 is more effective than Chorus, the original version of the pipeline, and OligoMiner for repeat removal. Chorus2 allows to select oligos that are conserved among related species, which extends the usage of oligo-FISH probes among phylogenetically related plant species. We also implemented a new function in Chorus2 that allows development of FISH probes from plant species without an assembled genome. We anticipate that Chorus2 can be used in plants as well as in mammalian and other non-plant species. Chorus2 will broadly facilitate the design of FISH probes for various types of application in molecular cytogenetics research.
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Affiliation(s)
- Tao Zhang
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Co‐Innovation Center for Modern Production Technology of Grain CropsAgricultural College of Yangzhou UniversityYangzhouChina
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Joint International Research Laboratory of Agriculture and Agri‐Product Safety of Ministry of Education of ChinaYangzhou UniversityYangzhouChina
| | - Guanqing Liu
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Co‐Innovation Center for Modern Production Technology of Grain CropsAgricultural College of Yangzhou UniversityYangzhouChina
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Joint International Research Laboratory of Agriculture and Agri‐Product Safety of Ministry of Education of ChinaYangzhou UniversityYangzhouChina
| | - Hainan Zhao
- Department of Plant BiologyMichigan State UniversityEast LansingMIUSA
| | - Guilherme T. Braz
- Department of Plant BiologyMichigan State UniversityEast LansingMIUSA
| | - Jiming Jiang
- Department of Plant BiologyMichigan State UniversityEast LansingMIUSA
- Department of HorticultureMichigan State UniversityEast LansingMIUSA
- Michigan State University AgBioResearchEast LansingMIUSA
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19
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Leal-Bertioli SCM, Nascimento EFMB, Chavarro MCF, Custódio AR, Hopkins MS, Moretzsohn MC, Bertioli DJ, Araújo ACG. Spontaneous generation of diversity in Arachis neopolyploids (Arachis ipaënsis × Arachis duranensis)4x replays the early stages of peanut evolution. G3-GENES GENOMES GENETICS 2021; 11:6353644. [PMID: 34510200 PMCID: PMC8527490 DOI: 10.1093/g3journal/jkab289] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 08/01/2021] [Indexed: 02/05/2023]
Abstract
Polyploidy is considered a driving force in plant evolution and domestication. Although in the genus Arachis, several diploid species were traditionally cultivated for their seeds, only the allotetraploid peanut Arachis hypogaea became the successful, widely spread legume crop. This suggests that polyploidy has given selective advantage for domestication of peanut. Here, we study induced allotetraploid (neopolyploid) lineages obtained from crosses between the peanut's progenitor species, Arachis ipaënsis and Arachis duranensis, at earlier and later generations. We observed plant morphology, seed dimensions, and genome structure using cytogenetics (FISH and GISH) and SNP genotyping. The neopolyploid lineages show more variable fertility and seed morphology than their progenitors and cultivated peanut. They also showed sexual and somatic genome instability, evidenced by changes of number of detectable 45S rDNA sites, and extensive homoeologous recombination indicated by mosaic patterns of chromosomes and changes in dosage of SNP alleles derived from the diploid species. Genome instability was not randomly distributed across the genome: the more syntenic chromosomes, the higher homoeologous recombination. Instability levels are higher than observed on peanut lines, therefore it is likely that more unstable lines tend to perish. We conclude that early stages of the origin and domestication of the allotetraploid peanut involved two genetic bottlenecks: the first, common to most allotetraploids, is composed of the rare hybridization and polyploidization events, followed by sexual reproductive isolation from its wild diploid relatives. Here, we suggest a second bottleneck: the survival of the only very few lineages that had stronger mechanisms for limiting genomic instability.
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Affiliation(s)
- Soraya C M Leal-Bertioli
- Institute of Plant Breeding, Genetics and Genomics, Athens, GA 30602-6810, USA.,Department of Plant Pathology, University of Georgia, Athens, GA 30602, USA
| | - Eliza F M B Nascimento
- Embrapa Genetic Resources and Biotechnology, Brasília, 70770-917, Brazill.,Institute of Biological Sciences, University of Brasilia, Brasília, 70910-000, Brazil
| | | | - Adriana R Custódio
- Embrapa Genetic Resources and Biotechnology, Brasília, 70770-917, Brazill
| | - Mark S Hopkins
- Institute of Plant Breeding, Genetics and Genomics, Athens, GA 30602-6810, USA
| | | | - David J Bertioli
- Institute of Plant Breeding, Genetics and Genomics, Athens, GA 30602-6810, USA.,Department of Crop and Soil Science, University of Georgia, Athens, GA 30602-6810, USA
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20
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Ribeiro T, Nascimento J, Santos A, Félix LP, Guerra M. Origin and evolution of highly polymorphic rDNA sites in Alstroemeria longistaminea (Alstroemeriaceae) and related species. Genome 2021; 64:833-845. [PMID: 33852822 DOI: 10.1139/gen-2020-0159] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Alstroemeria (Alstroemeriaceae) displays a conserved and highly asymmetric karyotype, where most rDNA sites can be properly recognized by the size and morphology of the chromosomes. We analyzed the intraspecific variation of rDNA sites in A. longistaminea and compared with their distribution in other species (A. caryophyllaea and A. piauhyensis) and a representative of a sister genus, Bomarea edulis. All three species of Alstroemeria presented 2n = 16, and one to six B chromosomes were found in some individuals of A. longistaminea. There was a set of 12 conserved rDNA sites (four 5S and eight 35S) and up to 11 variable sites. B chromosomes were almost entirely covered by 35S signals, coupled with tiny 5S sites. Noteworthy, most rDNA sites found in A. caryophyllaea and A. piauhyensis were localized in chromosome positions similar to those in A. longistaminea, suggesting the existence of conserved hotspots for rDNA accumulation. Some of these hotspots were absent in Chilean Alstromeria as well in B. edulis. We propose that insertions of rDNA sequences on chromosomes do not occur randomly but rather on preferential sites or hotspots for insertions. The maintenance of these arrays, however, may be favored/constrained by different factors, resulting in stable or polymorphic sites.
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Affiliation(s)
- Tiago Ribeiro
- Laboratório de Citogenética e Evolução Vegetal, Universidade Federal de Pernambuco, Departamento de Botânica, Recife, Pernambuco, Brasil
| | - Jéssica Nascimento
- Laboratório de Citogenética e Evolução Vegetal, Universidade Federal de Pernambuco, Departamento de Botânica, Recife, Pernambuco, Brasil
| | - Amanda Santos
- Laboratório de Citogenética e Evolução Vegetal, Universidade Federal de Pernambuco, Departamento de Botânica, Recife, Pernambuco, Brasil
| | - Leonardo P Félix
- Universidade Federal da Paraíba, Departamento de Biociências, Campus II, Areia, Paraíba, Brasil
| | - Marcelo Guerra
- Laboratório de Citogenética e Evolução Vegetal, Universidade Federal de Pernambuco, Departamento de Botânica, Recife, Pernambuco, Brasil
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21
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Aoki T, Kawaguchi M, Imaizumi-Anraku H, Akao S, Ayabe SI, Akashi T. Mutants of Lotus japonicus deficient in flavonoid biosynthesis. JOURNAL OF PLANT RESEARCH 2021; 134:341-352. [PMID: 33570676 PMCID: PMC7929969 DOI: 10.1007/s10265-021-01258-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 01/28/2021] [Indexed: 06/12/2023]
Abstract
Spatiotemporal features of anthocyanin accumulation in a model legume Lotus japonicus (Regel) K.Larsen were elucidated to develop criteria for the genetic analysis of flavonoid biosynthesis. Artificial mutants and wild accessions, with lower anthocyanin accumulation in the stem than the standard wild type (B-129 'Gifu'), were obtained by ethyl methanesulfonate (EMS) mutagenesis and from a collection of wild-grown variants, respectively. The loci responsible for the green stem of the mutants were named as VIRIDICAULIS (VIC). Genetic and chemical analysis identified two loci, namely, VIC1 and VIC2, required for the production of both anthocyanins and proanthocyanidins (condensed tannins), and two loci, namely, VIC3 and VIC4, required for the steps specific to anthocyanin biosynthesis. A mutation in VIC5 significantly reduced the anthocyanin accumulation. These mutants will serve as a useful system for examining the effects of anthocyanins and proanthocyanidins on the interactions with herbivorous pests, pathogenic microorganisms and nitrogen-fixing symbiotic bacteria, Mesorhizobium loti.
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Affiliation(s)
- Toshio Aoki
- Department of Applied Biological Sciences, Nihon University, Fujisawa, Kanagawa, 252-0880, Japan
| | - Masayoshi Kawaguchi
- Division of Symbiotic Systems, National Institute for Basic Biology, Okazaki, Aichi, 444-8585, Japan.
| | - Haruko Imaizumi-Anraku
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, 305-8634, Japan
| | - Shoichiro Akao
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, 305-8634, Japan
| | - Shin-Ichi Ayabe
- Department of Applied Biological Sciences, Nihon University, Fujisawa, Kanagawa, 252-0880, Japan
| | - Tomoyoshi Akashi
- Department of Applied Biological Sciences, Nihon University, Fujisawa, Kanagawa, 252-0880, Japan.
