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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 2024:10.1007/s00709-024-01944-z. [PMID: 38467939 DOI: 10.1007/s00709-024-01944-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [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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Mata-Sucre Y, Parteka LM, Ritz CM, Gatica-Arias A, Félix LP, Thomas WW, Souza G, Vanzela ALL, Pedrosa-Harand A, Marques A. Oligo-barcode illuminates holocentric karyotype evolution in Rhynchospora (Cyperaceae). Front Plant Sci 2024; 15:1330927. [PMID: 38384757 PMCID: PMC10879424 DOI: 10.3389/fpls.2024.1330927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 01/18/2024] [Indexed: 02/23/2024]
Abstract
Holocentric karyotypes are assumed to rapidly evolve through chromosome fusions and fissions due to the diffuse nature of their centromeres. Here, we took advantage of the recent availability of a chromosome-scale reference genome for Rhynchospora breviuscula, a model species of this holocentric genus, and developed the first set of oligo-based barcode probes for a holocentric plant. These probes were applied to 13 additional species of the genus, aiming to investigate the evolutionary dynamics driving the karyotype evolution in Rhynchospora. The two sets of probes were composed of 27,392 (green) and 23,968 (magenta) oligonucleotides (45-nt long), and generated 15 distinct FISH signals as a unique barcode pattern for the identification of all five chromosome pairs of the R. breviuscula karyotype. Oligo-FISH comparative analyzes revealed different types of rearrangements, such as fusions, fissions, putative inversions and translocations, as well as genomic duplications among the analyzed species. Two rounds of whole genome duplication (WGD) were demonstrated in R. pubera, but both analyzed accessions differed in the complex chain of events that gave rise to its large, structurally diploidized karyotypes with 2n = 10 or 12. Considering the phylogenetic relationships and divergence time of the species, the specificity and synteny of the probes were maintained up to species with a divergence time of ~25 My. However, karyotype divergence in more distant species hindered chromosome mapping and the inference of specific events. This barcoding system is a powerful tool to study chromosomal variations and genomic evolution in holocentric chromosomes of Rhynchospora species.
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Affiliation(s)
- Yennifer Mata-Sucre
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
- Laboratório de Citogenética e Evolução Vegetal, Departamento de Botânica, Centro de Biociências, Universidade Federal de Pernambuco, Recife, Brazil
| | - Letícia Maria Parteka
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
- Laboratory of Cytogenetics and Plant Diversity, Department of General Biology, Londrina State University, Londrina, Brazil
| | - Christiane M. Ritz
- Department of Botany, Senckenberg Museum for Natural History Görlitz, Senckenberg – Member of the Leibniz Association, Görlitz, Germany
- Technical University Dresden, International Institute (IHI) Zittau, Chair of Biodiversity of Higher Plants, Zittau, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | | | - Leonardo P. Félix
- Laboratory of Plant Cytogenetics, Department of Biosciences, Federal University of Paraíba, Areia, Brazil
| | - William Wayt Thomas
- Institute of Systematic Botany, New York Botanical Garden, Bronx, NY, United States
| | - Gustavo Souza
- Laboratório de Citogenética e Evolução Vegetal, Departamento de Botânica, Centro de Biociências, Universidade Federal de Pernambuco, Recife, Brazil
| | - André L. L. Vanzela
- Laboratory of Cytogenetics and Plant Diversity, Department of General Biology, Londrina State University, Londrina, Brazil
| | - Andrea Pedrosa-Harand
- Laboratório de Citogenética e Evolução Vegetal, Departamento de Botânica, Centro de Biociências, Universidade Federal de Pernambuco, Recife, Brazil
| | - André Marques
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
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Braz GT, Van-Lume B, de Resende KFM, Cardoso FP, Oliveira L, de Andrade MJG, Souza G, Torres GA. Cytomolecular trends in Chamaecrista Moench (Caesalpinioideae, Leguminosae) diversification. Genetica 2024; 152:51-61. [PMID: 38381186 DOI: 10.1007/s10709-024-00205-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 02/14/2024] [Indexed: 02/22/2024]
Abstract
Chamaecrista is a Pantropical legume genus of the tribe Cassieae, which includes six other genera. In contrast to most of the other Cassieae genera, Chamaecrista shows significant variability in chromosome number (from 2n = 14 to 2n = 56), with small and morphologically similar chromosomes. Here, we performed a new cytomolecular analysis on chromosome number, genome size, and rDNA site distribution in a molecular phylogenetic perspective to interpret the karyotype trends of Chamaecrista and other two genera of Cassieae, seeking to understand their systematics and evolution. Our phylogenetic analysis revealed that Chamaecrista is monophyletic and can be divided into four major clades corresponding to the four sections of the genus. Chromosome numbers ranged from 2n = 14, 16 (section Chamaecrista) to 2n = 28 (sections Absus, Apoucouita, and Baseophyllum). The number of 5S and 35S rDNA sites varied between one and three pairs per karyotype, distributed on different chromosomes or in synteny, with no obvious phylogenetic significance. Our data allowed us to propose x = 7 as the basic chromosome number of Cassieae, which was changed by polyploidy generating x = 14 (sections Absus, Apoucouita, and Baseophyllum) and by ascending dysploidy to x = 8 (section Chamaecrista). The DNA content values supported this hypothesis, with the genomes of the putative tetraploids being larger than those of the putative diploids. We hypothesized that ascending dysploidy, polyploidy, and rDNA amplification/deamplification are the major events in the karyotypic diversification of Chamaecrista. The chromosomal marks characterized here may have cytotaxonomic potential in future studies.
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Affiliation(s)
- Guilherme Tomaz Braz
- Departamento de Biologia Vegetal, Universidade Estadual de Campinas, Campinas, São Paulo, Brasil.
| | - Brena Van-Lume
- Programa de Pós-graduação em Biologia Vegetal, Centro de Biociências, Universidade Federal de Pernambuco, Recife, Pernambuco, Brasil
| | | | - Felipe Pereira Cardoso
- Departamento de Biologia, Instituto de Ciências Naturais, Universidade Federal de Lavras, Lavras, Minas Gerais, Brasil
| | - Ludmila Oliveira
- Biology Centre, Institute of Plant Molecular Biology, Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Maria José Gomes de Andrade
- Programa de Pós-graduação em Biodiversidade Vegetal, Departamento de Educação, Campus VIII, Universidade do Estado da Bahia, Bahia, Paulo Afonso, Brasil
| | - Gustavo Souza
- Programa de Pós-graduação em Biologia Vegetal, Centro de Biociências, Universidade Federal de Pernambuco, Recife, Pernambuco, Brasil
| | - Giovana Augusta Torres
- Departamento de Biologia, Instituto de Ciências Naturais, Universidade Federal de Lavras, Lavras, Minas Gerais, Brasil
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Cunha ACMC, Katz L, Amorim AFC, Coutinho IC, Souza AS, Katz S, Souza G, Souza G, Farias L, Lemos R, Mello MZ, Neves L, Albuquerque M, Feitosa FE, Paiva J, Lima C, Lima M, Amorim MM. Clinical, epidemiological and laboratory characteristics of cases of Covid-19-related maternal near miss and death at referral units in northeastern Brazil: a cohort study. J Matern Fetal Neonatal Med 2023; 36:2260056. [PMID: 37748920 DOI: 10.1080/14767058.2023.2260056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 09/09/2023] [Indexed: 09/27/2023]
Abstract
Objective: Covid-19 poses a major risk during pregnancy and postpartum, resulting in an increase in maternal mortality worldwide, including in Brazil; however, little research has been conducted into cases of a near miss. This study aimed to describe the frequency of COVID-19-related near miss and deaths during pregnancy or in the postpartum in referral centers in northeastern Brazil, as well as the clinical, epidemiological, and laboratory characteristics of the women who experienced a severe maternal outcome.Methods: A retrospective and prospective cohort study was performed between April 2020 and June 2021 with hospitalized pregnant and postpartum women with a diagnosis of COVID-19 confirmed by real-time polymerase chain reaction (RT-PCR). Data from five tertiary hospitals in northeastern Brazil were evaluated. Descriptive statistical analysis was performed using Epi Info, version 7.2.5.0.Results: A total of 463 patients were included. Of these, 64 (14% of the sample) had a severe maternal outcome, with 42 cases of near miss (9%) and 22 maternal deaths (5%). Patients who had a severe maternal outcome were predominantly young (median age 30 years) and 65.6% were black or brown-skinned. The women had between 6 and 16 years of schooling; 45.3% had a stable partner; 81.3% were pregnant at the time of admission to the study; and 76.6% required a Cesarean section. The great majority (82.8%) had severe acute respiratory syndrome (SARS). Other complications included hypertensive syndromes (40.6%), pneumonia (37.5%), urinary tract infections (29.7%), acute renal failure (25.0%) and postpartum hemorrhage (21.9%). Sepsis developed in 18.8% of cases, neurological dysfunction in 15.6%, and hepatic dysfunction and septic shock in 14.1% of cases each. The relative frequency of admission to an intensive care unit was 87.5%, while 67.2% of the patients required assisted mechanical ventilation, and 54.7% required noninvasive ventilation. Antibiotics were prescribed in 93.8% of cases and corticosteroids in 71.9%, while blood transfusion was required in 25.0% of cases and renal replacement therapy in 15.6%. Therapeutic anticoagulants were administered to 12.5% of the patients. Of the patients who had a severe maternal outcome, the frequency of respiratory dysfunction was 93.8%, with 50.0% developing neurological dysfunction and 37.5% cardiovascular dysfunction. Hematological dysfunction was found in 29.7%, renal dysfunction in 18.8%, and uterine dysfunction in 14.1%. Hepatic dysfunction occurred in 7.8% of the sample. The near-miss ratio for Covid-19 was 1.6/1000 live births and the maternal mortality ratio for Covid-19 was 84.8/100,000 live births, with a mortality index of 34.4% in the sample.Conclusion: This study revealed a low Covid-19-related maternal near miss (MNM) ratio of 1.6/1000 live births and a high Covid-19-related maternal mortality ratio (MMR) of 84.81/100,000 live births. The mortality index was also high. Most of the patients were admitted while pregnant, were young, married and black or brown-skinned, and none had completed university education. The majority had SARS and required admission to an intensive care unit and mechanical ventilation. Most were submitted to a Cesarean section.
