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Alves RM, de Abreu VAC, Oliveira RP, Almeida JVDA, de Oliveira MDM, Silva SR, Paschoal AR, de Almeida SS, de Souza PAF, Ferro JA, Miranda VFO, Figueira A, Domingues DS, Varani AM. Genomic decoding of Theobroma grandiflorum (cupuassu) at chromosomal scale: evolutionary insights for horticultural innovation. Gigascience 2024; 13:giae027. [PMID: 38837946 PMCID: PMC11152179 DOI: 10.1093/gigascience/giae027] [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: 12/23/2023] [Revised: 03/21/2024] [Accepted: 05/08/2024] [Indexed: 06/07/2024] Open
Abstract
BACKGROUND Theobroma grandiflorum (Malvaceae), known as cupuassu, is a tree indigenous to the Amazon basin, valued for its large fruits and seed pulp, contributing notably to the Amazonian bioeconomy. The seed pulp is utilized in desserts and beverages, and its seed butter is used in cosmetics. Here, we present the sequenced telomere-to-telomere genome of cupuassu, disclosing its genomic structure, evolutionary features, and phylogenetic relationships within the Malvaceae family. FINDINGS The cupuassu genome spans 423 Mb, encodes 31,381 genes distributed in 10 chromosomes, and exhibits approximately 65% gene synteny with the Theobroma cacao genome, reflecting a conserved evolutionary history, albeit punctuated with unique genomic variations. The main changes are pronounced by bursts of long-terminal repeat retrotransposons at postspecies divergence, retrocopied and singleton genes, and gene families displaying distinctive patterns of expansion and contraction. Furthermore, positively selected genes are evident, particularly among retained and dispersed tandem and proximal duplicated genes associated with general fruit and seed traits and defense mechanisms, supporting the hypothesis of potential episodes of subfunctionalization and neofunctionalization following duplication, as well as impact from distinct domestication process. These genomic variations may underpin the differences observed in fruit and seed morphology, ripening, and disease resistance between cupuassu and the other Malvaceae species. CONCLUSIONS The cupuassu genome offers a foundational resource for both breeding improvement and conservation biology, yielding insights into the evolution and diversity within the genus Theobroma.
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Affiliation(s)
| | - Vinicius A C de Abreu
- Laboratório de Bioinformática e Computação de Alto Desempenho (LaBioCad), Faculdade de Computação (FACOMP), Universidade Federal do Pará, 66075-110 Belém, PA, Brazil
| | - Rafaely Pantoja Oliveira
- Departamento de Biotecnologia Agropecuária e Ambiental, Universidade Estadual Paulista (UNESP), Faculdade de Ciências Agrárias e Veterinárias, 14884-900 Jaboticabal, SP, Brazil
| | - João Victor dos Anjos Almeida
- Departamento de Biotecnologia Agropecuária e Ambiental, Universidade Estadual Paulista (UNESP), Faculdade de Ciências Agrárias e Veterinárias, 14884-900 Jaboticabal, SP, Brazil
| | - Mauro de Medeiros de Oliveira
- Departamento de Biotecnologia Agropecuária e Ambiental, Universidade Estadual Paulista (UNESP), Faculdade de Ciências Agrárias e Veterinárias, 14884-900 Jaboticabal, SP, Brazil
| | - Saura R Silva
- Departamento de Biologia, Universidade Estadual Paulista (UNESP), Faculdade de Ciências Agrárias e Veterinárias, 14884-900 Jaboticabal, SP, Brazil
| | - Alexandre R Paschoal
- Departamento de Ciência da Computação (DACOM), Grupo de e Bioinformática e Reconhecimento de Padrões (bioinfo-cp), Universidade Tecnológica Federal do Paraná (UTFPR), 80230-901 Cornélio Procópio, PR, Brazil
- Artificial Intelligence and Informatics, The Rosalind Franklin Institute, OX110QX Didcot, UK
| | - Sintia S de Almeida
- Laboratório de Bioinformática e Computação de Alto Desempenho (LaBioCad), Faculdade de Computação (FACOMP), Universidade Federal do Pará, 66075-110 Belém, PA, Brazil
| | - Pedro A F de Souza