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22
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Aguilera PM, Debat HJ, Seijo JG, Grabiele M. A reference chromosomal map of the hot chili pepper Capsicum pubescens cv. “locoto” (Solanaceae). RODRIGUÉSIA 2021. [DOI: 10.1590/2175-7860202172062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Abstract Capsicum pubescens is a cultivated hot chili pepper, consumed in Latin American cuisine as a distinctive ingredient, and popularly known as “locoto” or “rocoto”. This taxon is also an outstanding source of resistance to biotic and abiotic stresses as well as other valuable fruit traits for breeding of the worldwidely cultivated C. annuum and related species. In this study, the chromosome complement of C. pubescens cv. “locoto” (2n = 24) was deeply characterized through a sequential combination of conventional and molecular cytogenetics approaches comprising: Ag-NOR staining, heterochromatic fluorescent C-DAPI, DAPI/AMD-CMA/DA bandings, fluorescence in situ hybridization (FISH) of Capsicum-derived probes of the 5S and 18S-25S rRNA genes and different regions of spacers of the ribosomal unit, as well as telomeric probe. The markers identified were systematically combined with morphological karyotype parameters - number, size, centromeres, satellites - to produce a physical map which allowed the identification of several landmarks in each individual chromosome. The reference chromosomal map of C. pubescens here presented is the most comprehensively developed in Capsicum so far. It is envisioned that this chromosomal map will serve as a reference framework for the upcoming sequencing projects and as starting point to assist future genetic mapping of important agronomic traits.
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Ferraz ME, Fonsêca A, Pedrosa-Harand A. Multiple and independent rearrangements revealed by comparative cytogenetic mapping in the dysploid Leptostachyus group (Phaseolus L., Leguminosae). Chromosome Res 2020; 28:395-405. [PMID: 33191473 DOI: 10.1007/s10577-020-09644-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 10/22/2020] [Accepted: 10/25/2020] [Indexed: 10/23/2022]
Abstract
Polyploidy and dysploidy have been reported as the main events in karyotype evolution of plants. In the genus Phaseolus L. (2n = 22), a small monophyletic group of three species, the Leptostachyus group, presents a dysploid karyotype with 2n = 20. It was shown in Phaseolus leptostachyus that the dysploidy was caused by a nested chromosome fusion (NCF) accompanied by several translocations, suggesting a high rate of karyotype evolution in the group. To verify if this karyotype restructuring was a single event or occurred progressively during the evolution of this group, we analysed P. macvaughii, sister to Phaseolus micranthus + P. leptostachyus. Twenty-four genomic clones of P. vulgaris previously mapped on P. leptostachyus, in addition to the 5S and 35S rDNA probes, were used for fluorescence in situ hybridization. Only a single rearrangement was common to the two species: the nested chromosome fusion (NCF) involving chromosomes 10 and 11. The translocation of chromosome 2 is not the same found in P. leptostachyus, and pericentric inversions in chromosomed 3 and 4 were exclusive of P. macvaughii. The other rearrangements observed in P. leptostachyus were not shared with this species, suggesting that they occurred after the separation of these lineages. The presence of private rearrangements indicates a progressive accumulation of karyotype changes in the Leptostachyus group instead of an instant genome-wide repatterning.
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Affiliation(s)
- Maria Eduarda Ferraz
- Laboratório de Citogenética e Evolução Vegetal, Departamento de Botânica, Universidade Federal de Pernambuco - UFPE, R. Prof. Moraes Rego, s/n, CDU, Recife, PE, 50670-420, Brazil
| | - Artur Fonsêca
- Laboratório de Citogenética e Evolução Vegetal, Departamento de Botânica, Universidade Federal de Pernambuco - UFPE, R. Prof. Moraes Rego, s/n, CDU, Recife, PE, 50670-420, Brazil
| | - Andrea Pedrosa-Harand
- Laboratório de Citogenética e Evolução Vegetal, Departamento de Botânica, Universidade Federal de Pernambuco - UFPE, R. Prof. Moraes Rego, s/n, CDU, Recife, PE, 50670-420, Brazil.
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24
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Mata-Sucre Y, Sader M, Van-Lume B, Gagnon E, Pedrosa-Harand A, Leitch IJ, Lewis GP, Souza G. How diverse is heterochromatin in the Caesalpinia group? Cytogenomic characterization of Erythrostemon hughesii Gagnon & G.P. Lewis (Leguminosae: Caesalpinioideae). PLANTA 2020; 252:49. [PMID: 32918627 DOI: 10.1007/s00425-020-03453-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 08/27/2020] [Indexed: 05/25/2023]
Abstract
Cytogenomic characterization of Erythrostemon hughesii reveals a heterogeneity of repeats in its subtelomeric heterochromatin. Comparative analyses with other Caesalpinia group species reveal a significant reduction in the abundance of Ty3-gypsy/Chromovirus Tekay retrotransposons during its evolution. In numerically stable karyotypes, repetitive DNA variability is one of the main causes of genome and chromosome variation and evolution. Species from the Caesalpinia group (Leguminosae) are karyotypically characterized by 2n = 24, with small chromosomes and highly variable CMA+ heterochromatin banding patterns that correlate with environmental variables. Erythrostemon hughesii differs from other species of the group examined to date for having subtelomeric CMA+ bands; this contrasts with most species in the group which have proximal bands. Here we analyse the repeatome of E. hughesii using genome skimming and chromosomal mapping approaches to characterize the identity of the most abundant repetitive elements and their physical location. The repetitive fraction of E. hughesii comprises 28.73% of the genome. The most abundant elements were retrotransposons (RT) with long terminal repeats (LTR-RT; 9.76%) and satellite DNAs (7.83%). Within the LTR-RTs, the most abundant lineages were: Ty1/copia-Ale (1%), Ty3/gypsy CRM (0.88%) and Ty3/gypsy Athila (0.75%). Using fluorescent in situ hybridization four satellite DNAs and several LTR-RT elements were shown to be present in most subtelomeric CMA+ bands. These results highlight how the repeatome in E. hughesii, a species from Oaxaca state in Mexico, is clearly distinct from Northeast Brazilian species of the Caesalpinia group, mainly due to its high diversity of repeats in its subtelomeric heterochromatic bands and low amount of LTR-RT Ty3/gypsy-Tekay elements. Comparative sequence analysis of Tekay elements from different species is congruent with a clade-specific origin of this LTR-RT after the divergence of the Caesalpinia group. We hypothesize that repeat-rich heterochromatin may play a role in leading to faster genomic divergence between individuals, increasing speciation and diversification.
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Affiliation(s)
- Yennifer Mata-Sucre
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Rua Nelson Chaves S/N, Cidade Universitaria, Recife, PE, 50670-420, Brazil
| | - Mariela Sader
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Rua Nelson Chaves S/N, Cidade Universitaria, Recife, PE, 50670-420, Brazil
| | - Brena Van-Lume
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Rua Nelson Chaves S/N, Cidade Universitaria, Recife, PE, 50670-420, Brazil
| | - Edeline Gagnon
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh, EH3 5NZ, UK
| | - Andrea Pedrosa-Harand
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Rua Nelson Chaves S/N, Cidade Universitaria, Recife, PE, 50670-420, Brazil
| | - Ilia J Leitch
- Comparative Plant and Fungal Biology Department, Royal Botanic Gardens, Kew, Richmond, TW9 3AB, Surrey, UK
| | - Gwilym P Lewis
- Comparative Plant and Fungal Biology Department, Royal Botanic Gardens, Kew, Richmond, TW9 3AB, Surrey, UK
| | - Gustavo Souza
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Rua Nelson Chaves S/N, Cidade Universitaria, Recife, PE, 50670-420, Brazil.
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Breaks of macrosynteny and collinearity among moth bean (Vigna aconitifolia), cowpea (V. unguiculata), and common bean (Phaseolus vulgaris). Chromosome Res 2020; 28:293-306. [PMID: 32654079 DOI: 10.1007/s10577-020-09635-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 06/29/2020] [Accepted: 07/01/2020] [Indexed: 10/23/2022]
Abstract
Comparative cytogenetic mapping is a powerful approach to gain insights into genome organization of orphan crops, lacking a whole sequenced genome. To investigate the cytogenomic evolution of important Vigna and Phaseolus beans, we built a BAC-FISH (fluorescent in situ hybridization of bacterial artificial chromosome) map of Vigna aconitifolia (Vac, subgenus Ceratotropis), species with no sequenced genome, and compared with V. unguiculata (Vu, subgenus Vigna) and Phaseolus vulgaris (Pv) maps. Seventeen Pv BACs, eight Vu BACs, and 5S and 35S rDNA probes were hybridized in situ on the 11 Vac chromosome pairs. Five Vac chromosomes (Vac6, Vac7, Vac9, Vac10, and Vac11) showed conserved macrosynteny and collinearity between V. unguiculata and P. vulgaris. On the other hand, we observed collinearity breaks, identified by pericentric inversions involving Vac2 (Vu2), Vac4 (Vu4), and Vac3 (Pv3). We also detected macrosynteny breaks of translocation type involving chromosomes 1 and 8 of V. aconitifolia and P. vulgaris; 2 and 3 of V. aconitifolia and P. vulgaris; and 1 and 5 of V. aconitifolia and V. unguiculata. Considering our data and previous BAC-FISH studies, six chromosomes (1, 2, 3, 4, 5, and 8) are involved in major karyotype divergences between genera and five (1, 2, 3, 4, and 5) between Vigna subgenera, including mechanisms such as duplications, inversions, and translocations. Macrosynteny breaks between Vigna and Phaseolus suggest that the major chromosomal rearrangements have occurred within the Vigna clade. Our cytogenomic comparisons bring new light on the degree of shared macrosynteny and mechanisms of karyotype diversification during Vigna and Phaseolus evolution.