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Affiliation(s)
- Anna Catharina M C Cunha
- Instituto de Medicina Integral Professor Fernando Figueira (IMIP), Recife, Brazil
- Stricto Sensu Postgraduate Program, IMIP, Recife, Brazl
| | - Leila Katz
- Instituto de Medicina Integral Professor Fernando Figueira (IMIP), Recife, Brazil
- Stricto Sensu Postgraduate Program, IMIP, Recife, Brazl
| | | | - Isabela Cristina Coutinho
- Instituto de Medicina Integral Professor Fernando Figueira (IMIP), Recife, Brazil
- Stricto Sensu Postgraduate Program, IMIP, Recife, Brazl
| | - Alex Sandro Souza
- Instituto de Medicina Integral Professor Fernando Figueira (IMIP), Recife, Brazil
| | - Sara Katz
- Universidade de Pernambuco, Recife, Brazil
| | | | | | | | - Raissa Lemos
- Universidade Catolica de Pernambuco, Recife, Brazil
| | | | - Lucas Neves
- Universidade Federal de Campina Grande, Campina Grande, Brazil
| | | | | | - Jordana Paiva
- Maternidade Escola Assis Chateaubriand, Fortaleza, Brazil
| | - Carolina Lima
- Maternidade Escola Assis Chateaubriand, Fortaleza, Brazil
| | - Marcelo Lima
- Instituto de Medicina Integral Professor Fernando Figueira (IMIP), Petrolina Brazil
| | - Melania Maria Amorim
- Instituto de Medicina Integral Professor Fernando Figueira (IMIP), Recife, Brazil
- Stricto Sensu Postgraduate Program, IMIP, Recife, Brazl
- Federal University of Campina Grande (UFCG), Campina Grande, Brazil
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Santos AS, Almeida EM, Aecyo P, Costa L, Wanderley A, Batalha-Filho H, Vaio M, Chase MW, Christenhusz MJM, Felix LP, Souza G. Macroevolutionary trends of the Neotropical genus Ameroglossum (Linderniaceae) in rocky outcrop environments. Mol Phylogenet Evol 2023; 189:107929. [PMID: 37726037 DOI: 10.1016/j.ympev.2023.107929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 09/04/2023] [Accepted: 09/14/2023] [Indexed: 09/21/2023]
Abstract
Ameroglossum is a rare plant genus endemic to northeastern of Brazil, initially monospecific (A. pernambucense) and recently expanded by the description of eight new species and two related genera. The genus was initially placed in the family Scrophulariaceae, but this has never been phylogenetically tested. This group is ecologically restricted to rocky inselberg habitats that function as island-like systems (ILS) with spatial fragmentation, limited area, environmental heterogeneity, temporal isolation and low connectivity. Here we use a phylogenetic perspective to test the hypothesis that Ameroglossum diversification was related to island-like radiation in inselbergs. Our results support that Ameroglossum is monophyletic only with the inclusion of Catimbaua and Isabelcristinia (named here as Ameroglossum sensu lato) and this group was well-supported in the family Linderniaceae. Biogeographic analyses suggest that the ancestral of Ameroglossum and related genus arrived in South America c.a. 15 million years ago by long-distance dispersal, given the ancestral distribution of Linderniaceae in Africa. In rocky outcrop habitats, Ameroglossum s.l. developed floral morphological specialization associated with pollinating hummingbirds, compatible with an island-like model. However, no increase in speciation rate was detected, which may be related to high extinction rates and/or slow diversification rate in this ecologically restrictive environment. Altogether, in Ameroglossum key innovations involving flowers seem to have offered opportunities for evolution of greater phenotypic diversity and occupation of new niches in rocky outcrop environments.
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Affiliation(s)
- Amanda S Santos
- Laboratory of Plant Cytogenetics and Evolution, Postgraduate Program Plant Biology, Department of Botany, Federal University of Pernambuco, Recife, Brazil
| | - Erton M Almeida
- Laboratory of Plant Cytogenetics and Evolution, Postgraduate Program Plant Biology, Department of Botany, Federal University of Pernambuco, Recife, Brazil
| | - Paulo Aecyo
- Laboratory of Plant Cytogenetics and Evolution, Postgraduate Program Plant Biology, Department of Botany, Federal University of Pernambuco, Recife, Brazil; Laboratory of Evolutionary Ecology and Genomic of Plants, Postgraduate Program in Plant Biology, Department of Plant Biology, Biology Institute, University of Campinas, São Paulo, Brazil
| | - Lucas Costa
- Laboratory of Plant Cytogenetics and Evolution, Postgraduate Program Plant Biology, Department of Botany, Federal University of Pernambuco, Recife, Brazil
| | - Artur Wanderley
- Laboratory of Plant Cytogenetics and Evolution, Postgraduate Program Plant Biology, Department of Botany, Federal University of Pernambuco, Recife, Brazil
| | - Henrique Batalha-Filho
- Laboratory of Evolution and Biogeography, Institute of Biology, Federal University of Bahia, Salvador, Brazil
| | - Magdalena Vaio
- Laboratory of Plant Genome Evolution and Domestication, Department of Plant Biology, Faculty of Agronomy, University of the Republic, Montevideo, Uruguay
| | - Mark W Chase
- Department of Environment and Agriculture, Curtin University, Perth, Western Australia, Australia, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3DS, United Kingdom
| | - Maarten J M Christenhusz
- Department of Environment and Agriculture, Curtin University, Perth, Western Australia, Australia, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3DS, United Kingdom
| | - Leonardo P Felix
- Laboratory of Plant Cytogenetics and Evolution, Postgraduate Program Plant Biology, Department of Botany, Federal University of Pernambuco, Recife, Brazil; Postgraduate Program Agronomy, Department of Biosciences, Federal University of Paraiba, Areia, Brazil
| | - Gustavo Souza
- Laboratory of Plant Cytogenetics and Evolution, Postgraduate Program Plant Biology, Department of Botany, Federal University of Pernambuco, Recife, Brazil.
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Jacobina UP, Pontes AI, Costa L, Souza G. Correction to: Macroevolutionary consequences of karyotypic changes in the neotropical Serrasalmidae fishes (Ostariophysi, Characiformes) diversification. Genetica 2023; 151:323. [PMID: 37698656 DOI: 10.1007/s10709-023-00195-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/13/2023]
Affiliation(s)
- Uedson Pereira Jacobina
- Laboratory of Molecular Integrative Systematics, Federal University of Alagoas, Campus Arapiraca, Arapiraca, 57076-100, Brazil.
| | - Alany Itala Pontes
- Laboratory of Molecular Integrative Systematics, Federal University of Alagoas, Campus Arapiraca, Arapiraca, 57076-100, Brazil
| | - Lucas Costa
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Recife, 50670-420, Brazil
| | - Gustavo Souza
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Recife, 50670-420, Brazil
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Jacobina UP, Pontes AI, Costa L, Souza G. Macroevolutionary consequences of karyotypic changes in the neotropical Serrasalmidae fishes (Ostariophysi, Characiformes) diversification. Genetica 2023; 151:311-321. [PMID: 37566292 DOI: 10.1007/s10709-023-00191-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 07/11/2023] [Indexed: 08/12/2023]
Abstract
In the Neotropical region, one of the most diverse families of freshwater fishes is the monophyletic Serrasalmidae. Karyotypically, the family shows high diversity in chromosome numbers (2n = 54 to 64). However, little is discussed about whether the chromosomal changes are associated with cladogenetic events within this family. In the present study, we evaluated the role of chromosomal changes in the evolutionary diversification of Serrasalmidae. Our phylogenetic sampling included 36 species and revealed three main clades. The ancestral chromosome number reconstruction revealed the basic number 2n = 54 and a high frequency of ascending dysploid events in the most derived lineages. Our biogeographic reconstruction suggests an Amazonian origin of the family at 48-38 Mya, with independent colonization of other basins between 15 and 8 Mya. We did not find specific chromosomal changes or increased diversification rates correlated with the colonization of a new environment. On the other hand, an increase in the diversification rate was detected involving the genus Serrasalmus and Pygocentrus in the Miocene, correlated with the stasis of 2n = 60. Our data demonstrate that chromosomal rearrangements might have played an important evolutionary role in major cladogenetic events in Serrasalmidae, revealing them as a possible evolutionary driver in their diversification.
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Affiliation(s)
- Uedson Pereira Jacobina
- Laboratory of Molecular Integrative Systematics, Federal University of Alagoas, Campus Arapiraca, Arapiraca, 57076-100, Brazil.
| | - Alany Itala Pontes
- Laboratory of Molecular Integrative Systematics, Federal University of Alagoas, Campus Arapiraca, Arapiraca, 57076-100, Brazil
| | - Lucas Costa
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Recife, 50670-420, Brazil
| | - Gustavo Souza
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Recife, 50670-420, Brazil
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Costa L, Marques A, Buddenhagen CE, Pedrosa-Harand A, Souza G. Investigating the diversification of holocentromeric satellite DNA Tyba in Rhynchospora (Cyperaceae). Ann Bot 2023; 131:813-825. [PMID: 36815646 PMCID: PMC10184444 DOI: 10.1093/aob/mcad036] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 02/21/2023] [Indexed: 05/16/2023]
Abstract
BACKGROUND AND AIMS Satellite DNAs (satDNAs) are repetitive sequences composed by tandemly arranged, often highly homogenized units called monomers. Although satDNAs are usually fast evolving, some satDNA families can be conserved across species separated by several millions of years, probably because of their functional roles in the genomes. Tyba was the first centromere-specific satDNA described for a holocentric organism, until now being characterized for only eight species of the genus Rhynchospora Vahl. (Cyperaceae). Here, we characterized Tyba across a broad sampling of the genus, analysing and comparing its evolutionary patterns with other satDNAs. METHODS We characterized the structure and sequence evolution of satDNAs across a robust dadated phylogeny based on Hybrid Target-Capture Sequencing (hyb-seq) of 70 species. We mined the repetitive fraction for Tyba-like satellites to compare its features with other satDNAs and to construct a Tyba-based phylogeny for the genus. KEY RESULTS Our results show that Tyba is present in the majority of examined species of the genus, spanning four of the five major clades and maintaining intrafamily pairwise identity of 70.9% over 31 Myr. In comparison, other satellite families presented higher intrafamily pairwise identity but are phylogenetically restricted. Furthermore, Tyba sequences could be divided into 12 variants grouped into three different clade-specific subfamilies, showing evidence of traditional models of satDNA evolution, such as the concerted evolution and library models. Besides, a Tyba-based phylogeny showed high congruence with the hyb-seq topology. Our results show structural indications of a possible relationship of Tyba with nucleosomes, given its high curvature peaks over conserved regions and overall high bendability values compared with other non-centromeric satellites. CONCLUSIONS Overall, Tyba shows a remarkable sequence conservation and phylogenetic significance across the genus Rhynchospora, which suggests that functional roles might lead to long-term stability and conservation for satDNAs in the genome.