- Laboratório de Bioinformática e Computação de Alto Desempenho (LaBioCad), Faculdade de Computação (FACOMP), Universidade Federal do Pará, 66075-110 Belém, PA, Brazil
| | - Jesus A Ferro
- Departamento de Biotecnologia Agropecuária e Ambiental, Universidade Estadual Paulista (UNESP), Faculdade de Ciências Agrárias e Veterinárias, 14884-900 Jaboticabal, SP, Brazil
| | - Vitor F O Miranda
- Departamento de Biologia, Universidade Estadual Paulista (UNESP), Faculdade de Ciências Agrárias e Veterinárias, 14884-900 Jaboticabal, SP, Brazil
| | - Antonio Figueira
- Centro de Energia Nuclear na Agricultura (CENA), Universidade de São Paulo, 13416-000 Piracicaba, SP, Brazil
| | - Douglas S Domingues
- Departamento de Genética, Universidade de São Paulo (USP), Escola Superior de Agricultura Luiz de Queiroz (ESALQ), 13418-900 Piracicaba, SP, Brazil
| | - Alessandro M Varani
- Departamento de Biotecnologia Agropecuária e Ambiental, Universidade Estadual Paulista (UNESP), Faculdade de Ciências Agrárias e Veterinárias, 14884-900 Jaboticabal, SP, Brazil
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Soares NR, Correa CTR, da Silva JC, da Silva Negreiros JR, Techio VH, Torres GA. Comparative cytogenetics of three economically important Piper L. species from the Brazilian Amazon. PROTOPLASMA 2022; 259:1099-1108. [PMID: 34762169 DOI: 10.1007/s00709-021-01721-2] [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: 06/30/2021] [Accepted: 11/01/2021] [Indexed: 06/13/2023]
Abstract
The species Piper hispidinervum, Piper aduncum, and Piper affinis hispidinervum have essential oils with high levels of safrole, dillapiole, and sarisan, respectively. Safrole is important for pharmaceutical and chemical industries, while dillapiole and sarisan are promising compounds to control insects and fungi. These species are very similar morphologically and their taxonomy is controversial. Divergent hypotheses consider P. aduncum and P. hispidinervum either as a single species or as distinct taxa, while P. affinis hispidinervum is inferred to be a natural hybrid or a chemotype of P. hispidinervum. Delimiting the taxonomic boundaries would be helpful for germplasm conservation and breeding programs. This study aimed to undertake a detailed analysis of P. aduncum, P. hispidinervum, and P. affinis hispidinervum karyotype and rDNA sites. Genomic in situ hybridization (GISH) was used to establish genomic homology among species and to test the natural hybridization hypothesis for origin of P. affinis hispidinervum. Karyotype traits were similar for all three species: 2n = 26 small chromosomes, predominantly metacentric. All three species exhibited CMA+ bands on the secondary constriction of chromosome pair 4. A size-heteromorphic 35S rDNA site was co-localized with the CMA+ band. A 5S rDNA site was located in the proximal region of chromosome pair 7. The patterns of genomic hybridization revealed that the repetitive DNA fraction of the species is highly similar in terms of proportion of genome, sequence type, and distribution. Our findings did not allow us to differentiate the three species and point to the importance of deeper genomic studies to elucidate the taxonomic controversy.
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Affiliation(s)
- Nina Reis Soares
- Departamento de Biologia, Instituto de Ciências Naturais, Universidade Federal de Lavas, Lavras, Minas Gerais, Brazil
| | - Caio Túlio Rodrigues Correa
- Departamento de Biologia, Instituto de Ciências Naturais, Universidade Federal de Lavas, Lavras, Minas Gerais, Brazil
| | - Jhonata Costa da Silva
- Departamento de Biologia, Instituto de Ciências Naturais, Universidade Federal de Lavas, Lavras, Minas Gerais, Brazil
| | | | - Vânia Helena Techio
- Departamento de Biologia, Instituto de Ciências Naturais, Universidade Federal de Lavas, Lavras, Minas Gerais, Brazil
| | - Giovana Augusta Torres
- Departamento de Biologia, Instituto de Ciências Naturais, Universidade Federal de Lavas, Lavras, Minas Gerais, Brazil.