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26
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Ibiapino A, García MÁ, Costea M, Stefanović S, Guerra M. Intense proliferation of rDNA sites and heterochromatic bands in two distantly related Cuscuta species (Convolvulaceae) with very large genomes and symmetric karyotypes. Genet Mol Biol 2020; 43:e20190068. [PMID: 32542306 PMCID: PMC7295182 DOI: 10.1590/1678-4685-gmb-2019-0068] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 04/06/2020] [Indexed: 11/21/2022] Open
Abstract
The genome size varies widely among angiosperms but only a few clades present huge variation at a low phylogenetic level. Among diploid species of the genus Cuscuta the genome size increased enormously in at least two independent lineages: in species of subgenus Monogynella and in at least one species (C. indecora) of the subgenus Grammica. Curiously, the independent events lead to similar karyotypes, with 2n = 30 mostly metacentric chromosomes. In this paper we compared the patterns of heterochromatic bands and rDNA sites of C. indecora and C. monogyna, aiming to evaluate the role of these repetitive fractions in these karyotypes. We found out that the large genomes of these species were incremented by a huge number of small heterochromatic CMA+ and DAPI+ bands and 5S and 35 rDNA sites, most of them clearly colocalized with CMA+ bands. Silver nitrate impregnation revealed that the maximum number of nucleoli per nucleus was low in both species, suggesting that some of these sites may be inactive. Noteworthy, the tandem repeats did not generate large bands or sites but rather dozens of small blocks dispersed throughout the chromosomes, apparently contributing to conserve the original karyotype symmetry.
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Affiliation(s)
- Amália Ibiapino
- Universidade Federal de Pernambuco, Departamento de Botânica,
Recife, PE, Brazil
| | - Miguel Ángel García
- University of Toronto Mississauga, Department of Biology,
Mississauga, ON, Canada
- Royal Botanic Gardens Kew, Richmond, Surrey, United Kingdom
| | - Mihai Costea
- Wilfrid Laurier University, Department of Biology, Waterloo, ON,
Canada
| | - Saša Stefanović
- University of Toronto Mississauga, Department of Biology,
Mississauga, ON, Canada
| | - Marcelo Guerra
- Universidade Federal de Pernambuco, Departamento de Botânica,
Recife, PE, Brazil
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27
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Li H, Jiang F, Wu P, Wang K, Cao Y. A High-Quality Genome Sequence of Model Legume Lotus japonicus (MG-20) Provides Insights into the Evolution of Root Nodule Symbiosis. Genes (Basel) 2020; 11:genes11050483. [PMID: 32365501 PMCID: PMC7290416 DOI: 10.3390/genes11050483] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Revised: 04/19/2020] [Accepted: 04/27/2020] [Indexed: 11/16/2022] Open
Abstract
Lotus japonicus is an important model legume for studying symbiotic nitrogen fixation as well as plant development. A genomic sequence of L. japonicus (MG20) has been available for more than ten years. However, the low quality of the genome limits its application in functional genomic studies. Therefore, it is necessary to assemble high-quality chromosome sequences of L. japonicus using new sequencing technology to facilitate the study of functional genomics. In this report, we used the third-generation sequencing combined with the Illumina HiSeq platform to sequence the genome of L. japonicus (MG20). We obtained 544 Mb of genomic sequence using third-generation assembly. Based on sequence analysis, 357 Mb of repeats, 28,251 genes, 626 tRNAs, 1409 rRNAs, and 1233 pseudogenes were predicted in the genome. A total of 27,991 genes were annotated into databases. Compared to the previously published data, the new genome database contains complete L. japonicus sequences in the proper order and orientation with a contig N50 2.81Mb and an excellent genome coverage, which provides more accurate genome information and more precise assembly for functional genomic study.
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Affiliation(s)
- Haoxing Li
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (H.L.); (P.W.); (K.W.)
| | - Fan Jiang
- College of Informatics, Huazhong Agricultural University, Wuhan 430070, China;
| | - Ping Wu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (H.L.); (P.W.); (K.W.)
| | - Ke Wang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (H.L.); (P.W.); (K.W.)
| | - Yangrong Cao
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (H.L.); (P.W.); (K.W.)
- Correspondence:
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28
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Franco AL, Figueredo A, Pereira LDM, de Sousa SM, Souza G, Carvalho MA, Simon MF, Viccini LF. Low cytomolecular diversification in the genus Stylosanthes Sw. (Papilionoideae, Leguminosae). Genet Mol Biol 2020; 43:e20180250. [PMID: 31429856 PMCID: PMC7197990 DOI: 10.1590/1678-4685-gmb-2018-0250] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 03/07/2019] [Indexed: 12/02/2022] Open
Abstract
Stylosanthes (Papilionoideae, Leguminosae) is a predominantly Neotropical genus with ~48 species that include worldwide important forage species. This study presents the chromosome number and morphology of eight species of the genus Stylosanthes (S. acuminata, S. gracilis, S. grandifolia, S. guianensis, S. hippocampoides, S. pilosa, S. macrocephala, and S. ruellioides). In addition, staining with CMA and DAPI, in situ hybridization with 5S and 35S rDNA probes, and estimation of DNA content were performed. The interpretation of Stylosanthes chromosome diversification was anchored by a comparison with the sister genus Arachis and a dated molecular phylogeny based on nuclear and plastid loci. Stylosanthes species showed 2n = 20, with low cytomolecular diversification regarding 5S rDNA, 35S rDNA, and genome size. Arachis has a more ancient diversification (~7 Mya in the Pliocene) than the relatively recent Stylosanthes (~2 Mya in the Pleistocene), and it seems more diverse than its sister lineage. Our data support the idea that the cytomolecular stability of Stylosanthes in relation to Arachis could be a result of its recent origin. The recent diversification of Stylosanthes could also be related to the low morphological differentiation among species, and to the recurrent formation of allopolyploid complexes.
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Affiliation(s)
- Ana Luiza Franco
- Universidade Federal de Juiz de Fora, Departamento de Biologia, Laboratório de Genética, Juiz de Fora, MG, Brazil
| | - Amanda Figueredo
- Universidade Federal de Pernambuco, Departamento de Botânica, Laboratório de Citogenética e Evolução Vegetal, CCB, Recife, PE, Brazil
| | - Lívia de Moraes Pereira
- Universidade Federal de Pernambuco, Departamento de Botânica, Laboratório de Citogenética e Evolução Vegetal, CCB, Recife, PE, Brazil
| | - Saulo Marçal de Sousa
- Universidade Federal de Juiz de Fora, Departamento de Biologia, Laboratório de Genética, Juiz de Fora, MG, Brazil
| | - Gustavo Souza
- Universidade Federal de Pernambuco, Departamento de Botânica, Laboratório de Citogenética e Evolução Vegetal, CCB, Recife, PE, Brazil
| | | | - Marcelo F. Simon
- Empresa Brasileira de Pesquisa Agropecuária, Embrapa Recursos Genéticos e Biotecnologia, PqEB, Brasília, DF, Brazil
| | - Lyderson Facio Viccini
- Universidade Federal de Juiz de Fora, Departamento de Biologia, Laboratório de Genética, Juiz de Fora, MG, Brazil
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29
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Souza RCD, Marques DDA, de Carvalho Filho MM, Oliveira ARDS, Siqueira WJ, Benko-Iseppon AM, Brasileiro-Vidal AC. Genome composition and pollen viability of Jatropha (Euphorbiaceae) interspecific hybrids by Genomic In Situ Hybridization (GISH). Genet Mol Biol 2020; 42:e20190112. [PMID: 32059051 PMCID: PMC7198012 DOI: 10.1590/1678-4685-gmb-2019-0112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 11/10/2019] [Indexed: 11/24/2022] Open
Abstract
Interspecific hybridization is required for the development of Jatropha
curcas L. improved cultivars, due to its narrow genetic basis. The
present study aimed to analyze the parental genomic composition of F1
and BC1F1 generations derived from interspecific crosses
(J. curcas/J. integerrima and J. curcas/J.
multifida) by GISH (Genomic In Situ
Hybridization), and the meiotic index and pollen viability of F1
hybrids. In F1 cells from both hybrids, 11 chromosomes of each
parental was observed, as expected, but chromosome rearrangement events could be
detected using rDNA chromosome markers, suggesting unbalanced cells. In the
BC1F1, both hybrids had 22 chromosomes, suggesting
that only n = 11 gametes were viable in the next generation.
However, GISH allowed the identification of three and two alien chromosomes in
J. curcas//J. integerrima and J. curcas//J.
multifida BC1F1 hybrids, respectively,
suggesting a preferential transmission of J. curcas chromosomes
for both hybrids. Pollen viability in F1 hybrids derived from
J. curcas/J. integerrima crosses were higher (82-83%) than
those found for J. curcas/J. multifida (68%), showing
post-meiotic problems in these last hybrids, with dyads, triads, polyads, and
micronuclei as post-meiosis results. The here presented cytogenetic
characterization of interspecific hybrids and their backcross progenies can
contribute to the selection of the best genotypes for future assisted breeding
of J. curcas.