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Affiliation(s)
- Lucas Costa
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Recife-PE, Brazil
| | - André Marques
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | | | - Andrea Pedrosa-Harand
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Recife-PE, Brazil
| | - Gustavo Souza
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Recife-PE, Brazil
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Quiroga MP, Zattara EE, Souza G, Pedrosa-Harand A, Premoli AC. Plastome sequencing of South American Podocarpus species reveals low rearrangement rates despite ancient gondwanan disjunctions. Mol Biol Rep 2023; 50:309-318. [PMID: 36331753 DOI: 10.1007/s11033-022-07969-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 09/22/2022] [Indexed: 11/06/2022]
Abstract
BACKGROUND Historical reconstructions within Podocarpaceae have provided valuable information to disentangle biogeographic scenarios that begun 65 Mya. However, early molecular phylogenies of Podocarpaceae failed to agree on the intergeneric relationships within the family. The aims of this study were to test whether plastome organization is stable within the genus Podocarpus, to estimate the selective regimes affecting plastome protein-coding genes, and to strengthen our understanding of the phylogenetic relationships and biogeographic history. METHODS AND RESULTS We sequenced the plastomes of four South American species from Patagonia, southern Yungas, and Brazilian subtropical forests. We compared their plastomes to those published from Brazil, Africa, New Zealand, and Southeast Asia, along with representatives from other genera within Podocarpaceae as outgroups. The four newly sequenced plastomes ranged in size between 133,791 bp and 133,991 bp. Gene content and order among chloroplasts from South American, African and Asian Podocarpus were conserved and different from the plastome of P. totara, from New Zealand. Most genes showed substitution patterns consistent with a conservative selective regime. Phylogenies inferred from either complete sequences or protein coding regions were mostly congruent with previous studies, but showed earlier branching of P. salignus, P. totara and P. sellowii. CONCLUSIONS Highly similar and conserved plastomes of African, South American and Asian species suggest that P. totara plastome should be revised and compared to other species from Oceanic distribution. Furthermore, given such structural conservation, we suggest plastome sequencing is not useful to test whether genomic order can be climatically or geologically structured.
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Affiliation(s)
- M Paula Quiroga
- INIBIOMA, Universidad Nacional del Comahue, CONICET, 8400, Bariloche, Quintral 1250, Argentina.
| | - Eduardo E Zattara
- INIBIOMA, Universidad Nacional del Comahue, CONICET, 8400, Bariloche, Quintral 1250, Argentina
| | - Gustavo Souza
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, R. Prof. Moraes Rego, s/n, CDU, 50670-420, Recife, PE, Brazil
| | - Andrea Pedrosa-Harand
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, R. Prof. Moraes Rego, s/n, CDU, 50670-420, Recife, PE, Brazil
| | - Andrea C Premoli
- INIBIOMA, Universidad Nacional del Comahue, CONICET, 8400, Bariloche, Quintral 1250, Argentina
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Sader MA, Costa LA, Souza G, Urdampilleta JD, Simon J, Vaio M. South American Plant Chromosome Numbers Databases: The Information We Have and the Information We Lack on the Most Plant-Diverse Continent. Methods Mol Biol 2023; 2703:211-225. [PMID: 37646948 DOI: 10.1007/978-1-0716-3389-2_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
Chromosome numbers have been used in plant taxonomy, and they are still fundamental for taxon delimitation and genome evolution studies. South America is one of the most diverse continents in terms of plant species and there is a considerable number of species not yet analyzed. Accumulated knowledge about plant chromosome numbers has been compiled from online databases, and here we present an overview. The CCDB is one of the largest plant cytological databases and includes data for around 18% of known vascular plants in the world. In this work, we review the information contained in CCDB and in three databases with exclusive information for South America. At present, the three existing databases comprise information on around 1800 plant taxa related to specific regions, countries, or biomes. Efforts are necessary to expand cytological knowledge and to collect all the available information in a plant chromosome database for this continent.
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Affiliation(s)
- Mariela A Sader
- Instituto Multidisciplinario de Biología Vegetal (IMBIV), Universidad de Córdoba - CONICET, Córdoba, Argentina
| | - Lucas A Costa
- Laboratorio de Citogenética Vegetal, Departamento de Botânica, Universidade Federal de Pernambuco, Recife, Brazil
| | - Gustavo Souza
- Laboratorio de Citogenética Vegetal, Departamento de Botânica, Universidade Federal de Pernambuco, Recife, Brazil
| | - Juan D Urdampilleta
- Instituto Multidisciplinario de Biología Vegetal (IMBIV), Universidad de Córdoba - CONICET, Córdoba, Argentina
| | - Joan Simon
- BioC (GReB, IRBio) - Laboratori de Botànica, Facultat de Farmàcia i Ciències de l'Alimentació, Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Magdalena Vaio
- Laboratorio de Evolución y Domesticación de las Plantas, Departamento de Biología Vegetal, Facultad de Agronomía, Universidad de la República, Montevideo, Uruguay.
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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] [What about the content of this article? (0)] [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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Oliveira AV, Lanna EAT, Motta NC, Souza G, Souza GA, Oliveira JM, Freato TA, Santos FM. Extenders and cryosolutions for Grumata (Prochilodus vimboides) sperm preservation. Cryo Letters 2022; 43:246-254. [PMID: 36626128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
BACKGROUND Prochilodus vimboides populations are being reduced in rivers due to changes in their habitat, overfishing, urbanization, and pollution. OBJECTIVE To evaluate the effect of sperm extender solutions for short-term storage and cryosolutions for freezing sperm of Prochilodus vimboides. MATERIALS AND METHODS For short-term storage, the sperm was diluted in 0.9% NaCl, 1.2% NaCl, 5% glucose, 5% BTS, or 6% MIII. Sperm motility was evaluated after 0, 24, 48, and 72 h of short-term storage at 4-6 degree C. For cryopreservation, sperm samples were diluted in the same extenders and factorially combined with three cryoprotectants (dimethylsulfoxide, methyl glycol, and ethylene glycol). After thawing, sperm motility and oxidative stress parameters were evaluated. RESULTS Dilution of samples in BTS preserved sperm motility >40% for up to 48 h. Samples cryopreserved in 5% glucose and methylglycol presented higher sperm motility, lower catalase, and lipid peroxidation activities. CONCLUSION Prochilodus vimboides sperm can be cooled for up to 48 h in an extender solution of 5% BTS and cryopreserved in 5% glucose and methyl glycol. doi.org/10.54680/fr22410110612.
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Affiliation(s)
- A V Oliveira
- Agricultural Research Company of Minas Gerais, EPAMIG, Viçosa, MG, Brazil.
| | - E A T Lanna
- Department of Animal Science, Federal University of Viçosa, Viçosa, MG, Brazil
| | - N C Motta
- Department of Animal Science, Federal University of Lavras, Lavras, MG, Brazil
| | - G Souza
- Non-governmental Organization, Piabanha Project, Itaocara, RJ, Brazil
| | - G A Souza
- Department of Forest Engineering, Federal University of Viçosa, MG, Brazil
| | - J M Oliveira
- Department of Animal Biology, Federal University of Viçosa, MG, Brazil
| | - T A Freato
- Meteorological and Climate Research Center Applied to Agriculture, State University of Campinas, Campinas, SP, Brazil
| | - F M Santos
- Department of Animal Biology, Federal University of Viçosa, MG, Brazil
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Vieira LA, Tabarelli M, Souza G, Queiroz RT, Santos BA. Divergent herb communities in drier and chronically disturbed areas of the Brazilian Caatinga. Perspect Ecol Conserv 2022. [DOI: 10.1016/j.pecon.2021.12.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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Costa L, Marques A, Buddenhagen C, Thomas WW, Huettel B, Schubert V, Dodsworth S, Houben A, Souza G, Pedrosa-Harand A. Aiming off the target: recycling target capture sequencing reads for investigating repetitive DNA. Ann Bot 2021; 128:835-848. [PMID: 34050647 PMCID: PMC8577205 DOI: 10.1093/aob/mcab063] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 05/26/2021] [Indexed: 05/28/2023]
Abstract
BACKGROUND AND AIMS With the advance of high-throughput sequencing, reduced-representation methods such as target capture sequencing (TCS) emerged as cost-efficient ways of gathering genomic information, particularly from coding regions. As the off-target reads from such sequencing are expected to be similar to genome skimming (GS), we assessed the quality of repeat characterization in plant genomes using these data. METHODS Repeat composition obtained from TCS datasets of five Rhynchospora (Cyperaceae) species were compared with GS data from the same taxa. In addition, a FISH probe was designed based on the most abundant satellite found in the TCS dataset of Rhynchospora cephalotes. Finally, repeat-based phylogenies of the five Rhynchospora species were constructed based on the GS and TCS datasets and the topologies were compared with a gene-alignment-based phylogenetic tree. KEY RESULTS All the major repetitive DNA families were identified in TCS, including repeats that showed abundances as low as 0.01 % in the GS data. Rank correlations between GS and TCS repeat abundances were moderately high (r = 0.58-0.85), increasing after filtering out the targeted loci from the raw TCS reads (r = 0.66-0.92). Repeat data obtained by TCS were also reliable in developing a cytogenetic probe of a new variant of the holocentromeric satellite Tyba. Repeat-based phylogenies from TCS data were congruent with those obtained from GS data and the gene-alignment tree. CONCLUSIONS Our results show that off-target TCS reads can be recycled to identify repeats for cyto- and phylogenomic investigations. Given the growing availability of TCS reads, driven by global phylogenomic projects, our strategy represents a way to recycle genomic data and contribute to a better characterization of plant biodiversity.