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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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de Oliveira OLS, Souza MM, de Melo CAF. Cytogenetics and morphological delimitation between three species of Passiflora L. (subgenus Distephana Cervi). PLANT BIOLOGY (STUTTGART, GERMANY) 2019; 21:662-669. [PMID: 30676681 DOI: 10.1111/plb.12967] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 01/20/2019] [Indexed: 06/09/2023]
Abstract
Several studies on cytogenetic characterisation of passion flowers are helpful to elucidate doubts about taxa relationships, delimitation and classification into more coherent groups based on karyomorphological data. Molecular and conventional cytogenetic techniques were applied to three Passiflora species with red flowers, P. coccinea, P. vitifolia and P. tholozanii, for species karyotype relationships. Additionally, for descriptive morphology, were used flowers, leaves and seeds. Results describe for the first time the karyomorphological and chromosome number (2n = 18) for P. tholozanii. anova was performed (P < 0.05) and statistical significance for average chromosome size (CV: 16.53%) between species. Genomic in situ hybridisation (GISH) proved relationships between P. coccinea and P. tholozanii, which suggests a common origin, however, we could not identify hybridisation between genomic probes from P. vitifolia in P. tholozanii chromosomes. Among the species analysed, P. tholozanii has great similarity in karyotypic and morphology to P. coccinea but not to P. vitifolia. We suggest the inclusion of P. tholozanii in the same subgenus and section as P. coccinea based on the similarity in karyomorphological and morphological traits between the species. Additionally, GISH might indicate a common or hybrid origin of P. tholozanii.
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Affiliation(s)
- O L S de Oliveira
- Laboratório de Melhoramento de Plantas, Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz (UESC), Ilhéus, Brazil
| | - M M Souza
- Laboratório de Melhoramento de Plantas, Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz (UESC), Ilhéus, Brazil
| | - C A F de Melo
- Laboratório de Melhoramento de Plantas, Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz (UESC), Ilhéus, Brazil
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Bolaños-Villegas P, Argüello-Miranda O. Meiosis Research in Orphan and Non-orphan Tropical Crops. FRONTIERS IN PLANT SCIENCE 2019; 10:74. [PMID: 30891046 PMCID: PMC6411703 DOI: 10.3389/fpls.2019.00074] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 01/17/2019] [Indexed: 05/04/2023]
Abstract
Plant breeding is directly linked to the development of crops that can effectively adapt to challenging conditions such as soil nutrient depletion, water pollution, drought, and anthropogenic climate change. These conditions are extremely relevant in developing countries already burdened with population growth and unchecked urban expansion, especially in the tropical global southern hemisphere. Engineering new crops thus has potential to enhance food security, prevent hunger, and spur sustainable agricultural growth. A major tool for the improvement of plant varieties in this context could be the manipulation of homologous recombination and genome haploidization during meiosis. The isolation or the design of mutations in key meiotic genes may facilitate DNA recombination and transmission of important genes quickly and efficiently. Genome haploidization through centromeric histone mutants could be an option to create new crosses rapidly. This review covers technical approaches to engineer key meiotic genes in tropical crops as a blueprint for future work and examples of tropical crops in which such strategies could be applied are given.
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Affiliation(s)
- Pablo Bolaños-Villegas
- Laboratory of Molecular and Cell Biology, Fabio Baudrit Agricultural Research Station, University of Costa Rica, Alajuela, Costa Rica
- *Correspondence: Pablo Bolaños-Villegas,
| | - Orlando Argüello-Miranda
- Department of Cell Biology, The University of Texas Southwestern Medical Center, Dallas, TX, United States
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Osorio-Guarín JA, Quackenbush CR, Cornejo OE. Ancestry informative alleles captured with reduced representation library sequencing in Theobroma cacao. PLoS One 2018; 13:e0203973. [PMID: 30332408 PMCID: PMC6192562 DOI: 10.1371/journal.pone.0203973] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 10/04/2018] [Indexed: 12/18/2022] Open
Abstract
As the source of chocolate, cacao has become one of the most important crops in the world. The identification of molecular markers to understand the demographic history, genetic diversity and population structure plays a pivotal role in cacao breeding programs. Here, we report the use of a modified genotyping-by-sequencing (GBS) approach for large-scale single nucleotide polymorphism (SNP) discovery and allele ancestry mapping. We identified 12,357 bi-allelic SNPs after filtering, of which, 7,009 variants were ancestry informative. The GBS approach proved to be rapid, cost-effective, and highly informative for ancestry assignment in this species.