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Affiliation(s)
- Rosilda Cintra de Souza
- Universidade Federal de Pernambuco, Departamento de Genética, Recife, PE, Brazil.,Universidade Federal Rural de Pernambuco, Departamento de Agronomia, Recife, Pernambuco, Brazil
| | | | | | | | | | | | - Ana Christina Brasileiro-Vidal
- Universidade Federal de Pernambuco, Departamento de Genética, Recife, PE, Brazil.,Universidade Federal Rural de Pernambuco, Departamento de Agronomia, Recife, Pernambuco, Brazil
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30
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Sahruzaini NA, Rejab NA, Harikrishna JA, Khairul Ikram NK, Ismail I, Kugan HM, Cheng A. Pulse Crop Genetics for a Sustainable Future: Where We Are Now and Where We Should Be Heading. FRONTIERS IN PLANT SCIENCE 2020; 11:531. [PMID: 32431724 PMCID: PMC7212832 DOI: 10.3389/fpls.2020.00531] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 04/07/2020] [Indexed: 05/12/2023]
Abstract
The last decade has witnessed dramatic changes in global food consumption patterns mainly because of population growth and economic development. Food substitutions for healthier eating, such as swapping regular servings of meat for protein-rich crops, is an emerging diet trend that may shape the future of food systems and the environment worldwide. To meet the erratic consumer demand in a rapidly changing world where resources become increasingly scarce due largely to anthropogenic activity, the need to develop crops that benefit both human health and the environment has become urgent. Legumes are often considered to be affordable plant-based sources of dietary proteins. Growing legumes provides significant benefits to cropping systems and the environment because of their natural ability to perform symbiotic nitrogen fixation, which enhances both soil fertility and water-use efficiency. In recent years, the focus in legume research has seen a transition from merely improving economically important species such as soybeans to increasingly turning attention to some promising underutilized species whose genetic resources hold the potential to address global challenges such as food security and climate change. Pulse crops have gained in popularity as an affordable source of food or feed; in fact, the United Nations designated 2016 as the International Year of Pulses, proclaiming their critical role in enhancing global food security. Given that many studies have been conducted on numerous underutilized pulse crops across the world, we provide a systematic review of the related literature to identify gaps and opportunities in pulse crop genetics research. We then discuss plausible strategies for developing and using pulse crops to strengthen food and nutrition security in the face of climate and anthropogenic changes.
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Affiliation(s)
- Nurul Amylia Sahruzaini
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Nur Ardiyana Rejab
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
- Centre for Research in Biotechnology for Agriculture (CEBAR), University of Malaya, Kuala Lumpur, Malaysia
| | - Jennifer Ann Harikrishna
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
- Centre for Research in Biotechnology for Agriculture (CEBAR), University of Malaya, Kuala Lumpur, Malaysia
| | - Nur Kusaira Khairul Ikram
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
- Centre for Research in Biotechnology for Agriculture (CEBAR), University of Malaya, Kuala Lumpur, Malaysia
| | - Ismanizan Ismail
- Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, Bangi, Malaysia
| | - Hazel Marie Kugan
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Acga Cheng
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
- *Correspondence: Acga Cheng,
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31
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Báez M, Vaio M, Dreissig S, Schubert V, Houben A, Pedrosa-Harand A. Together But Different: The Subgenomes of the Bimodal Eleutherine Karyotypes Are Differentially Organized. FRONTIERS IN PLANT SCIENCE 2019; 10:1170. [PMID: 31649686 PMCID: PMC6791338 DOI: 10.3389/fpls.2019.01170] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 08/27/2019] [Indexed: 06/10/2023]
Abstract
Bimodal karyotypes are characterized by the presence of two sets of chromosomes of contrasting size. Eleutherine bulbosa (2n = 12) presents a bimodal karyotype with a large chromosome pair, which has a pericentric inversion in permanent heterozygosity with suppressed recombination, and five pairs of three to four times smaller chromosomes. Aiming to understand whether high copy number sequence composition differs between both chromosome sets, we investigated the repetitive DNA fraction of E. bulbosa and compared it to the chromosomal organization of the related Eleutherine latifolia species, not containing the pericentric inversion. We also compared the repetitive sequence proportions between the heteromorphic large chromosomes of E. bulbosa and between E. bulbosa and E. latifolia to understand the influence of the chromosome inversion on the dynamics of repetitive sequences. The most abundant repetitive families of the genome showed a similar chromosomal distribution in both homologs of the large pair and in both species, apparently not influenced by the species-specific inversions. The repeat families Ebusat1 and Ebusat4 are localized interstitially only on the large chromosome pair, while Ebusat2 is located in the centromeric region of all chromosomes. The four most abundant retrotransposon lineages are accumulated in the large chromosome pair. Replication timing and distribution of epigenetic and transcriptional marks differ between large and small chromosomes. The differential distribution of retroelements appears to be related to the bimodal condition and is not influenced by the nonrecombining chromosome inversions in these species. Thus, the large and small chromosome subgenomes of the bimodal Eleutherine karyotype are differentially organized and probably evolved by repetitive sequences accumulation on the large chromosome set.
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Affiliation(s)
- Mariana Báez
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Recife, Brazil
| | - Magdalena Vaio
- Laboratory of Genetics, Department of Plant Biology, College of Agronomy, University of the Republic, Montevideo, Uruguay
| | - Steven Dreissig
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Veit Schubert
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Andreas Houben
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Andrea Pedrosa-Harand
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Recife, Brazil
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Sader MA, Dias Y, Costa ZP, Munhoz C, Penha H, Bergès H, Vieira MLC, Pedrosa-Harand A. Identification of passion fruit (Passiflora edulis) chromosomes using BAC-FISH. Chromosome Res 2019; 27:299-311. [PMID: 31321607 DOI: 10.1007/s10577-019-09614-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 06/13/2019] [Accepted: 07/05/2019] [Indexed: 12/11/2022]
Abstract
Passiflora edulis, the yellow passion fruit, is the main crop from the Passiflora genus, which comprises 525 species with its diversity center in South America. Genetic maps and a BAC (bacterial artificial chromosome) genomic library are available, but the nine chromosome pairs of similar size and morphology (2n = 18) hamper chromosome identification, leading to different proposed karyotypes. Thus, the aim of this study was to establish chromosome-specific markers for the yellow passion fruit using single-copy and repetitive sequences as probes in fluorescent in situ hybridizations (FISH) to allow chromosome identification and future integration with whole genome data. Thirty-six BAC clones harboring genes and three retrotransposons (Ty1-copy, Ty3-gypsy, and LINE) were selected. Twelve BACs exhibited a dispersed pattern similar to that revealed by retroelements, and one exhibited subtelomeric distribution. Twelve clones showed unique signals in terminal or subterminal regions of the chromosomes, allowing their genes to be anchored to six chromosome pairs that can be identified with single-copy markers. The markers developed herein will provide an important tool for genomic and evolutionary studies in the Passiflora genus.
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Affiliation(s)
- M A Sader
- Department of Botany, Federal University of Pernambuco, Recife, Brazil
| | - Y Dias
- Department of Botany, Federal University of Pernambuco, Recife, Brazil
| | - Z P Costa
- Department of Genetics, "Luiz de Queiroz" College of Agriculture, University of São Paulo, Piracicaba, Brazil
| | - C Munhoz
- Department of Genetics, "Luiz de Queiroz" College of Agriculture, University of São Paulo, Piracicaba, Brazil
| | - H Penha
- Department of Technology, Faculty of Agricultural and Veterinary Sciences, São Paulo State University (UNESP), Jaboticabal, Brazil
| | - H Bergès
- French Plant Genomic Resources Center (CNRGV)/ INRA, Toulouse, France
| | - M L C Vieira
- Department of Genetics, "Luiz de Queiroz" College of Agriculture, University of São Paulo, Piracicaba, Brazil
| | - Andrea Pedrosa-Harand
- Department of Botany, Federal University of Pernambuco, Recife, Brazil.
- Laboratório de Citogenética e Evolução Vegetal, Departamento de Botânica, Centro de Biociências, Universidade Federal de Pernambuco, R. Prof. Moraes Rego, s/n, CDU, Recife, PE, 50670-901, Brazil.
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Ibiapino A, García MA, Ferraz ME, Costea M, Stefanović S, Guerra M. Allopolyploid origin and genome differentiation of the parasitic species Cuscuta veatchii (Convolvulaceae) revealed by genomic in situ hybridization. Genome 2019; 62:467-475. [PMID: 31071271 DOI: 10.1139/gen-2018-0184] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Interspecific hybridization and genome duplication to form allopolyploids are major evolutionary events in angiosperms. In the parasitic genus Cuscuta (Convolvulaceae), molecular data suggested the existence of species of hybrid origin. One of them, C. veatchii, has been proposed as a hybrid between C. denticulata and C. nevadensis, both included in sect. Denticulatae. To test this hypothesis, a cytogenetic analysis was performed with CMA/DAPI staining and fluorescent in situ hybridization using 5S and 35S rDNA and genomic probes. Chromosomes of C. denticulata were small with a well-defined centromeric region, whereas C. nevadensis had larger, densely stained chromosomes, and less CMA+ heterochromatic bands. Cuscuta veatchii had 2n = 60 chromosomes, about 30 of them similar to those of C. denticulata and the remaining to C. nevadensis. GISH analysis confirmed the presence of both subgenomes in the allotetraploid C. veatchii. However, the number of rDNA sites and the haploid karyotype length in C. veatchii were not additive. The diploid parentals had already diverged in their chromosomes structure, whereas the reduction in the number of rDNA sites more probably occurred after hybridization. As phylogenetic data suggested a recent divergence of the progenitors, these species should have a high rate of karyotype evolution.