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Affiliation(s)
- Lucas Costa
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Recife-PE, Brazil
| | - André Marques
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | | | | | - Bruno Huettel
- Max Planck Genome Centre Cologne, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Veit Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | | | - Andreas Houben
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Gustavo Souza
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Recife-PE, Brazil
| | - Andrea Pedrosa-Harand
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Recife-PE, Brazil
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Oliveira MAS, Nunes T, Dos Santos MA, Ferreira Gomes D, Costa I, Van-Lume B, Marques Da Silva SS, Oliveira RS, Simon MF, Lima GSA, Gissi DS, Almeida CCDS, Souza G, Marques A. High-Throughput Genomic Data Reveal Complex Phylogenetic Relationships in Stylosanthes Sw (Leguminosae). Front Genet 2021; 12:727314. [PMID: 34630521 PMCID: PMC8495327 DOI: 10.3389/fgene.2021.727314] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 09/08/2021] [Indexed: 11/22/2022] Open
Abstract
Allopolyploidy is widely present across plant lineages. Though estimating the correct phylogenetic relationships and origin of allopolyploids may sometimes become a hard task. In the genus Stylosanthes Sw. (Leguminosae), an important legume crop, allopolyploidy is a key speciation force. This makes difficult adequate species recognition and breeding efforts on the genus. Based on comparative analysis of nine high-throughput sequencing (HTS) samples, including three allopolyploids (S. capitata Vogel cv. “Campo Grande,” S. capitata “RS024” and S. scabra Vogel) and six diploids (S. hamata Taub, S. viscosa (L.) Sw., S. macrocephala M. B. Ferreira and Sousa Costa, S. guianensis (Aubl.) Sw., S. pilosa M. B. Ferreira and Sousa Costa and S. seabrana B. L. Maass & 't Mannetje) we provide a working pipeline to identify organelle and nuclear genome signatures that allowed us to trace the origin and parental genome recognition of allopolyploids. First, organelle genomes were de novo assembled and used to identify maternal genome donors by alignment-based phylogenies and synteny analysis. Second, nuclear-derived reads were subjected to repetitive DNA identification with RepeatExplorer2. Identified repeats were compared based on abundance and presence on diploids in relation to allopolyploids by comparative repeat analysis. Third, reads were extracted and grouped based on the following groups: chloroplast, mitochondrial, satellite DNA, ribosomal DNA, repeat clustered- and total genomic reads. These sets of reads were then subjected to alignment and assembly free phylogenetic analyses and were compared to classical alignment-based phylogenetic methods. Comparative analysis of shared and unique satellite repeats also allowed the tracing of allopolyploid origin in Stylosanthes, especially those with high abundance such as the StyloSat1 in the Scabra complex. This satellite was in situ mapped in the proximal region of the chromosomes and made it possible to identify its previously proposed parents. Hence, with simple genome skimming data we were able to provide evidence for the recognition of parental genomes and understand genome evolution of two Stylosanthes allopolyploids.
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Affiliation(s)
| | - Tomáz Nunes
- Laboratory of Genetic Resources, Federal University of Alagoas, Arapiraca, Brazil
| | | | | | - Iara Costa
- Laboratory of Genetic Resources, Federal University of Alagoas, Arapiraca, Brazil
| | - Brena Van-Lume
- Laboratory of Plant Cytogenetics and Evolution, Federal University of Pernambuco, Recife, Brazil
| | | | - Ronaldo Simão Oliveira
- Campus Xique Xique, Federal Institute of Education, Science and Technology of Bahia, Xique-Xique, Brazil
| | | | - Gaus S A Lima
- Center of Agronomic Sciences, Federal University of Alagoas, Rio Largo, Brazil
| | - Danilo Soares Gissi
- Department of Biostatistics, Institute of Biosciences-IBB, Plant Biology, Parasitology and Zoology, São Paulo State University-UNESP, Botucatu, Brazil
| | | | - Gustavo Souza
- Laboratory of Plant Cytogenetics and Evolution, Federal University of Pernambuco, Recife, Brazil
| | - André Marques
- Laboratory of Genetic Resources, Federal University of Alagoas, Arapiraca, Brazil.,Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
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Aecyo P, Marques A, Huettel B, Silva A, Esposito T, Ribeiro E, Leal IR, Gagnon E, Souza G, Pedrosa-Harand A. Plastome evolution in the Caesalpinia group (Leguminosae) and its application in phylogenomics and populations genetics. Planta 2021; 254:27. [PMID: 34236509 DOI: 10.1007/s00425-021-03655-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 06/03/2021] [Indexed: 06/13/2023]
Abstract
The chloroplast genomes of Caesalpinia group species are structurally conserved, but sequence level variation is useful for both phylogenomic and population genetic analyses. Variation in chloroplast genomes (plastomes) has been an important source of information in plant biology. The Caesalpinia group has been used as a model in studies correlating ecological and genomic variables, yet its intergeneric and infrageneric relationships are not fully solved, despite densely sampled phylogenies including nuclear and plastid loci by Sanger sequencing. Here, we present the de novo assembly and characterization of plastomes from 13 species from the Caesalpinia group belonging to eight genera. A comparative analysis was carried out with 13 other plastomes previously available, totalizing 26 plastomes and representing 15 of the 26 known Caesalpinia group genera. All plastomes showed a conserved quadripartite structure and gene repertoire, except for the loss of four ndh genes in Erythrostemon gilliesii. Thirty polymorphic regions were identified for inter- or intrageneric analyses. The 26 aligned plastomes were used for phylogenetic reconstruction, revealing a well-resolved topology, and dividing the Caesalpinia group into two fully supported clades. Sixteen microsatellite (cpSSR) loci were selected from Cenostigma microphyllum for primer development and at least two were cross-amplified in different Leguminosae subfamilies by in vitro or in silico approaches. Four loci were used to assess the genetic diversity of C. microphyllum in the Brazilian Caatinga. Our results demonstrate the structural conservation of plastomes in the Caesalpinia group, offering insights into its systematics and evolution, and provides new genomic tools for future phylogenetic, population genetics, and phylogeographic studies.
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Affiliation(s)
- Paulo Aecyo
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Recife, Brazil
| | - André Marques
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Bruno Huettel
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Ana Silva
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Recife, Brazil
| | - Tiago Esposito
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Recife, Brazil
| | - Elâine Ribeiro
- Laboratory of Plant-Animal Interaction, Department of Botany, Federal University of Pernambuco, Recife, Brazil
- Laboratory of Biodiversity and Evolutionary Genetics, University of Pernambuco - Campus Petrolina, Petrolina, Brazil
| | - Inara R Leal
- Laboratory of Plant-Animal Interaction, Department of Botany, Federal University of Pernambuco, Recife, Brazil
| | - Edeline Gagnon
- Royal Botanic Garden of Edinburgh, University of Edinburgh, Edinburgh, UK
| | - Gustavo Souza
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Recife, Brazil
| | - Andrea Pedrosa-Harand
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Recife, Brazil.
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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: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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20
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Costa L, Jimenez H, Carvalho R, Carvalho-Sobrinho J, Escobar I, Souza G. Divide to Conquer: Evolutionary History of Allioideae Tribes (Amaryllidaceae) Is Linked to Distinct Trends of Karyotype Evolution. Front Plant Sci 2020; 11:320. [PMID: 32318079 PMCID: PMC7155398 DOI: 10.3389/fpls.2020.00320] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 03/04/2020] [Indexed: 06/11/2023]
Abstract
Allioideae (e.g., chives, garlics, onions) comprises three mainly temperate tribes: Allieae (800 species from the northern hemisphere), Gilliesieae (80 South American species), and Tulbaghieae (26 Southern African species). We reconstructed the phylogeny of Allioideae (190 species plus 257 species from Agapanthoideae and Amaryllidoideae) based on ITS, matK, ndhF, and rbcL to investigate its historical biogeography and karyotype evolution using newly generated cytomolecular data for Chilean Gilliesieae genera Gethyum, Miersia, Solaria, and Speea. The crown group of Allioideae diversified ∼62 Mya supporting a Gondwanic origin for the subfamily and vicariance as the cause of the intercontinental disjunction of the tribes. Our results support the hypothesis of the Indian tectonic plate carrying Allieae to northern hemisphere ('out-of-India' hypothesis). The colonization of the northern hemisphere (∼30 Mya) is correlated with a higher diversification rate in Allium associated to stable x = 8, increase of polyploidy and the geographic expansion in Europe and North America. Tulbaghieae presented x = 6, but with numerical stability (2n = 12). In contrast, the tribe Gilliesieae (x = 6) varied considerably in genome size (associated with Robertsonian translocations), rDNA sites distribution and chromosome number. Our data indicate that evolutionary history of Allioideae tribes is linked to distinct trends of karyotype evolution.
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Affiliation(s)
- Lucas Costa
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Recife, Brazil
| | - Horace Jimenez
- Laboratory of Plant Cytogenetics, Department of Biology, Federal Rural University of Pernambuco, Recife, Brazil
| | - Reginaldo Carvalho
- Laboratory of Plant Cytogenetics, Department of Biology, Federal Rural University of Pernambuco, Recife, Brazil
| | - Jefferson Carvalho-Sobrinho
- Laboratory of Plant Cytogenetics, Department of Biology, Federal Rural University of Pernambuco, Recife, Brazil
| | - Inelia Escobar
- Department of Botany, University of Concepción, Concepción, Chile
| | - Gustavo Souza
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Recife, Brazil
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Báez M, Souza G, Guerra M. Does the chromosomal position of 35S rDNA sites influence their transcription? A survey on Nothoscordum species (Amaryllidaceae). Genet Mol Biol 2020; 43:e20180194. [PMID: 31469154 PMCID: PMC7197985 DOI: 10.1590/1678-4685-gmb-2018-0194] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 03/21/2019] [Indexed: 11/22/2022] Open
Abstract
35S ribosomal DNA (rDNA) sites are the regions where the ribosomal genes 18S, 5.8S and 25S, responsible for the formation of the nucleoli, are found. The fact that rDNA sites have non-random distribution on chromosomes suggests that their positions may influence their transcription. To identify if the preferentially transcribed rDNA sites occupy specific position, six species (nine cytotypes) of the genus Nothoscordum were analyzed using two different techniques to impregnate the nucleolar organizer regions (NORs) with silver nitrate. Both techniques strongly stained NORs, but one of them also stained the proximal region of all chromosomes, suggesting the existence of another group of argentophilic proteins in this region. In species with rDNA sites in acrocentric and metacentric chromosomes, sites located on the short arms of the acrocentric chromosomes were preferentially activated. On the other hand, in species with rDNA sites restricted to the short arms of the acrocentrics, all of them were activated, whereas in those species with sites restricted to the terminal region of metacentric chromosomes, the frequency of active sites was always lower than expected. This indicate that, at least in Nothoscordum, the transcription of an rDNA site is influenced by its chromosomal position, and may explain, at least partially, the strongly non-random distribution of these sites in plant and animal chromosomes.