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Affiliation(s)
- Jaime A. Osorio-Guarín
- Centro de Investigación Tibaitatá, Corporación Colombiana de Investigación Agropecuaria–Agrosavia, Mosquera, Cundinamarca, Colombia
| | - Corey R. Quackenbush
- School of Biological Sciences, Washington State University, Pullman, WA, United States of America
| | - Omar E. Cornejo
- School of Biological Sciences, Washington State University, Pullman, WA, United States of America
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Feitoza L, Costa L, Guerra M. Condensation patterns of prophase/prometaphase chromosome are correlated with H4K5 histone acetylation and genomic DNA contents in plants. PLoS One 2017; 12:e0183341. [PMID: 28854212 PMCID: PMC5576753 DOI: 10.1371/journal.pone.0183341] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 08/02/2017] [Indexed: 02/05/2023] Open
Abstract
Mitotic prophase chromosome condensation plays an essential role in nuclear division being therefore regulated by highly conserved mechanisms. However, degrees of chromatin condensation in prophase-prometaphase cells may vary along the chromosomes resulting in specific condensation patterns. We examined different condensation patterns (CPs) of prophase and prometaphase chromosomes and investigated their relationship with genome size and distribution of histone H4 acetylated at lysine 5 (H4K5ac) in 17 plant species. Our results showed that most species with small genomes (2C < 5 pg) (Arachis pusilla, Bixa orellana, Costus spiralis, Eleutherine bulbosa, Indigofera campestris, Phaseolus lunatus, P. vulgaris, Poncirus trifoliata, and Solanum lycopersicum) displayed prophase chromosomes with late condensing terminal regions that were highly enriched in H4K5ac, and early condensing regions with apparently non-acetylated proximal chromatin. The species with large genomes (Allium cepa, Callisia repens, Araucaria angustifolia and Nothoscordum pulchellum) displayed uniformly condensed and acetylated prophase/prometaphase chromosomes. Three species with small genomes (Eleocharis geniculata, Rhynchospora pubera, and R. tenuis) displayed CP and H4K5ac labeling patterns similar to species with large genomes, whereas a forth species (Emilia sonchifolia) exhibited a gradual chromosome labeling, being more acetylated in the terminal regions and less acetylated in the proximal ones. The nucleolus organizer chromatin was the only chromosomal region that in prometaphase or metaphase could be hyperacetylated, hypoacetylated or non-acetylated, depending on the species. Our data indicate that the CP of a plant chromosome complement is influenced but not exclusively determined by nuclear and chromosomal DNA contents, whereas the CP of individual chromosomes is clearly correlated with H4K5ac distribution.
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Affiliation(s)
- Lidiane Feitoza
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Recife, PE, Brazil
| | - Lucas Costa
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Recife, PE, Brazil
| | - Marcelo Guerra
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Recife, PE, Brazil
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Genome size, cytogenetic data and transferability of EST-SSRs markers in wild and cultivated species of the genus Theobroma L. (Byttnerioideae, Malvaceae). PLoS One 2017; 12:e0170799. [PMID: 28187131 PMCID: PMC5302445 DOI: 10.1371/journal.pone.0170799] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2016] [Accepted: 01/11/2017] [Indexed: 11/19/2022] Open
Abstract
The genus Theobroma comprises several trees species native to the Amazon. Theobroma cacao L. plays a key economic role mainly in the chocolate industry. Both cultivated and wild forms are described within the genus. Variations in genome size and chromosome number have been used for prediction purposes including the frequency of interspecific hybridization or inference about evolutionary relationships. In this study, the nuclear DNA content, karyotype and genetic diversity using functional microsatellites (EST-SSR) of seven Theobroma species were characterized. The nuclear content of DNA for all analyzed Theobroma species was 1C = ~ 0.46 pg. These species presented 2n = 20 with small chromosomes and only one pair of terminal heterochromatic bands positively stained (CMA+/DAPI− bands). The small size of Theobroma ssp. genomes was equivalent to other Byttnerioideae species, suggesting that the basal lineage of Malvaceae have smaller genomes and that there was an expansion of 2C values in the more specialized family clades. A set of 20 EST-SSR primers were characterized for related species of Theobroma, in which 12 loci were polymorphic. The polymorphism information content (PIC) ranged from 0.23 to 0.65, indicating a high level of information per locus. Combined results of flow cytometry, cytogenetic data and EST-SSRs markers will contribute to better describe the species and infer about the evolutionary relationships among Theobroma species. In addition, the importance of a core collection for conservation purposes is highlighted.