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Affiliation(s)
- Amália Ibiapino
- a Laboratory of Plant Cytogenetics and Evolution - Federal University of Pernambuco, Department of Botany, Recife 50.372-970, PE, Brazil
| | - Miguel A García
- b Department of Biology, University of Toronto Mississauga, Mississauga, ON L5L 1C6, Canada.,c Royal Botanic Gardens Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | - Maria Eduarda Ferraz
- a Laboratory of Plant Cytogenetics and Evolution - Federal University of Pernambuco, Department of Botany, Recife 50.372-970, PE, Brazil
| | - Mihai Costea
- d Department of Biology, Wilfrid Laurier University, Waterloo, ON N2L 3C5, Canada
| | - Saša Stefanović
- b Department of Biology, University of Toronto Mississauga, Mississauga, ON L5L 1C6, Canada
| | - Marcelo Guerra
- a Laboratory of Plant Cytogenetics and Evolution - Federal University of Pernambuco, Department of Botany, Recife 50.372-970, PE, Brazil
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Marques A, Moraes L, Aparecida Dos Santos M, Costa I, Costa L, Nunes T, Melo N, Simon MF, Leitch AR, Almeida C, Souza G. Origin and parental genome characterization of the allotetraploid Stylosanthes scabra Vogel (Papilionoideae, Leguminosae), an important legume pasture crop. ANNALS OF BOTANY 2018; 122:1143-1159. [PMID: 29982475 PMCID: PMC6324754 DOI: 10.1093/aob/mcy113] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 06/28/2018] [Indexed: 05/04/2023]
Abstract
BACKGROUNDS AND AIMS The genus Stylosanthes includes nitrogen-fixing and drought-tolerant species of considerable economic importance for perennial pasture, green manure and land recovery. Stylosanthes scabra is adapted to variable soil conditions, being cultivated to improve pastures and soils worldwide. Previous studies have proposed S. scabra as an allotetraploid species (2n = 40) with a putative diploid A genome progenitor S. hamata or S. seabrana (2n = 20) and the B genome progenitor S. viscosa (2n = 20). We aimed to provide conclusive evidence for the origin of S. scabra. METHODS We performed fluorescence in situ hybridization (FISH) and genomic in situ hybridization (GISH) experiments and Illumina paired-end sequencing of S. scabra, S. hamata and S. viscosa genomic DNA, to assemble and compare complete ribosomal DNA (rDNA) units and chloroplast genomes. Plastome- and genome-wide single nucleotide variation detection was also performed. KEY RESULTS GISH and phylogenetic analyses of plastid DNA and rDNA sequences support that S. scabra is an allotetraploid formed from 0.63 to 0.52 million years ago (Mya), from progenitors with a similar genome structure to the maternal donor S. hamata and the paternal donor S. viscosa. FISH revealed a non-additive number of 35S rDNA sites in S. scabra compared with its progenitors, indicating the loss of one locus from A genome origin. In S. scabra, most 5S rDNA units were similar to S. viscosa, while one 5S rDNA site of reduced size most probably came from an A genome species as revealed by GISH and in silico analysis. CONCLUSIONS Our approach combined whole-plastome and rDNA assembly with additional cytogenetic analysis to shed light successfully on the allotetraploid origin of S. scabra. We propose a Middle Pleistocene origin for S. scabra involving species with maternal A and paternal B genomes. Our data also suggest that variation found in rDNA units in S. scabra and its progenitors reveals differences that can be explained by homogenization, deletion and amplification processes that have occurred since its origin.
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Affiliation(s)
- André Marques
- Laboratory of Genetic Resources, Federal University of Alagoas, Arapiraca, AL, Brazil
| | - Lívia Moraes
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Recife, Brazil
| | | | - Iara Costa
- Laboratory of Genetic Resources, Federal University of Alagoas, Arapiraca, AL, Brazil
| | - Lucas Costa
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Recife, Brazil
| | - Tomáz Nunes
- Laboratory of Genetic Resources, Federal University of Alagoas, Arapiraca, AL, Brazil
| | - Natoniel Melo
- Laboratory of Biotechnology, Embrapa Semi-arid, Petrolina, Brazil
| | | | | | - Cicero Almeida
- Laboratory of Genetic Resources, Federal University of Alagoas, Arapiraca, AL, Brazil
| | - Gustavo Souza
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Recife, Brazil
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Karyotype heterogeneity in Philodendron s.l. (Araceae) revealed by chromosome mapping of rDNA loci. PLoS One 2018; 13:e0207318. [PMID: 30440003 PMCID: PMC6237374 DOI: 10.1371/journal.pone.0207318] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 10/29/2018] [Indexed: 12/18/2022] Open
Abstract
Philodendron s.l. (Araceae) has been recently focus of taxonomic and phylogenetic studies, but karyotypic data are limited to chromosome numbers and a few published genome sizes. In this work, karyotypes of 34 species of Philodendron s.l. (29 species of Philodendron and five of Thaumatophyllum), ranging from 2n = 28 to 36 chromosomes, were analyzed by fluorescence in situ hybridization (FISH) with rDNA and telomeric probes, aiming to understand the evolution of the karyotype diversity of the group. Philodendron presented a high number variation of 35S rDNA, ranging from two to 16 sites, which were mostly in the terminal region of the short arms, with nine species presenting heteromorphisms. In the case of Thaumatophyllum species, we observed a considerably lower variation, which ranged from two to four terminal sites. The distribution of the 5S rDNA clusters was more conserved, with two sites for most species, being preferably located interstitially in the long chromosome arms. For the telomeric probe, while exclusively terminal sites were observed for P. giganteum (2n = 30) chromosomes, P. callosum (2n = 28) presented an interstitial distribution associated with satellite DNA. rDNA sites of the analyzed species of Philodendron s.l. species were randomly distributed considering the phylogenetic context, probably due to rapid evolution and great diversity of these genomes. The observed heteromorphisms suggest the accumulation of repetitive DNA in the genomes of some species and the occurrence of chromosomal rearrangements along the karyotype evolution of the group.
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Liu H, Sandal N, Andersen KR, James EK, Stougaard J, Kelly S, Kawaharada Y. A genetic screen for plant mutants with altered nodulation phenotypes in response to rhizobial glycan mutants. THE NEW PHYTOLOGIST 2018; 220:526-538. [PMID: 29959893 DOI: 10.1111/nph.15293] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2018] [Accepted: 05/24/2018] [Indexed: 05/08/2023]
Abstract
Nodule primordia induced by rhizobial glycan mutants often remain uninfected. To identify processes involved in infection and organogenesis we used forward genetics to identify plant genes involved in perception and responses to bacterial glycans. To dissect the mechanisms underlying the negative plant responses to the Mesorhizobium loti R7AexoU and ML001cep mutants, a screen for genetic suppressors of the nodulation phenotypes was performed on a chemically mutagenized Lotus population. Two mutant lines formed infected nitrogen-fixing pink nodules, while five mutant lines developed uninfected large white nodules, presumably altered in processes controlling organogenesis. Genetic mapping identified a mutation in the cytokinin receptor Lhk1 resulting in an alanine to valine substitution adjacent to a coiled-coil motif in the juxta-membrane region of LHK1. This results in a spontaneous nodulation phenotype and increased ethylene production. The allele was renamed snf5, and segregation studies of snf5 together with complementation studies suggest that snf5 is a gain-of-function allele. This forward genetic approach to investigate the role of glycans in the pathway synchronizing infection and organogenesis shows that a combination of plant and bacterial genetics opens new possibilities to study glycan responses in plants as well as identification of mutant alleles affecting nodule organogenesis.
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Affiliation(s)
- Huijun Liu
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, DK-8000, Aarhus C, Denmark
| | - Niels Sandal
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, DK-8000, Aarhus C, Denmark
| | - Kasper R Andersen
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, DK-8000, Aarhus C, Denmark
| | - Euan K James
- The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | - Jens Stougaard
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, DK-8000, Aarhus C, Denmark
| | - Simon Kelly
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, DK-8000, Aarhus C, Denmark
| | - Yasuyuki Kawaharada
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, DK-8000, Aarhus C, Denmark
- Department of Plant BioSciences, Faculty of Agriculture, Iwate University, 3-18-8-Ueda, Morioka, Iwate, Japan
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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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do Nascimento EFDMB, Dos Santos BV, Marques LOC, Guimarães PM, Brasileiro ACM, Leal-Bertioli SCM, Bertioli DJ, Araujo ACG. The genome structure of Arachis hypogaea (Linnaeus, 1753) and an induced Arachis allotetraploid revealed by molecular cytogenetics. COMPARATIVE CYTOGENETICS 2018; 12:111-140. [PMID: 29675140 PMCID: PMC5904367 DOI: 10.3897/compcytogen.v12i1.20334] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 01/23/2018] [Indexed: 05/03/2023]
Abstract
Peanut, Arachis hypogaea (Linnaeus, 1753) is an allotetraploid cultivated plant with two subgenomes derived from the hybridization between two diploid wild species, A. duranensis (Krapovickas & W. C. Gregory, 1994) and A. ipaensis (Krapovickas & W. C. Gregory, 1994), followed by spontaneous chromosomal duplication. To understand genome changes following polyploidy, the chromosomes of A. hypogaea, IpaDur1, an induced allotetraploid (A. ipaensis × A. duranensis)4x and the diploid progenitor species were cytogenetically compared. The karyotypes of the allotetraploids share the number and general morphology of chromosomes; DAPI+ bands pattern and number of 5S rDNA loci. However, one 5S rDNA locus presents a heteromorphic FISH signal in both allotetraploids, relative to corresponding progenitor. Whilst for A. hypogaea the number of 45S rDNA loci was equivalent to the sum of those present in the diploid species, in IpaDur1, two loci have not been detected. Overall distribution of repetitive DNA sequences was similar in both allotetraploids, although A. hypogaea had additional CMA3+ bands and few slight differences in the LTR-retrotransposons distribution compared to IpaDur1. GISH showed that the chromosomes of both allotetraploids had preferential hybridization to their corresponding diploid genomes. Nevertheless, at least one pair of IpaDur1 chromosomes had a clear mosaic hybridization pattern indicating recombination between the subgenomes, clear evidence that the genome of IpaDur1 shows some instability comparing to the genome of A. hypogaea that shows no mosaic of subgenomes, although both allotetraploids derive from the same progenitor species. For some reasons, the chromosome structure of A. hypogaea is inherently more stable, or, it has been at least, partially stabilized through genetic changes and selection.