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Affiliation(s)
- Mariana Báez
- Universidade Federal de Pernambuco, Departamento de Botânica, Laboratório de Citogenética e Evolução de Plantas, Recife, PE, Brazil
| | - Gustavo Souza
- Universidade Federal de Pernambuco, Departamento de Botânica, Laboratório de Citogenética e Evolução de Plantas, Recife, PE, Brazil
| | - Marcelo Guerra
- Universidade Federal de Pernambuco, Departamento de Botânica, Laboratório de Citogenética e Evolução de Plantas, Recife, PE, Brazil
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Pavoski G, Kalikoski R, Souza G, Baldisserotto D, Brum LF, dos Santos C, Bergmann C, Brandelli A, Jacobi M, Galland G. Antimicrobial High-Density Polyethylene (HDPE)/ZnO Nanocomposites Obtained by in situ Polymerization. J BRAZIL CHEM SOC 2020. [DOI: 10.21577/0103-5053.20200042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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Antunes A, Targueta C, Castro A, Souza G, Soares T, Telles M. Research Article Genome size and chromosome number of <i>Dipteryx</i> <i>alata</i> (Leguminosae): a model candidate for comparative genomics in Papilionoideae. Genet Mol Res 2020. [DOI: 10.4238/gmr18640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Van-Lume B, Mata-Sucre Y, Báez M, Ribeiro T, Huettel B, Gagnon E, Leitch IJ, Pedrosa-Harand A, Lewis GP, Souza G. Evolutionary convergence or homology? Comparative cytogenomics of Caesalpinia group species (Leguminosae) reveals diversification in the pericentromeric heterochromatic composition. Planta 2019; 250:2173-2186. [PMID: 31696317 DOI: 10.1007/s00425-019-03287-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 09/25/2019] [Indexed: 05/02/2023]
Abstract
We demonstrated by cytogenomic analysis that the proximal heterochromatin of the Northeast Brazilian species of Caesalpinia group is enriched with phylogenetically conserved Ty3/Gypsy-Tekay RT, but diverge in the presence of Ty3/Gypsy-Athila RT and satDNA. The Caesalpinia Group includes 225 species and 27 monophyletic genera of which four occur in Northeastern Brazil: Erythrostemon (1 sp.), Cenostigma (7 spp.), Libidibia (1 sp.), and Paubrasilia (1 sp.). The last three genera are placed in different clades in the Caesalpinia Group phylogeny, and yet they are characterized by having a numerically stable karyotype 2n = 24 (16 M+8A) and GC-rich heterochromatic bands (chromomycin A3 positive/CMA+ bands) in the proximal chromosome regions. To characterize the composition of their heterochromatin and test for the homology of these chromosomal regions, genomic DNA was extracted from Cenostigma microphyllum, Libidibia ferrea, and Paubrasilia echinata, and sequenced at low coverage using the Illumina platform. The genomic repetitive fractions were characterized using a Galaxy/RepeatExplorer-Elixir platform. The most abundant elements of each genome were chromosomally located by fluorescent in situ hybridization (FISH) and compared to the CMA+ heterochromatin distribution. The repetitive fraction of the genomes of C. microphyllum, L. ferrea, and P. echinata were estimated to be 41.70%, 38.44%, and 72.51%, respectively. Ty3/Gypsy retrotransposons (RT), specifically the Tekay lineage, were the most abundant repeats in each of the three genomes. FISH mapping revealed species-specific patterns for the Tekay elements in the proximal regions of the chromosomes, co-localized with CMA+ bands. Other species-specific patterns were observed, e.g., for the Ty3/Gypsy RT Athila elements which were found in all the proximal heterochromatin of L. ferrea or restricted to the acrocentric chromosomes of C. microphyllum. This Athila labeling co-localized with satellite DNAs (satDNAs). Although the Caesalpinia Group diverged around 55 Mya, our results suggest an ancestral colonization of Tekay RT in the proximal heterochromatin. Thus, the present-day composition of the pericentromeric heterochromatin in these Northeast Brazilian species is a combination of the maintenance of an ancestral Tekay distribution with a species-specific accumulation of other repeats.
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Affiliation(s)
- Brena Van-Lume
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Rua Nelson Chaves S/N, Cidade Universitária, Recife, PE, 50670-420, Brazil
| | - Yennifer Mata-Sucre
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Rua Nelson Chaves S/N, Cidade Universitária, Recife, PE, 50670-420, Brazil
| | - Mariana Báez
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Rua Nelson Chaves S/N, Cidade Universitária, Recife, PE, 50670-420, Brazil
| | - Tiago Ribeiro
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Rua Nelson Chaves S/N, Cidade Universitária, Recife, PE, 50670-420, Brazil
- Department of Botany and Ecology, Institute of Biosciences, Federal University of Mato Grosso, Av. Fernando Correa da Costa, 2.367, Boa Esperança, Cuiabá, MT, 78060-900, Brazil
| | | | - Edeline Gagnon
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh, EH3 5NZ, UK
| | - Ilia J Leitch
- Department of Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB, UK
| | - Andrea Pedrosa-Harand
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Rua Nelson Chaves S/N, Cidade Universitária, Recife, PE, 50670-420, Brazil
| | - Gwilym P Lewis
- Department of Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB, UK
| | - Gustavo Souza
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Rua Nelson Chaves S/N, Cidade Universitária, Recife, PE, 50670-420, Brazil.
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Amorim BS, Vasconcelos TN, Souza G, Alves M, Antonelli A, Lucas E. Advanced understanding of phylogenetic relationships, morphological evolution and biogeographic history of the mega-diverse plant genus Myrcia and its relatives (Myrtaceae: Myrteae). Mol Phylogenet Evol 2019; 138:65-88. [DOI: 10.1016/j.ympev.2019.05.014] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2018] [Revised: 02/18/2019] [Accepted: 05/17/2019] [Indexed: 01/10/2023]
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Marinho MAO, Souza G, Felix LP, De Carvalho R. Comparative cytogenetics of the ACPT clade (Anacampserotaceae, Cactaceae, Portulacaceae, and Talinaceae): a very diverse group of the suborder Cactineae, Caryophyllales. Protoplasma 2019; 256:805-814. [PMID: 30604246 DOI: 10.1007/s00709-018-01334-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2018] [Accepted: 11/26/2018] [Indexed: 06/09/2023]
Abstract
The clade ACPT (Anacampserotaceae, Cactaceae, Portulacaceae, and Talinaceae) is the most diverse lineage of the subordem Cactineae. The relationships between these families are still uncertain, with different topologies suggested by phylogenetic analyses with several combinations of markers. Different basic numbers (x) have been suggested for each family and for the subord, often in a contestable way. Comparative cytogenetic has helped to understand the evolutionary relationships of phylogenetically poorly resolved groups, as well as their mechanisms of karyotype evolution. The karyotype evolution in representatives of Cactineae was analyzed, focusing on the ACPT clade, through the analysis of chromosome number in a phylogenetic bias. The phylogeny obtained showed a well-resolved topology with support for the monophyly of the five families. Although a chromosomal number is known for less than 30% of the Cactineae species, the analyses revealed a high karyotype variability, from 2n = 8 to 2n = 110. The analysis of character reconstruction of the ancestral haploid numbers (p) suggested p = 12 for Cactineae, with distinct basic numbers for the clade family ACPT: Cactaceae and Montiaceae (p = 11), Talinaceae (p = 12), and Anacampserotaceae and Portulacaceae (p = 9). Talinaceae, Anacampserotaceae, and Cactaceae were stable, while Portulaca and Montiaceae were karyotypically variable. The chromosome evolution of this group was mainly due to events of descending disploidy and poliploidy. Our data confirm that the low phylogenetic resolution among the families of the ACPT clade is due to a divergence of this clade in a short period of time. However, each of these families can be characterized by basic chromosome numbers and unique karyotype evolution events.