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The Impact of Polyoxyethylene Sorbitan Surfactants in the Microstructure and Rheological Behaviour of Emulsions Made With Melted Fat From Cupuassu (Theobroma grandiflorum). J SURFACTANTS DETERG 2016. [DOI: 10.1007/s11743-016-1820-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Royaert S, Jansen J, da Silva DV, de Jesus Branco SM, Livingstone DS, Mustiga G, Marelli JP, Araújo IS, Corrêa RX, Motamayor JC. Identification of candidate genes involved in Witches' broom disease resistance in a segregating mapping population of Theobroma cacao L. in Brazil. BMC Genomics 2016; 17:107. [PMID: 26865216 PMCID: PMC4750280 DOI: 10.1186/s12864-016-2415-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Accepted: 01/26/2016] [Indexed: 01/17/2023] Open
Abstract
Background Witches’ broom disease (WBD) caused by the fungus Moniliophthora perniciosa is responsible for considerable economic losses for cacao producers. One of the ways to combat WBD is to plant resistant cultivars. Resistance may be governed by a few genetic factors, mainly found in wild germplasm. Results We developed a dense genetic linkage map with a length of 852.8 cM that contains 3,526 SNPs and is based on the MP01 mapping population, which counts 459 trees from a cross between the resistant ‘TSH 1188’ and the tolerant ‘CCN 51’ at the Mars Center for Cocoa Science in Barro Preto, Bahia, Brazil. Seven quantitative trait loci (QTL) that are associated with WBD were identified on five different chromosomes using a multi-trait QTL analysis for outbreeders. Phasing of the haplotypes at the major QTL region on chromosome IX on a diversity panel of genotypes clearly indicates that the major resistance locus comes from a well-known source of WBD resistance, the clone ‘SCAVINA 6’. Various potential candidate genes identified within all QTL may be involved in different steps leading to disease resistance. Preliminary expression data indicate that at least three of these candidate genes may play a role during the first 12 h after infection, with clear differences between ‘CCN 51’ and ‘TSH 1188’. Conclusions We combined the information from a large mapping population with very distinct parents that segregate for WBD, a dense set of mapped markers, rigorous phenotyping capabilities and the availability of a sequenced genome to identify several genomic regions that are involved in WBD resistance. We also identified a novel source of resistance that most likely comes from the ‘CCN 51’ parent. Thanks to the large population size of the MP01 population, we were able to pick up QTL and markers with relatively small effects that can contribute to the creation and selection of more tolerant/resistant plant material. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2415-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Stefan Royaert
- Mars Center for Cocoa Science, CP 55, Itajuípe, BA, CEP 45.630-000, Brazil.
| | - Johannes Jansen
- Biometris, Wageningen University and Research Centre, P.O. Box 100, 6700 AC, Wageningen, The Netherlands.
| | - Daniela Viana da Silva
- Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Rodovia Ilhéus-Itabuna, Km 16, Bairro Salobrinho, Ilhéus, BA, CEP 45.662-900, Brazil.
| | - Samuel Martins de Jesus Branco
- Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Rodovia Ilhéus-Itabuna, Km 16, Bairro Salobrinho, Ilhéus, BA, CEP 45.662-900, Brazil.
| | | | - Guiliana Mustiga
- Mars, Incorporated, 13601 Old Cutler Road, Miami, FL, 33158, USA.
| | | | - Ioná Santos Araújo
- Departamento de Ciências Vegetais, Universidade Federal Rural do Semi-Arido, BR 110 - Km 47, Bairro Pres. Costa e Silva, Mossoró, RN, CEP 59.625-900, Brazil.
| | - Ronan Xavier Corrêa
- Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Rodovia Ilhéus-Itabuna, Km 16, Bairro Salobrinho, Ilhéus, BA, CEP 45.662-900, Brazil.