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Affiliation(s)
- Eliza F de M B do Nascimento
- University of Brasilia, Institute of Biological Sciences, Campus Darcy Ribeiro, CEP 70.910-900, Brasília, DF, Brazil
- Embrapa Genetic Resources and Biotechnology, PqEB W5 Norte Final, CP 02372, CEP 70.770-917, Brasília, DF, Brazil
| | - Bruna V Dos Santos
- Embrapa Genetic Resources and Biotechnology, PqEB W5 Norte Final, CP 02372, CEP 70.770-917, Brasília, DF, Brazil
| | - Lara O C Marques
- Embrapa Genetic Resources and Biotechnology, PqEB W5 Norte Final, CP 02372, CEP 70.770-917, Brasília, DF, Brazil
- Catholic University of Brasilia, Campus I, CEP 71966-700, Brasília, DF, Brazil
| | - Patricia M Guimarães
- Embrapa Genetic Resources and Biotechnology, PqEB W5 Norte Final, CP 02372, CEP 70.770-917, Brasília, DF, Brazil
| | - Ana C M Brasileiro
- Embrapa Genetic Resources and Biotechnology, PqEB W5 Norte Final, CP 02372, CEP 70.770-917, Brasília, DF, Brazil
| | - Soraya C M Leal-Bertioli
- Center for Applied Genetic Technologies, University of Georgia, 111 Riverbend Road, 30602-6810, Athens, Georgia, USA
| | - David J Bertioli
- Center for Applied Genetic Technologies, University of Georgia, 111 Riverbend Road, 30602-6810, Athens, Georgia, USA
| | - Ana C G Araujo
- Embrapa Genetic Resources and Biotechnology, PqEB W5 Norte Final, CP 02372, CEP 70.770-917, Brasília, DF, Brazil
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Majka J, Książczyk T, Kiełbowicz-Matuk A, Kopecký D, Kosmala A. Exploiting repetitive sequences and BAC clones in Festuca pratensis karyotyping. PLoS One 2017; 12:e0179043. [PMID: 28591168 PMCID: PMC5462415 DOI: 10.1371/journal.pone.0179043] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 05/23/2017] [Indexed: 11/24/2022] Open
Abstract
The Festuca genus is thought to be the most numerous genus of the Poaceae family. One of the most agronomically important forage grasses, Festuca pratensis Huds. is treated as a model plant to study the molecular mechanisms associated with tolerance to winter stresses, including frost. However, the precise mapping of the genes governing stress tolerance in this species is difficult as its karyotype remains unrecognized. Only two F. pratensis chromosomes with 35S and 5S rDNA sequences can be easily identified, but its remaining chromosomes have not been distinguished to date. Here, two libraries derived from F. pratensis nuclear DNA with various contents of repetitive DNA sequences were used as sources of molecular probes for fluorescent in situ hybridisation (FISH), a BAC library and a library representing sequences most frequently present in the F. pratensis genome. Using FISH, six groups of DNA sequences were revealed in chromosomes on the basis of their signal position, including dispersed-like sequences, chromosome painting-like sequences, centromeric-like sequences, knob-like sequences, a group without hybridization signals, and single locus-like sequences. The last group was exploited to develop cytogenetic maps of diploid and tetraploid F. pratensis, which are presented here for the first time and provide a remarkable progress in karyotype characterization.
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Affiliation(s)
- Joanna Majka
- Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland
- * E-mail:
| | - Tomasz Książczyk
- Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland
| | | | - David Kopecký
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Arkadiusz Kosmala
- Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland
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Moraes AP, Koehler S, Cabral JS, Gomes SSL, Viccini LF, Barros F, Felix LP, Guerra M, Forni-Martins ER. Karyotype diversity and genome size variation in Neotropical Maxillariinae orchids. PLANT BIOLOGY (STUTTGART, GERMANY) 2017; 19:298-308. [PMID: 27917576 DOI: 10.1111/plb.12527] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 11/28/2016] [Indexed: 06/06/2023]
Abstract
Orchidaceae is a widely distributed plant family with very diverse vegetative and floral morphology, and such variability is also reflected in their karyotypes. However, since only a low proportion of Orchidaceae has been analysed for chromosome data, greater diversity may await to be unveiled. Here we analyse both genome size (GS) and karyotype in two subtribes recently included in the broadened Maxillariinea to detect how much chromosome and GS variation there is in these groups and to evaluate which genome rearrangements are involved in the species evolution. To do so, the GS (14 species), the karyotype - based on chromosome number, heterochromatic banding and 5S and 45S rDNA localisation (18 species) - was characterised and analysed along with published data using phylogenetic approaches. The GS presented a high phylogenetic correlation and it was related to morphological groups in Bifrenaria (larger plants - higher GS). The two largest GS found among genera were caused by different mechanisms: polyploidy in Bifrenaria tyrianthina and accumulation of repetitive DNA in Scuticaria hadwenii. The chromosome number variability was caused mainly through descending dysploidy, and x=20 was estimated as the base chromosome number. Combining GS and karyotype data with molecular phylogeny, our data provide a more complete scenario of the karyotype evolution in Maxillariinae orchids, allowing us to suggest, besides dysploidy, that inversions and transposable elements as two mechanisms involved in the karyotype evolution. Such karyotype modifications could be associated with niche changes that occurred during species evolution.
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Affiliation(s)
- A P Moraes
- Departamento de Biologia Vegetal, Instituto de Biociências, Universidade Estadual de Campinas, Campinas, Brazil
- Departamento de Genética, Instituto de Biociências, Universidade Estadual Paulista Julio de Mesquita Filho, Botucatu, Brazil
- Instituto de Ciências e Tecnologia, Universidade Federal de São Paulo, São José dos Campos, Brazil
| | - S Koehler
- Departamento de Biologia Vegetal, Instituto de Biociências, Universidade Estadual de Campinas, Campinas, Brazil
| | - J S Cabral
- Departamento de Botânica, Centro de Ciências Biológicas, Cidade Universitária, Universidade Federal de Pernambuco, Recife, Brazil
- Synthesis Centre, German Centre for Integrative Biodiversity Research, Leipzig, Germany
- Center for Computational and Theoretical Biology, Ecosystem Modeling, University of Würzburg, Würzburg, Germany
| | - S S L Gomes
- Departamento de Biologia, Instituto de Ciências Biológicas, Universidade Federal de Juiz de Fora, Juiz de Fora, Brazil
| | - L F Viccini
- Departamento de Biologia, Instituto de Ciências Biológicas, Universidade Federal de Juiz de Fora, Juiz de Fora, Brazil
| | - F Barros
- Instituto de Botânica, Núcleo de Pesquisa Orquidário do Estado de São Paulo, São Paulo, Brazil
| | - L P Felix
- Departamento de Ciências Biológicas, Centro de Ciências Agrárias, Universidade Federal da Paraíba, Rodovia, Areias, Brazil
| | - M Guerra
- Departamento de Botânica, Centro de Ciências Biológicas, Cidade Universitária, Universidade Federal de Pernambuco, Recife, Brazil
| | - E R Forni-Martins
- Departamento de Biologia Vegetal, Instituto de Biociências, Universidade Estadual de Campinas, Campinas, Brazil
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Detecting Mechanisms of Karyotype Evolution in Heterotaxis (Orchidaceae). PLoS One 2016; 11:e0165960. [PMID: 27832130 PMCID: PMC5104408 DOI: 10.1371/journal.pone.0165960] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 10/20/2016] [Indexed: 01/22/2023] Open
Abstract
The karyotype is shaped by different chromosome rearrangements during species evolution. However, determining which rearrangements are responsible for karyotype changes is a challenging task and the combination of a robust phylogeny with refined karyotype characterization, GS measurements and bioinformatic modelling is necessary. Here, this approach was applied in Heterotaxis to determine what chromosome rearrangements were responsible for the dysploidy variation. We used two datasets (nrDNA and cpDNA, both under MP and BI) to infer the phylogenetic relationships among Heterotaxis species and the closely related genera Nitidobulbon and Ornithidium. Such phylogenies were used as framework to infer how karyotype evolution occurred using statistical methods. The nrDNA recovered Ornithidium, Nitidobulbon and Heterotaxis as monophyletic under both MP and BI; while cpDNA could not completely separate the three genera under both methods. Based on the GS, we recovered two groups within Heterotaxis: (1) "small GS", corresponding to the Sessilis grade, composed of plants with smaller genomes and smaller morphological structure, and (2) "large GS", corresponding to the Discolor clade, composed of plants with large genomes and robust morphological structures. The robust karyotype modeling, using both nrDNA phylogenies, allowed us to infer that the ancestral Heterotaxis karyotype presented 2n = 40, probably with a proximal 45S rDNA on a metacentric chromosome pair. The chromosome number variation was caused by ascending dysploidy (chromosome fission involving the proximal 45S rDNA site resulting in two acrocentric chromosome pairs holding a terminal 45S rDNA), with subsequent descending dysploidy (fusion) in two species, H. maleolens and H. sessilis. However, besides dysploidy, our analysis detected another important chromosome rearrangement in the Orchidaceae: chromosome inversion, that promoted 5S rDNA site duplication and relocation.