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Affiliation(s)
- Maria Angélica Oliveira Marinho
- Graduate Program in Botany, Department of Biology, Universidade Federal Rural de Pernambuco, Rua Dom Manoel de Medeiros, s/n, Dois Irmãos, Recife, Pernambuco, 52171-900, Brazil.
| | - Gustavo Souza
- Laboratory of Cytogenetics and Evolution of Plants, Department of Botany, Universidade Federal de Pernambuco, Av. Professor Moraes Rego s/n, Cidade Universitária, Recife, PE, 50670-901, Brazil
| | - Leonardo P Felix
- Center of Agrarian Sciences, Universidade Federal da Paraíba, Campus II, Areia, Paraíba, 58397-000, Brazil
| | - Reginaldo De Carvalho
- Graduate Program in Botany, Department of Biology, Universidade Federal Rural de Pernambuco, Rua Dom Manoel de Medeiros, s/n, Dois Irmãos, Recife, Pernambuco, 52171-900, Brazil
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Pavoski G, Kalikoski R, Souza G, Brum LFW, Santos CD, Markeb AA, Santos JHZD, Font X, dell'Erba I, Galland GB. Corrigendum to: "Synthesis of polyethylene/silica-silver nanocomposites with antibacterial properties by in situ polymerization" [European Polymer Journal 106 (2018) 92–101]. Eur Polym J 2019. [DOI: 10.1016/j.eurpolymj.2019.01.055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Sader MA, Amorim BS, Costa L, Souza G, Pedrosa-Harand A. The role of chromosome changes in the diversification of Passiflora L. (Passifloraceae). SYST BIODIVERS 2019. [DOI: 10.1080/14772000.2018.1546777] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Mariela A. Sader
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Recife, PE, 50670-901, Brazil
| | - Bruno S. Amorim
- Museu da Amazônia, MUSA, Manaus, Amazonas, 69099-415, Brazil
- Pós-Graduação em Biotecnologia e Recursos Naturais, Universidade do Estado do Amazonas, Manaus, Amazonas, 69058-807, Brazil
| | - Lucas Costa
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Recife, PE, 50670-901, Brazil
| | - Gustavo Souza
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Recife, PE, 50670-901, Brazil
| | - Andrea Pedrosa-Harand
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Recife, PE, 50670-901, 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. Ann Bot 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] [What about the content of this article? (0)] [Affiliation(s)] [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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Jacobina UP, Lima SMQ, Maia DG, Souza G, Batalha-Filho H, Torres RA. DNA barcode sheds light on systematics and evolution of neotropical freshwater trahiras. Genetica 2018; 146:505-515. [DOI: 10.1007/s10709-018-0043-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2018] [Accepted: 10/09/2018] [Indexed: 02/04/2023]
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Pavoski G, Kalikoski R, Souza G, Brum LFW, dos Santos C, Abo Markeb A, dos Santos JHZ, Font X, dell'Erba I, Galland GB. Synthesis of polyethylene/silica-silver nanocomposites with antibacterial properties by in situ polymerization. Eur Polym J 2018. [DOI: 10.1016/j.eurpolymj.2018.07.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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Costa L, Crosa O, Souza G. Evidencing genome downsizing as a result of multiple robertsonian translocations in the subfamily allioideae (Amararyllidaceae). Semin Cienc Biol Saude 2018. [DOI: 10.5433/1679-0367.2017v38n1suplp168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Large genomes and a history of chromosome rearrangements have made the subfamily Allioideae an interesting model to understand chromosome evolution. The majority of its genera show high karyotype diversity mainly due to polyploidy and Robertsonian translocations (RT) events. The three lineages of Allioideae present different levels of RT, evidenced by metacentric-rich karyotypes observed in Allieae and Tulbaghieae, and a variable proportion between metacentric/acrocentrics in Gilliesieae. Extreme condition of centric fissions occurs in the genera Ipheion, Zoellnerallium and Miersia, whose results in karyotypes formed almost exclusively by acrocentric chromosomes. In this work we investigate how RT drives genome size and chromosome number variation in species of Allioideae. For this, we estimated the genome size by flow cytometry and compiled chromosome number data for 37 species of Allioideae. We employed comparative phylogenetic methods in a Bayesian tree based on ITS1-5.8S-ITS2 sequences. Genome size ranged from 1C = 9.03 picograms (pg) in Ipheon uniflorum to 1C = 54.97 pg in Leucocoryne ixioides. Our analyses revealed that metacentric-rich karyotype is the plesiomorphic state in the subfamily Allioideae and RT as a driving force in genome size variation. This is demonstrated in the relationships Leucocoryne (2n = 14M+4A) /Zoellnerallium (2n = 8M+16A) and Tristagma (2n = 6M+2A)/Ipheion (2n = 14A) with a strong reduction of DNA content (49.5% and 61.47%, respectively) associated to multiple fissions. These changes in Zoellnerallium and Ipheon genomes occurred independently around 12 myr. This relationship was not observed in the Chilean species Speea humilis (2n = 8M+2SM+2A)/ Miersia chilensis (2n = 2SM+18A) with recent differentiation (5 mya), suggesting that multiple centric fusions may require additional evolutionary time to decrease genome size. Our phylogenetic independent contrast analysis of genome size and chromosome number revealed that these traits have a negative correlation (r²=0.18 and p=0.01). This corroborates a tendency of decrease in genome size after events that increase chromosome number such as fissions. Possibly, changes in chromosome linkage may increase meiotic recombination frequency, which might lead to higher probability of unequal crossing over. This mechanism could associate the loss of repetitive sequences to centric fission, explaining downsizing in Allioideae acrocentric-rich genomes.
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Costa I, Aparecida M, Moraes L, Melo NFD, Almeida C, Souza G, Marques A. Análise citogenômica confirma a origem alotetraploide de Stylosanthes scabra a partir de S. viscosa x S. hamata. Semin Cienc Biol Saude 2018. [DOI: 10.5433/1679-0367.2017v38n1suplp80] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
O gênero Stylosanthes (Fabaceae) possui grande importância agronômica por seu uso forrageiro e sua associação com bactérias nitrificantes, que o torna ideal para adubação verde e recuperação de solos degradados. O gênero tem o Brasil como principal centro de diversidade, sendo citogeneticamente conhecido por apresentar cariótipos estáveis com 2n = 20 e ocorrência de alotetraploides naturais, dentre esses S. scabra. Este trabalho teve como objetivo confirmar a origem desse alotetraploide a partir de S. hamata × S. viscosa. Para isso foi realizado o sequenciamento do DNA genômico total de S. scabra, S. viscosa e S. hamata utilizando a plataforma Illumina HiSeq 2000 com reads pareados. A caracterização da fração repetitiva dos genomas das três espécies foi feita individualmente e comparativamente no programa RepeatExplorer, no qual foi identificado a proporção das famílias de sequências repetitivas para cada espécie. Também foi feito a montagem do genoma plastidial (plastoma) das três espécies utilizando os programas NOVOPlasty v. 2.5.6 e Geneious v.9.1.8. A análise dos clusters obtidos no RepeatExplorer revelou vários grupos de DNA repetitivo presentes em S. scabra que eram específicos do genoma de S. hamata ou de S. viscosa, sendo esses principalmente pertencentes a famílias de DNA satélite. Uma análise dos contigs do DNA ribossomal (DNAr) mostrou alta similaridade de ambos DNAr 5S e 45S entre S. scabra e S. viscosa. A análise dos plastomas revelou uma alta similaridade (99,8%) entre o plastoma de S. scabra e S. hamata indicando que S. hamata seja seu possível parental materno. Análises de GISH corroboram essa relação de parentesco, mostrando que metade do complemento cromossômico de S. scabra é marcada com cada um do parentais S. hamata e S. viscosa. A análise comparativa dos sítios de DNAr 5S e 45S por hibridização in situ fluorescente (FISH) revela que S. scabra não possui o somatório dos sítios observados nos seus parentais, sugerindo algum grau de diploidização. A FISH das famílias de DNA satélite específicas e retroelementos de S. hamata e S. viscosa nos cromossomos do híbrido S. scabra poderá contribuir para o entendimento dos mecanismos de evolução e estabilização genômica desse alotetraploide.
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Ribeiro T, Buddenhagen CE, Thomas WW, Souza G, Pedrosa-Harand A. Are holocentrics doomed to change? Limited chromosome number variation in Rhynchospora Vahl (Cyperaceae). Protoplasma 2018; 255:263-272. [PMID: 28844108 DOI: 10.1007/s00709-017-1154-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 08/14/2017] [Indexed: 05/23/2023]
Abstract
Karyotype evolution in species with non-localised centromeres (holocentric chromosomes) is usually very dynamic and associated with recurrent fission and fusion (also termed agmatoploidy/symploidy) events. In Rhynchospora (Cyperaceae), one of the most species-rich sedge genera, all analysed species have holocentric chromosomes and their numbers range from 2n = 4 to 2n = 84. Agmatoploidy/symploidy and polyploidy were suggested as the main processes in the reshuffling of Rhynchospora karyotypes, although testing different scenarios of chromosome number evolution in a phylogenetic framework has not been attempted until now. Here, we used maximum likelihood and model-based analyses, in combination with genome size estimation and ribosomal DNA distribution, to understand chromosome evolution in Rhynchospora. Overall, chromosome number variation showed a significant phylogenetic signal and the majority of the lineages maintained a karyotype of 2n = 10 (~48% of the species), the most likely candidate for the ancestral number of the genus. Higher and lower chromosome numbers were restricted to specific clades, whilst polyploidy and/or fusion/fission events were present in specific branches. Variation in genome size and ribosomal DNA site number showed no correlation with ploidy level or chromosome number. Although different mechanisms of karyotype evolution (polyploidy, fusion and fission) seem to be acting in distinct lineages, the degree of chromosome variation and the main mechanisms involved are comparable to those found in some monocentric genera and lower than expected for a holocentric genus.
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Affiliation(s)
- Tiago Ribeiro
- Departamento de Botânica, Centro de Biociências, Laboratório de Citogenética e Evolução Vegetal, Universidade Federal de Pernambuco, Av. Prof. Moraes Rego, s/n, Cidade Universitária, Recife, PE, 50670-901, Brazil
| | | | | | - Gustavo Souza
- Departamento de Botânica, Centro de Biociências, Laboratório de Citogenética e Evolução Vegetal, Universidade Federal de Pernambuco, Av. Prof. Moraes Rego, s/n, Cidade Universitária, Recife, PE, 50670-901, Brazil
| | - Andrea Pedrosa-Harand
- Departamento de Botânica, Centro de Biociências, Laboratório de Citogenética e Evolução Vegetal, Universidade Federal de Pernambuco, Av. Prof. Moraes Rego, s/n, Cidade Universitária, Recife, PE, 50670-901, Brazil.
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Cordeiro JMP, Kaehler M, Souza G, Felix LP. Karyotype analysis in Bignonieae (Bignoniaceae): chromosome numbers and heterochromatin. AN ACAD BRAS CIENC 2017; 89:2697-2706. [PMID: 29236867 DOI: 10.1590/0001-3765201720170363] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 07/31/2017] [Indexed: 11/21/2022] Open
Abstract
Chromosome numbers and heterochromatin banding pattern variability have been shown to be useful for taxonomic and evolutionary studies of different plant taxa. Bignonieae is the largest tribe of Bignoniaceae, composed mostly by woody climber species whose taxonomies are quite complicated. We reviewed and added new data concerning chromosome numbers in Bignonieae and performed the first analyses of heterochromatin banding patterns in that tribe based on the fluorochromes chromomycin A3 (CMA) and 4'-6-diamidino-2-phenylindole (DAPI). We confirmed the predominant diploid number 2n = 40, as well as variations reported in the literature (dysploidy in Mansoa [2n = 38] and polyploidy in Dolichandra ungis-cati [2n = 80] and Pyrostegia venusta [2n = 80]). We also found a new cytotype for the genus Anemopaegma (Anemopaegma citrinum, 2n = 60) and provide the first chromosome counts for five species (Adenocalymma divaricatum, Amphilophium scabriusculum, Fridericia limae, F. subverticillata, and Xylophragma myrianthum). Heterochromatin analyses revealed only GC-rich regions, with six different arrangements of those bands. The A-type (one large and distal telomeric band) were the most common, although the presence and combinations of the other types appear to be the most promising for taxonomic studies.