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Roa F, Guerra M. Distribution of 45S rDNA sites in chromosomes of plants: structural and evolutionary implications. BMC Evol Biol 2012. [PMID: 23181612 PMCID: PMC3583730 DOI: 10.1186/1471-2148-12-225] [Citation(s) in RCA: 101] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Background 45S rDNA sites are the most widely documented chromosomal regions in eukaryotes. The analysis of the distribution of these sites along the chromosome in several genera has suggested some bias in their distribution. In order to evaluate if these loci are in fact non-randomly distributed and what is the influence of some chromosomal and karyotypic features on the distribution of these sites, a database was built with the position and number of 45S rDNA sites obtained by FISH together with other karyotypic data from 846 plant species. Results In angiosperms the most frequent numbers of sites per diploid karyotype were two and four, suggesting that in spite of the wide dispersion capacity of these sequences the number of rDNA sites tends to be restricted. The sites showed a preferential distribution on the short arms, mainly in the terminal regions. Curiously, these sites were frequently found on the short arms of acrocentric chromosomes where they usually occupy the whole arm. The trend to occupy the terminal region is especially evident in holokinetic chromosomes, where all of them were terminally located. In polyploids there is a trend towards reduction in the number of sites per monoploid complement. In gymnosperms, however, the distribution of rDNA sites varied strongly among the sampled families. Conclusions The location of 45S rDNA sites do not vary randomly, occurring preferentially on the short arm and in the terminal region of chromosomes in angiosperms. The meaning of this preferential location is not known, but some hypotheses are considered and the observed trends are discussed.
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Affiliation(s)
- Fernando Roa
- Department of Botany Laboratory of Plant Cytogenetics and Evolution, Federal University of Pernambuco Center of Biological Sciences, Rua Nelson Chaves, s/n Cidade Universitária, Recife, PE, 50,670-420, Brazil
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Feitoza L, Guerra M. Different types of plant chromatin associated with modified histones H3 and H4 and methylated DNA. Genetica 2011; 139:305-14. [PMID: 21327493 DOI: 10.1007/s10709-011-9550-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2010] [Accepted: 01/12/2011] [Indexed: 11/26/2022]
Abstract
Eukaryotic chromosomes are organized into two large and distinct domains, euchromatin and heterochromatin, which are cytologically characterized by different degrees of chromatin compaction during interphase/prophase and by post-synthesis modifications of histones and DNA methylation. Typically, heterochromatin remains condensed during the entire cell cycle whereas euchromatin is decondensed at interphase. However, a fraction of the euchromatin can also remain condensed during interphase and appears as early condensing prophase chromatin. 5S and 45S rDNA sites and telomere DNA were used to characterize these regions in metaphase and interphase nuclei. We investigated the chromosomal distribution of modified histones and methylated DNA in the early and late condensing prophase chromatin of two species with clear differentiation between these domains. Both species, Costus spiralis and Eleutherine bulbosa, additionally have a small amount of classical heterochromatin detected by CMA/DAPI staining. The distribution of H4 acetylated at lysine 5 (H4K5ac), H3 phosphorylated at serine 10 (H3S10ph), H3 dimethylated at lysine 4 or 9 (H3K4me2, H3K9me2), and 5-methylcytosine was compared in metaphase, prophase, and interphase cells by immunostaining with specific antibodies. In both species, the late condensing prophase chromatin was highly enriched in H4K5ac and H3K4me2 whereas the early condensing chromatin was very poor in these marks. H3K9me2 was apparently uniformly distributed along the chromosomes whereas the early condensing chromatin was slightly enriched in 5-methylcytosine. Signals of H3S10ph were restricted to the pericentromeric region of all chromosomes. Notably, none of these marks distinguished classical heterochromatin from the early condensing euchromatin. It is suggested that the early condensing chromatin is an intermediate type between classical heterochromatin and euchromatin.
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Affiliation(s)
- Lidiane Feitoza
- Laboratory of Plant Cytogenetics, Department of Botany, Federal University of Pernambuco, Recife, Brazil
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