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Shah N, Hirakawa H, Kusakabe S, Sandal N, Stougaard J, Schierup MH, Sato S, Andersen SU. High-resolution genetic maps of Lotus japonicus and L. burttii based on re-sequencing of recombinant inbred lines. DNA Res 2016; 23:487-494. [PMID: 27374610 PMCID: PMC5066174 DOI: 10.1093/dnares/dsw033] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 06/01/2016] [Indexed: 11/13/2022] Open
Abstract
Recombinant inbred lines (RILs) derived from bi-parental populations are stable genetic resources, which are widely used for constructing genetic linkage maps. These genetic maps are essential for QTL mapping and can aid contig and scaffold anchoring in the final stages of genome assembly. In this study, two Lotus sp. RIL populations, Lotus japonicus MG-20 × Gifu and Gifu × L. burttii, were characterized by Illumina re-sequencing. Genotyping of 187 MG-20 × Gifu RILs at 87,140 marker positions and 96 Gifu × L. burttii RILs at 357,973 marker positions allowed us to accurately identify 1,929 recombination breakpoints in the MG-20 × Gifu RILs and 1,044 breakpoints in the Gifu × L. burttii population. The resulting high-density genetic maps now facilitate high-accuracy QTL mapping, identification of reference genome mis-assemblies, and characterization of structural variants.
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Affiliation(s)
- Niraj Shah
- Center for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus, Denmark
| | | | - Shohei Kusakabe
- Graduate School of Life Sciences, Tohoku University, Aoba-ku, Sendai 980-8577, Japan
| | - Niels Sandal
- Center for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus, Denmark
| | - Jens Stougaard
- Center for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus, Denmark
| | | | - Shusei Sato
- Kazusa DNA Research Institute, Chiba 292-0818, Japan.,Graduate School of Life Sciences, Tohoku University, Aoba-ku, Sendai 980-8577, Japan
| | - Stig Uggerhøj Andersen
- Center for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus, Denmark
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Fonsêca A, Ferraz ME, Pedrosa-Harand A. Speeding up chromosome evolution in Phaseolus: multiple rearrangements associated with a one-step descending dysploidy. Chromosoma 2015; 125:413-21. [PMID: 26490170 DOI: 10.1007/s00412-015-0548-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Revised: 10/01/2015] [Accepted: 10/05/2015] [Indexed: 11/28/2022]
Abstract
The genus Phaseolus L. has been subject of extensive cytogenetic studies due to its global economic importance. It is considered karyotypically stable, with most of its ca. 75 species having 2n = 22 chromosomes, and only three species (Phaseolus leptostachyus, Phaseolus macvaughii, and Phaseolus micranthus), which form the Leptostachyus clade, having 2n = 20. To test whether a simple chromosomal fusion was the cause of this descending dysploidy, mitotic chromosomes of P. leptostachyus (2n = 20) were comparatively mapped by fluorescent in situ hybridization (FISH) using bacterial artificial chromosomes (BACs) and ribosomal DNA (rDNA) probes. Our results corroborated the conservation of the 5S and 45S rDNA sites on ancestral chromosomes 10 and 6, respectively. The reduction from x = 11 to x = 10 was the result of the insertion of chromosome 10 into the centromeric region of chromosome 11, supporting a nested chromosome fusion (NCF) as the main cause of this dysploidy. Additionally, the terminal region of the long arm of chromosome 6 was translocated to this larger chromosome. Surprisingly, the NCF was accompanied by several additional translocations and inversions previously unknown for the genus, suggesting that the dysploidy may have been associated to a burst of genome reorganization in this otherwise stable, diploid plant genus.
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Affiliation(s)
- Artur Fonsêca
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Rua Nelson Chaves s/n, Recife, PE, 50670-420, Brazil
| | - Maria Eduarda Ferraz
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Rua Nelson Chaves s/n, Recife, PE, 50670-420, Brazil
| | - Andrea Pedrosa-Harand
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Rua Nelson Chaves s/n, Recife, PE, 50670-420, Brazil.
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Rocha LC, Bustamante FDO, Silveira RAD, Torres GA, Mittelmann A, Techio VH. Functional repetitive sequences and fragile sites in chromosomes of Lolium perenne L. PROTOPLASMA 2015; 252:451-60. [PMID: 25141824 DOI: 10.1007/s00709-014-0690-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Accepted: 08/13/2014] [Indexed: 05/26/2023]
Abstract
Lolium perenne is considered a high-quality forage widely used in temperate regions to meet the shortage of forage during the winter. In this species, some peculiarities related to cytogenetic aspects have already been described, as the variability in number and position of 45S ribosomal DNA (rDNA) sites and the expression of fragile sites, which require further studies to support the understanding of their causes and consequences. In this way, this study aimed to evaluate the relationship between the expression of fragile sites and functional repetitive sequences (rDNA and telomeric) in chromosomes of diploid and polyploid cultivars of L. perenne. The techniques of FISH, Ag-NOR and fluorescence banding were used to assess the distribution of sites of 45S rDNA, 5S, telomeric sequences, and the transcriptional activity of the 45S ribosomal genes and the distribution of AT- and/or GC-rich sequences in L. perenne, respectively. There was variability in the number and location of 45S rDNA sites, which was not observed for 5S rDNA sites. One of the genotypes showed two 45S rDNA sites on the same chromosome, located in different chromosome arms. Breaks and gaps were found in 45S rDNA sites in most metaphases evaluated for both cultivars. Telomeric sequences were not detected at the end of the chromosomal fragments corresponding to the location of breaks at 45S sites. Apparently, the transcriptional activity was modified in fragile sites. Variation in the number and size of nucleoli, nucleolar fusions and dissociations were observed. All CMA(+) bands were colocalized with the 45S sites.
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Affiliation(s)
- Laiane Corsini Rocha
- Department of Biology, Federal University of Lavras, P.O. Box 3037, 37200-000, Lavras, Minas Gerais State, Brazil
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Intra- and interchromosomal rearrangements between cowpea [Vigna unguiculata (L.) Walp.] and common bean (Phaseolus vulgaris L.) revealed by BAC-FISH. Chromosome Res 2015; 23:253-66. [PMID: 25634499 DOI: 10.1007/s10577-014-9464-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Revised: 12/22/2014] [Accepted: 12/26/2014] [Indexed: 12/22/2022]
Abstract
Cowpea (Vigna unguiculata) is an annual legume grown in tropical and subtropical regions, which is economically relevant due to high protein content in dried beans, green pods, and leaves. In this work, a comparative cytogenetic study between V. unguiculata and Phaseolus vulgaris (common bean) was conducted using BAC-FISH. Sequences previously mapped in P. vulgaris chromosomes (Pv) were used as probes in V. unguiculata chromosomes (Vu), contributing to the analysis of macrosynteny between both legumes. Thirty-seven clones from P. vulgaris 'BAT93' BAC library, corresponding to its 11 linkage groups, were hybridized in situ. Several chromosomal rearrangements were identified, such as translocations (between BACs from Pv1 and Pv8; Pv2 and Pv3; as well as Pv2 and Pv11), duplications (BAC from Pv3), as well as paracentric and pericentric inversions (BACs from Pv3, and Pv4, respectively). Two BACs (from Pv2 and Pv7), which hybridized at terminal regions in almost all P. vulgaris chromosomes, showed single-copy signal in Vu. Additionally, 17 BACs showed no signal in V. unguiculata chromosomes. The present results demonstrate the feasibility of using BAC libraries in comparative chromosomal mapping and karyotype evolution studies between Phaseolus and Vigna species, and revealed several macrosynteny and collinearity breaks among both legumes.
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Książkiewicz M, Zielezinski A, Wyrwa K, Szczepaniak A, Rychel S, Karlowski W, Wolko B, Naganowska B. Remnants of the Legume Ancestral Genome Preserved in Gene-Rich Regions: Insights from Lupinus angustifolius Physical, Genetic, and Comparative Mapping. PLANT MOLECULAR BIOLOGY REPORTER 2015; 33:84-101. [PMID: 25620837 PMCID: PMC4295026 DOI: 10.1007/s11105-014-0730-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The narrow-leafed lupin (Lupinus angustifolius) was recently considered as a legume reference species. Genetic resources have been developed, including a draft genome sequence, linkage maps, nuclear DNA libraries, and cytogenetic chromosome-specific landmarks. Here, we used a complex approach, involving DNA fingerprinting, sequencing, genetic mapping, and molecular cytogenetics, to localize and analyze L. angustifolius gene-rich regions (GRRs). A L. angustifolius genomic bacterial artificial chromosome (BAC) library was screened with short sequence repeat (SSR)-based probes. Selected BACs were fingerprinted and assembled into contigs. BAC-end sequence (BES) annotation allowed us to choose clones for sequencing, targeting GRRs. Additionally, BESs were aligned to the scaffolds of the genome sequence. The genetic map was supplemented with 35 BES-derived markers, distributed in 14 linkage groups and tagging 37 scaffolds. The identified GRRs had an average gene density of 19.6 genes/100 kb and physical-to-genetic distance ratios of 11 to 109 kb/cM. Physical and genetic mapping was supported by multi-BAC-fluorescence in situ hybridization (FISH), and five new linkage groups were assigned to the chromosomes. Syntenic links to the genome sequences of five legume species (Medicago truncatula, Glycine max, Lotus japonicus, Phaseolus vulgaris, and Cajanus cajan) were identified. The comparative mapping of the two largest lupin GRRs provides novel evidence for ancient duplications in all of the studied species. These regions are conserved among representatives of the main clades of Papilionoideae. Furthermore, despite the complex evolution of legumes, some segments of the nuclear genome were not substantially modified and retained their quasi-ancestral structures. Cytogenetic markers anchored in these regions constitute a platform for heterologous mapping of legume genomes.