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Affiliation(s)
- Joel M P Cordeiro
- Centro de Ciências Agrárias, Departamento de Ciências Biológicas, Universidade Federal da Paraíba, Campus II, Rodovia PB 079, Km 12, 58397-000 Areia, PB, Brazil
| | - Miriam Kaehler
- Mülleriana, Sociedade Fritz Müller de Ciências Naturais, Rua Humberto Morona, 26, 80050-402 Curitiba, PR, Brazil
| | - Gustavo Souza
- Centro de Ciências Biológicas, Departamento de Botânica, Universidade Federal de Pernambuco, Campus I, Av. Prof. Moraes Rego, 1235, 50670-901 Recife, PE, Brazil
| | - Leonardo P Felix
- Centro de Ciências Agrárias, Departamento de Ciências Biológicas, Universidade Federal da Paraíba, Campus II, Rodovia PB 079, Km 12, 58397-000 Areia, PB, Brazil
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Sodré F, Souza G, Feitosa R, Pereira C, Maldaner A. Illicit Drugs, Metabolites and Adulterants in Wastewater: Monitoring Community Drug Abuse in the Brazilian Federal District during the 2014 Soccer World Cup. J BRAZIL CHEM SOC 2017. [DOI: 10.21577/0103-5053.20170063] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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Gomes GMF, Philipssen C, Bard EK, Souza G. DOLOMITE DESULFURIZATION BEHAVIOR IN A BUBBLING FLUIDIZED BED PILOT PLANT FOR HIGH ASH COAL. Braz J Chem Eng 2016. [DOI: 10.1590/0104-6632.20160332s20140237] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Affiliation(s)
- G. M. F. Gomes
- Fundação de Ciência e Tecnologia do Estado do Rio Grande do Sul, Brasil; Universidade do Vale do Rio dos Sinos, Brazil
| | | | - E. K. Bard
- Fundação de Ciência e Tecnologia do Estado do Rio Grande do Sul, Brasil
| | - G. Souza
- Fundação de Ciência e Tecnologia do Estado do Rio Grande do Sul, Brasil
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Ribeiro EMS, Santos BA, Arroyo-Rodríguez V, Tabarelli M, Souza G, Leal IR. Phylogenetic impoverishment of plant communities following chronic human disturbances in the Brazilian Caatinga. Ecology 2016; 97:1583-92. [DOI: 10.1890/15-1122.1] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Elâine M. S. Ribeiro
- Departamento de Botânica; Universidade Federal de Pernambuco; Programa de Pós-Graduação em Botânica; Cidade Universitária Av. Professor Moraes Rego, s/n CEP: 50670-901 Recife PE Brasil
| | - Bráulio A. Santos
- Departamento de Sistemática e Ecologia; Universidade Federal da Paraíba; Centro de Ciências Exatas e da Natureza; Cidade Universitária CEP: 58051-900 João Pessoa PB Brasil
| | - Víctor Arroyo-Rodríguez
- Instituto de Investigaciones en Ecosistemas y Sustentabilidad; Universidad Nacional Autónoma de Mexico; Morelia C.P. 58190 Michoacán Mexico
| | - Marcelo Tabarelli
- Departamento de Botânica; Universidade, Federal de Pernambuco; Cidade, Universitária Av. Professor Moraes Rego, s/n CEP: 50670-901 Recife PE Brasil
| | - Gustavo Souza
- Departamento de Botânica; Universidade, Federal de Pernambuco; Cidade, Universitária Av. Professor Moraes Rego, s/n CEP: 50670-901 Recife PE Brasil
| | - Inara R. Leal
- Departamento de Botânica; Universidade, Federal de Pernambuco; Cidade, Universitária Av. Professor Moraes Rego, s/n CEP: 50670-901 Recife PE Brasil
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Souza G, Vanzela ALL, Crosa O, Guerra M. Interstitial telomeric sites and Robertsonian translocations in species of Ipheion and Nothoscordum (Amaryllidaceae). Genetica 2016; 144:157-66. [PMID: 26869260 DOI: 10.1007/s10709-016-9886-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 02/04/2016] [Indexed: 10/22/2022]
Abstract
The genera Nothoscordum and Ipheion (Allioideae, Amaryllidaceae) are cytologically characterized by a dysploid series with variable numbers of metacentric and acrocentric chromosomes typical of karyotypes rearranged by Robertsonian translocations (RT). Since they have large chromosomes, low diploid numbers, and possess two telomeric motifs [the vertebrate-type (TTAGGG) n and the Arabidopsis-type (TTTAGGG) n ] they are suitable for investigating the occurrence and possible role of interstitial telomeric sites (ITS) associated with RT. We analyzed the distributions of telomeric sites in 12 species of Nothoscordum and Ipheion and found that both telomeric probes colocalized in all chromosome termini. Cloning and sequencing PCR products obtained using both telomeric primers simultaneously revealed long stretches of (TTAGGG) n and (TTTAGGG) n sequences together with degenerated telomeric sequences. Most acrocentric chromosomes have a 45S rDNA site at the terminal region of the short arms adjacent to the most distal telomeric sites. Telomeric signals were found at all chromosome ends, but ITS were also detected in a few proximal and subterminal regions in some Nothoscordum species. Although RT are common in this group of plants, our findings suggest that proximal positioning of telomeric motifs are not necessarily related to that kind of rearrangement. Rather, transposition of telomeric sequences followed by amplification, could better explain the presence of (TTAGGG) n and (TTTAGGG) n repeats at those sites. Furthermore, a few small interstitial sites found in some Nothoscordum species indicate that dispersion of these sequences was not restricted to the proximal region.
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Affiliation(s)
- Gustavo Souza
- Laboratory of Plant Cytogenetics and Evolution, Centro de Ciências Biológicas, Department of Botany, Federal University of Pernambuco, Rua Nelson Chaves S/N, Cidade Universitária, Recife, PE, 50670-420, Brazil.
| | - Andre L L Vanzela
- Laboratory of Cytogenetics and Plant Diversity, Department of General Biology, State University of Londrina, Londrina, Paraná, Brazil
| | - Orfeo Crosa
- Laboratory of Genetics, Department of Plant Biology, Faculty of Agronomy, University of the Republic, Montevideo, Uruguay
| | - Marcelo Guerra
- Laboratory of Plant Cytogenetics and Evolution, Centro de Ciências Biológicas, Department of Botany, Federal University of Pernambuco, Rua Nelson Chaves S/N, Cidade Universitária, Recife, PE, 50670-420, Brazil
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Jacobina UP, Martinez PA, Torres RA, Souza G. Trends on the Karyotype Acrocentrization Within Carangidae (Perciformes): A New Phylogenetic Evidence About a Traditional Marine Paradigm. Zebrafish 2015; 13:45-53. [PMID: 26716977 DOI: 10.1089/zeb.2015.1143] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
Carangidae is a morphologically diverse family of marine fish, characterized by stable karyotypes, predominantly with 2n = 48, composed of acrocentric chromosomes (A). This stability is shared with other families of the order Perciformes, which resulted in the hypothesis that 48A is a plesiomorphic karyotype of the group. We tested this hypothesis in the Carangidae family using comparative phylogenetic methods, investigating the evolution of karyotype characters (including chromosome number, morphology, and number of chromosome arms per karyotype [fundamental number, FN]). Our analyses revealed that 2n = 48 is most likely the ancestral chromosome number for the family. However, an extremely variable number of FNs, always above 48, was observed in basal clades within the family and sister groups. On the other hand, the reduced FN = 48 was consistently observed only in the most derived clades, indicating a tendency for acrocentrization. The number of acrocentric chromosomes apparently was accompanied by a trend of reduction in the genome size (1C-value), suggesting that these changes might be correlated. Our data contradict the marine fish hypothesis that the 2n = 48 acrocentric karyotype is plesiomorphic, at least for Carangidae, and reveal the importance for the correct interpretation of karyotype in a temporal and phylogenetic context.
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Affiliation(s)
- Uedson Pereira Jacobina
- 1 Laboratório de Genômica Evolutiva e Ambiental, Departamento de Zoologia/UFPE, Cidade Universitária , Recife, Brazil
| | - Pablo Ariel Martinez
- 2 BioMa: Biodiversity and Macroecology Lab, Universidad Rey Juan Carlos , Mostoles, Madrid
| | - Rodrigo Augusto Torres
- 1 Laboratório de Genômica Evolutiva e Ambiental, Departamento de Zoologia/UFPE, Cidade Universitária , Recife, Brazil
| | - Gustavo Souza
- 3 Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco , Recife, Brazil
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Bocchi EA, Tanigawa RY, Brandão SMG, Cruz F, Issa V, Ayub-Ferreira S, Chizzola P, Souza G, Fiorelli AI, Bacal F, Pomerantzeff PMA, Honorato R, Lourenço-Filho D, Guimarães G, Benvenuti LA. Immunohistochemical quantification of inflammatory cells in endomyocardial biopsy fragments after heart transplantation: a new potential method to improve the diagnosis of rejection after heart transplantation. Transplant Proc 2015; 46:1489-96. [PMID: 24935318 DOI: 10.1016/j.transproceed.2013.12.062] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Revised: 10/09/2013] [Accepted: 12/16/2013] [Indexed: 11/30/2022]
Abstract
Inconsistencies in cardiac rejection grading systems corroborate the concept that the evaluation of inflammatory intensity and myocyte damage seems to be subjective. We studied in 36 patients the potential role of the immunohistochemical (IHC) counting of inflammatory cells in endomyocardial biopsy (EMB) as an objective tool, testing the hypothesis of correlation between the International Society for Heart and Lung Transplantation 2004 rejection and IHC counting of inflammatory cells. We observed a progressive increment in CD68+ cells/mm(2) (P = .000) and CD3+ cells/mm(2) (P = .000) with higher rejection grade. A strong correlation between the grade of cellular rejection and both CD68+ cells/mm(2) and CD3+ cells/mm(2) was obtained (P = .000). One patient with CD3+ and CD68+ cells/mm(2) above the upper limit of the 95% confidence interval for cells/mm(2) found in rejection grade 1R evolved to rejection grade 2R without treatment. In patients with 2R that did not respond to treatment the values of CD68+ or CD3+ cells were higher than the overall median values for rejection grade 2R. For diagnosis of rejection needing treatment, the CD68+ and CD3+ cells/mm(2) areas under the receiver operating characteristic curves were 0.956 and 0.934, respectively. IHC counting of mononuclear inflammatory infiltrate in EMB seems to have additive potential role in evaluation of EMB for the diagnosis and prognosis of rejection episodes.
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Affiliation(s)
- E A Bocchi
- Heart Institute (Incor), University of São Paulo Medical School, São Paulo, Brazil.
| | - R Y Tanigawa
- Heart Institute (Incor), University of São Paulo Medical School, São Paulo, Brazil
| | - S M G Brandão
- Heart Institute (Incor), University of São Paulo Medical School, São Paulo, Brazil
| | - F Cruz
- Heart Institute (Incor), University of São Paulo Medical School, São Paulo, Brazil
| | - V Issa
- Heart Institute (Incor), University of São Paulo Medical School, São Paulo, Brazil
| | - S Ayub-Ferreira
- Heart Institute (Incor), University of São Paulo Medical School, São Paulo, Brazil
| | - P Chizzola
- Heart Institute (Incor), University of São Paulo Medical School, São Paulo, Brazil
| | - G Souza
- Heart Institute (Incor), University of São Paulo Medical School, São Paulo, Brazil
| | - A I Fiorelli
- Heart Institute (Incor), University of São Paulo Medical School, São Paulo, Brazil
| | - F Bacal
- Heart Institute (Incor), University of São Paulo Medical School, São Paulo, Brazil
| | - P M A Pomerantzeff
- Heart Institute (Incor), University of São Paulo Medical School, São Paulo, Brazil
| | - R Honorato
- Heart Institute (Incor), University of São Paulo Medical School, São Paulo, Brazil
| | - D Lourenço-Filho
- Heart Institute (Incor), University of São Paulo Medical School, São Paulo, Brazil
| | - G Guimarães
- Heart Institute (Incor), University of São Paulo Medical School, São Paulo, Brazil
| | - L A Benvenuti
- Heart Institute (Incor), University of São Paulo Medical School, São Paulo, Brazil
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Sartori SB, Ferreira LFR, Messias TG, Souza G, Pompeu GB, Monteiro RTR. Pleurotus biomass production on vinasse and its potential use for aquaculture feed. Mycology 2014; 6:28-34. [PMID: 26000196 PMCID: PMC4409041 DOI: 10.1080/21501203.2014.988769] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Accepted: 10/25/2014] [Indexed: 11/02/2022] Open
Abstract
The vinasse is a by-product generated during the manufacture of alcohol from sugarcane fermentation. Rich in organic matter, it is known that the vinasse has the potential to be used as a source of nutrients for plants as well as microorganisms. In this study, the fungi Pleurotus sajor-caju, P. ostreatus, P. albidus and P. flabellatus were cultivated in vinasse and utilised as a complementary diet for Danio rerio fish. The fungi mycelia cultured in vinasse for 15 days were lyophilised and offered to the fishes at a rate of 2% (medium/body weight) for 28 days. P. albidus produced the highest biomass (16.27 g L-1). Bromatological analysis of mycelia showed similar values to commercial rations. Toxicity tests showed that fish survival was 100% and no significant biomass loss was observed, indicating that the tested fungi grown in vinasse showed no toxicity. Our results showed that vinasse is a promising by-product for fungal growth and the mycelia of Pleurotus sp. fungi can be included in the diets of fish as a nutritional supplement.
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Affiliation(s)
- S B Sartori
- Escola Superior de Agricultura 'Luiz de Queiroz'/USP , Av. Pádua Dias, 11, Piracicaba , SP , Brazil
| | - L F R Ferreira
- Centro de Energia Nuclear na Agricultura/USP , Caixa Postal 96. Av. Centenário, 303, Piracicaba , SP , Brazil
| | - T G Messias
- Centro de Energia Nuclear na Agricultura/USP , Caixa Postal 96. Av. Centenário, 303, Piracicaba , SP , Brazil
| | - G Souza
- Centro de Energia Nuclear na Agricultura/USP , Caixa Postal 96. Av. Centenário, 303, Piracicaba , SP , Brazil
| | - G B Pompeu
- Escola Superior de Agricultura 'Luiz de Queiroz'/USP , Av. Pádua Dias, 11, Piracicaba , SP , Brazil
| | - R T R Monteiro
- Centro de Energia Nuclear na Agricultura/USP , Caixa Postal 96. Av. Centenário, 303, Piracicaba , SP , Brazil
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Abstract
Implantation of penile nodules under the foreskin aims at improving male and female sexual pleasures during intercourse. This case discusses the characteristics of the South American penile adornment ‘Bouglou’ as well as the risk factors for penile cancer in this region of Amazonia. This is a case report of a 48-year-old man whose penis presented a destructive gland/penile shaft lesion and three adornments in the penile shaft, reported as ‘Bouglou’. The diagnosis of penile cancer was confirmed after total penectomy. This study is the first that suggests a possible association between squamous cell carcinoma and these penile adornments.
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Affiliation(s)
- Thiago Teixeira
- Urology Department, Hospital de Clínicas Dr. Alberto Lima Federal University of Amapa, Macapa, Brazil
| | - Gustavo Souza
- Urology Department, Hospital de Clínicas Dr. Alberto Lima Federal University of Amapa, Macapa, Brazil
| | - Raiza Campos
- Medical School, Federal University of Amapa, Macapa, Brazil
| | - Luis Pena
- Medical School, Federal University of Amapa, Macapa, Brazil
| | - Jorge Hallak
- Medical School, São Paulo University, São Paulo, Brazil
| | - Maira Tongu
- Medical School, Federal University of Amapa, Macapa, Brazil
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Fernandes-Charpiot I, Souza G, Nogueira M, Baptista M, Sorrenti A, Abbud-Filho M. Clinical Outcomes and Virus Characteristics of Dengue in Kidney Transplant Recipients: Report of 11 Cases From a Single Center. Transplantation 2014. [DOI: 10.1097/00007890-201407151-00793] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Oliveira AP, Silva RR, Souza G, Carvalho F, Silva A, Lisboa G, Pereira MMS, Carvalho VM, Mendes FBL, Oliveira AC. Consumo e deposição de ácidos graxos no longissimus de novilhos Nelore suplementados em pastagens. ARCH ZOOTEC 2013. [DOI: 10.21071/az.v63i241.566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Objetivou-se estudar a correlação entre consumo e deposição de ácidos graxos no músculo Longissimus de novilhos nelore suplementados em pastagens. O trabalho de campo foi implantado numa área de 52 ha, formada de Brachiaria brizantha. Foram utilizados 40 novilhos da raça Nelore com peso inicial médio de 373,7 ± 14,9 kg e 26 meses de idade, distribuídos em quatro tratamentos:Controle= T00 (fornecimento apenas de sal mineral), T03= fornecimento de 0,3% concentrado em função do peso vivo; T06= fornecimento de 0,6 % concentrado em função do peso vivo; T09= fornecimento de 0,9 % concentrado em função do peso vivo. Amostras dos concentrados e da forragem foram coletadas para análise da composição de ácidos graxos. O período experimental foi de 98 dias. Após este período, os animais foram abatidos. Os resultados foram analisados por Correlação Linear de Pearson e teste t. Constatou-se que existem correlações entre os ácidos graxos consumidos e depositados no músculo.
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Pinna A, Martins G, Souza G, Lilenbaum W. Influence of Seroreactivity toLeptospiraand Reproductive Failures in Recipient Mares of Equine Embryo Transfer Programmes. Reprod Domest Anim 2013; 48:e55-7. [DOI: 10.1111/rda.12166] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2012] [Accepted: 02/14/2013] [Indexed: 11/27/2022]
Affiliation(s)
- A Pinna
- Laboratory of Veterinary Bacteriology; Universidade Federal Fluminense; Niterói; RJ; Brazil
| | - G Martins
- Laboratory of Veterinary Bacteriology; Universidade Federal Fluminense; Niterói; RJ; Brazil
| | - G Souza
- Empresa Brasileira de Pesquisa Agropecuária - Gado de leite; Juiz de Fora; MG; Brazil
| | - W Lilenbaum
- Laboratory of Veterinary Bacteriology; Universidade Federal Fluminense; Niterói; RJ; Brazil
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48
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Bocchi E, Benvenutti L, Tanigawa R, Brandão S, Issa V, Ayub-Ferreira S, Cruz F, Pomerantzeff P, Honorato R, Lourenço-Filho D, Fiorelli A, Chizzola P, Souza G, Bacal F. Immunohistochemical Counting of Mononuclear Infiltrates in Endomyocardial Biopsy Fragments: A New Method To Improve the Diagnosis of Rejection after Heart Transplantation. J Heart Lung Transplant 2013. [DOI: 10.1016/j.healun.2013.01.186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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49
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Anicete-Santos M, Lima RC, Orhan E, Maurera MAMA, Simões LGP, Souza G, PIZANI PS, Leite ER, Varela JA, Longo E. Visible PL Phenomenon at Room Temperature in Disordered Structure of SrWO4 Powder. ACTA ACUST UNITED AC 2006. [DOI: 10.1007/s10820-006-9002-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Guimaraes G, Silva M, d’Avila V, Issa V, Souza G, Ciolac E, Pereira C, Ferras A, Bocchi E. 34. J Heart Lung Transplant 2006. [DOI: 10.1016/j.healun.2005.11.036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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