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Affiliation(s)
- Michał Książkiewicz
- Department of Genomics, Institute of Plant Genetics of the Polish Academy of Sciences, Strzeszyńska 34, 60-479 Poznan, Poland
| | - Andrzej Zielezinski
- Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznan, Poland
| | - Katarzyna Wyrwa
- Department of Genomics, Institute of Plant Genetics of the Polish Academy of Sciences, Strzeszyńska 34, 60-479 Poznan, Poland
| | - Anna Szczepaniak
- Department of Genomics, Institute of Plant Genetics of the Polish Academy of Sciences, Strzeszyńska 34, 60-479 Poznan, Poland
| | - Sandra Rychel
- Department of Genomics, Institute of Plant Genetics of the Polish Academy of Sciences, Strzeszyńska 34, 60-479 Poznan, Poland
| | - Wojciech Karlowski
- Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznan, Poland
| | - Bogdan Wolko
- Department of Genomics, Institute of Plant Genetics of the Polish Academy of Sciences, Strzeszyńska 34, 60-479 Poznan, Poland
| | - Barbara Naganowska
- Department of Genomics, Institute of Plant Genetics of the Polish Academy of Sciences, Strzeszyńska 34, 60-479 Poznan, Poland
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Joshi A, Das SK, Samanta P, Paria P, Sen SK, Basu A. Chromosome-specific physical localisation of expressed sequence tag loci in Corchorus olitorius L. PLANT BIOLOGY (STUTTGART, GERMANY) 2014; 16:1133-1139. [PMID: 24628982 DOI: 10.1111/plb.12158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2013] [Accepted: 12/20/2013] [Indexed: 06/03/2023]
Abstract
Jute (Corchorus spp.), as a natural fibre-producing species, ranks next only to cotton. Inadequate understanding of its genetic architecture is a major lacuna for genetic improvement of this crop in terms of yield and quality. Establishment of a physical map provides a genomic tool that helps in positional cloning of valuable genes. In this report, an attempt was initiated to study association and localisation of single copy expressed sequence tag (EST) loci in the genome of Corchorus olitorius. The chromosome-specific association of EST was determined based on the appearance of an extra signal for a single copy cDNA probe in mitotic interphase nuclei of specific trisomic(s) for fluorescence in situ hybridisation, and validated using a cDNA fragment of the 26S rRNA gene (600 bp) as molecular probe. The probe exhibited three signals in meiotic interphase nuclei of trisomic 5, instead of two as observed in diploids and other trisomics, indicating its association with chromosome 5. Subsequent hybridisation of the same probe on the pachytene chromosomes of diploids confirmed that 26S rRNA occupies the terminal end of the short arm of chromosome 5 in C. olitorius. Subsequently, chromosome-specific association of 63 single copy EST and their physical localisation were determined on chromosomes 2, 4, 5 and 7. The study describes chromosome-specific physical localisation of genes in jute. The approach used here could be a step towards construction of genome-wide physical maps for any recalcitrant plant species like jute.
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Affiliation(s)
- A Joshi
- Advanced Laboratory for Plant Genetic Engineering, Indian Institute of Technology, Kharagpur, India
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Cabral G, Marques A, Schubert V, Pedrosa-Harand A, Schlögelhofer P. Chiasmatic and achiasmatic inverted meiosis of plants with holocentric chromosomes. Nat Commun 2014; 5:5070. [PMID: 25295686 PMCID: PMC4190664 DOI: 10.1038/ncomms6070] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Accepted: 08/25/2014] [Indexed: 11/09/2022] Open
Abstract
Meiosis is a specialized cell division in sexually reproducing organisms before gamete formation. Following DNA replication, the canonical sequence in species with monocentric chromosomes is characterized by reductional segregation of homologous chromosomes during the first and equational segregation of sister chromatids during the second meiotic division. Species with holocentric chromosomes employ specific adaptations to ensure regular disjunction during meiosis. Here we present the analysis of two closely related plant species with holocentric chromosomes that display an inversion of the canonical meiotic sequence, with the equational division preceding the reductional. In-depth analysis of the meiotic divisions of Rhynchospora pubera and R. tenuis reveals that during meiosis I sister chromatids are bi-oriented, display amphitelic attachment to the spindle and are subsequently separated. During prophase II, chromatids are connected by thin chromatin threads that appear instrumental for the regular disjunction of homologous non-sister chromatids in meiosis II. The absence of a defined centromere in organisms with holocentric chromosomes presents particular problems for the control of chromosome segregation during meiosis. Cabral et al. present evidence that two plant species overcome this challenge by inverting the conventional sequence of meiotic divisions.
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Affiliation(s)
- Gabriela Cabral
- 1] Department of Botany, Laboratory of Plant Cytogenetics and Evolution, Federal University of Pernambuco, Rua Nelson Chaves s/n, Recife, Pernambuco 50670-420, Brazil [2] Department of Chromosome Biology, Max F. Perutz Laboratories, University of Vienna, Dr Bohr-Gasse 9, Vienna A-1030, Austria
| | - André Marques
- Department of Botany, Laboratory of Plant Cytogenetics and Evolution, Federal University of Pernambuco, Rua Nelson Chaves s/n, Recife, Pernambuco 50670-420, Brazil
| | - Veit Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research, Corrensstraße 3, Gatersleben 06466, Germany
| | - Andrea Pedrosa-Harand
- Department of Botany, Laboratory of Plant Cytogenetics and Evolution, Federal University of Pernambuco, Rua Nelson Chaves s/n, Recife, Pernambuco 50670-420, Brazil
| | - Peter Schlögelhofer
- Department of Chromosome Biology, Max F. Perutz Laboratories, University of Vienna, Dr Bohr-Gasse 9, Vienna A-1030, Austria
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Santos AA, Penha HA, Bellec A, Munhoz CDF, Pedrosa-Harand A, Bergès H, Vieira MLC. Begin at the beginning: A BAC-end view of the passion fruit (Passiflora) genome. BMC Genomics 2014; 15:816. [PMID: 25260959 PMCID: PMC4189760 DOI: 10.1186/1471-2164-15-816] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Accepted: 09/22/2014] [Indexed: 12/16/2022] Open
Abstract
Background The passion fruit (Passiflora edulis) is a tropical crop of economic importance both for juice production and consumption as fresh fruit. The juice is also used in concentrate blends that are consumed worldwide. However, very little is known about the genome of the species. Therefore, improving our understanding of passion fruit genomics is essential and to some degree a pre-requisite if its genetic resources are to be used more efficiently. In this study, we have constructed a large-insert BAC library and provided the first view on the structure and content of the passion fruit genome, using BAC-end sequence (BES) data as a major resource. Results The library consisted of 82,944 clones and its levels of organellar DNA were very low. The library represents six haploid genome equivalents, and the average insert size was 108 kb. To check its utility for gene isolation, successful macroarray screening experiments were carried out with probes complementary to eight Passiflora gene sequences available in public databases. BACs harbouring those genes were used in fluorescent in situ hybridizations and unique signals were detected for four BACs in three chromosomes (n = 9). Then, we explored 10,000 BES and we identified reads likely to contain repetitive mobile elements (19.6% of all BES), simple sequence repeats and putative proteins, and to estimate the GC content (~42%) of the reads. Around 9.6% of all BES were found to have high levels of similarity to plant genes and ontological terms were assigned to more than half of the sequences analysed (940). The vast majority of the top-hits made by our sequences were to Populus trichocarpa (24.8% of the total occurrences), Theobroma cacao (21.6%), Ricinus communis (14.3%), Vitis vinifera (6.5%) and Prunus persica (3.8%). Conclusions We generated the first large-insert library for a member of Passifloraceae. This BAC library provides a new resource for genetic and genomic studies, as well as it represents a valuable tool for future whole genome study. Remarkably, a number of BAC-end pair sequences could be mapped to intervals of the sequenced Arabidopsis thaliana, V. vinifera and P. trichocarpa chromosomes, and putative collinear microsyntenic regions were identified. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-816) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | - Maria Lucia Carneiro Vieira
- Departamento de Genética, Universidade de São Paulo, Escola Superior de Agricultura "Luiz de Queiroz", P,O, Box 83, 13400-970 Piracicaba, Brazil.
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50
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Tek AL, Kashihara K, Murata M, Nagaki K. Identification of the centromere-specific histone H3 variant in Lotus japonicus. Gene 2014; 538:8-11. [PMID: 24462968 DOI: 10.1016/j.gene.2014.01.034] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Revised: 12/02/2013] [Accepted: 01/11/2014] [Indexed: 11/15/2022]
Abstract
The centromere is a structurally and functionally specialized region present on every eukaryotic chromosome. Lotus japonicus is a model legume species for which there is very limited information on the centromere structure. Here we cloned and characterized the L. japonicus homolog of the centromere-specific histone H3 gene (LjCenH3) encoding a 159-amino acid protein. Using an Agrobacterium-based transformation system, LjCenH3 tagged with a green fluorescent protein was transferred into L. japonicus cells. The centromeric position of LjCENH3 protein was revealed on L. japonicus metaphase chromosomes by an immunofluorescence assay. The identification of LjCenH3 as a critical centromere landmark could pave the way for a better understanding of centromere structure in this model and other agriculturally important legume species.
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Affiliation(s)
- Ahmet L Tek
- Institute of Plant Science and Resources, Okayama University, Kurashiki 710-0046, Japan.
| | - Kazunari Kashihara
- Institute of Plant Science and Resources, Okayama University, Kurashiki 710-0046, Japan
| | - Minoru Murata
- Institute of Plant Science and Resources, Okayama University, Kurashiki 710-0046, Japan
| | - Kiyotaka Nagaki
- Institute of Plant Science and Resources, Okayama University, Kurashiki 710-0046, Japan.
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