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Staggemeier VG, Amorim B, Bünger M, Costa IR, de Faria JEQ, Flickinger J, Giaretta A, Kubo MT, Lima DF, Dos Santos LL, Lourenço AR, Lucas E, Mazine FF, Murillo-A J, de Oliveira MIU, Parra-O C, Proença CEB, Reginato M, Rosa PO, Santos MF, Stadnik A, Tuler AC, Valdemarin KS, Vasconcelos T. Towards a species-level phylogeny for Neotropical Myrtaceae: Notes on topology and resources for future studies. AMERICAN JOURNAL OF BOTANY 2024; 111:e16330. [PMID: 38725388 DOI: 10.1002/ajb2.16330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 02/22/2024] [Accepted: 02/23/2024] [Indexed: 05/29/2024]
Abstract
PREMISE Increasingly complete phylogenies underpin studies in systematics, ecology, and evolution. Myrteae (Myrtaceae), with ~2700 species, is a key component of the exceptionally diverse Neotropical flora, but given its complicated taxonomy, automated assembling of molecular supermatrices from public databases often lead to unreliable topologies due to poor species identification. METHODS Here, we build a taxonomically verified molecular supermatrix of Neotropical Myrteae by assembling 3909 published and 1004 unpublished sequences from two nuclear and seven plastid molecular markers. We infer a time-calibrated phylogenetic tree that covers 712 species of Myrteae (~28% of the total diversity in the clade) and evaluate geographic and taxonomic gaps in sampling. RESULTS The tree inferred from the fully concatenated matrix mostly reflects the topology of the plastid data set and there is a moderate to strong incongruence between trees inferred from nuclear and plastid partitions. Large, species-rich genera are still the poorest sampled within the group. Eastern South America is the best-represented area in proportion to its species diversity, while Western Amazon, Mesoamerica, and the Caribbean are the least represented. CONCLUSIONS We provide a time-calibrated tree that can be more reliably used to address finer-scale eco-evolutionary questions that involve this group in the Neotropics. Gaps to be filled by future studies include improving representation of taxa and areas that remain poorly sampled, investigating causes of conflict between nuclear and plastid partitions, and the role of hybridization and incomplete lineage sorting in relationships that are poorly supported.
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Affiliation(s)
- Vanessa G Staggemeier
- Departamento de Ecologia, Centro de Biociências, Universidade Federal do Rio Grande do Norte, Natal, 59092-970, RN, Brazil
| | - Bruno Amorim
- Programa de Pós-Graduação em Biotecnologia e Recursos Naturais da Amazônia, Universidade do Estado do Amazonas, Manaus, AM, Brazil
| | - Mariana Bünger
- Programa de Pós-Graduação em Sistemática, Uso e Conservação da Biodiversidade, Department de Biologia, Universidade Federal do Ceará, Fortaleza, 60355-636, CE, Brazil
| | - Itayguara R Costa
- Programa de Pós-Graduação em Sistemática, Uso e Conservação da Biodiversidade, Department de Biologia, Universidade Federal do Ceará, Fortaleza, 60355-636, CE, Brazil
| | - Jair Eustáquio Quintino de Faria
- Instituto Interamericano de Cooperação para a Agricultura - IICA - SHIS QI 5, Chácara 16, Lago Sul, Brasília, 71600-530, DF, Brazil
| | - Jonathan Flickinger
- Lady Bird Johnson Wildflower Center, The University of Texas at Austin, 4801 La Crosse Ave., Austin, 78739, TX, USA
| | - Augusto Giaretta
- Universidade Federal da Grande Dourados, Faculdade de Ciências Biológicas e Ambientais, Unidade II, Dourados, 79804-970, MS, Brazil
| | - Marcelo T Kubo
- Departamento de Botânica, Laboratório de Sistemática Vegetal, Instituto de Biociências, Universidade de São Paulo, São Paulo, 05508-900, São Paulo, Brazil
| | - Duane Fernandes Lima
- Programa de Pós-Graduação em Biologia de Fungos, Algas e Plantas, Centro de Ciências Biológicas, Universidade Federal de Santa Catarina, Florianópolis, 88040-900, SC, Brazil
| | | | | | - Eve Lucas
- Herbarium, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB, UK
| | - Fiorella Fernanda Mazine
- Universidade Federal de São Carlos, Campus Sorocaba, Rodovia João Leme dos Santos (SP-264), km 110, Sorocaba, 18052-780, SP, Brazil
| | - José Murillo-A
- Instituto de Ciencias Naturales, Universidad Nacional de Colombia, Carrera 30 No. 45-03, Bogotá, Colombia
| | - Marla Ibrahim Uehbe de Oliveira
- Departamento de Biologia, Universidade Federal de Sergipe, Av. Marcelo Déda Chagas, s/n, Bairro Jardim Rosa Elze, São Cristóvão, 49107-230, SE, Brazil
| | - Carlos Parra-O
- Instituto de Ciencias Naturales, Universidad Nacional de Colombia, Carrera 30 No. 45-03, Bogotá, Colombia
| | - Carolyn E B Proença
- Departamento de Botânica, Universidade de Brasília, Brasília, 70910-900, DF, Brazil
| | - Marcelo Reginato
- Departamento de Botânica, Universidade Federal do Rio Grande do Sul, Porto Alegre, 90650-001, RS, Brazil
| | - Priscila Oliveira Rosa
- Jardim Botânico de Brasília, Diretoria de Vegetação e Flora, Área Especial SMDB Estação Ecológica Jardim Botânico de Brasília, Brasília, 71.680-001, DF, Brazil
| | - Matheus Fortes Santos
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Alameda da Universidade s/n, Anchieta, São Bernardo do Campo, 09606-045, SP, Brazil
| | - Aline Stadnik
- Instituto Interamericano de Cooperação para a Agricultura - IICA - SHIS QI 5, Chácara 16, Lago Sul, Brasília, 71600-530, DF, Brazil
- Programa de Pós-Graduação em Botânica, Universidade Estadual de Feira de Santana, Departamento de Ciências Biológicas, Av. Transnordestina s/n, Feira de Santana, 44036-900, BA, Brazil
| | - Amélia Carlos Tuler
- Centro de Estudos da Biodiversidade, Universidade Federal de Roraima, Campus Paricarana, Av. Cap. Ene Garcez, 2413, Boa Vista, 69304-000, RR, Brazil
| | - Karinne Sampaio Valdemarin
- Departamento de Ciências Biológicas, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, Piracicaba, 13418-260, SP, Brazil
| | - Thais Vasconcelos
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, 48109, MI, USA
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Pires GP, Fioresi VS, Canal D, Canal DC, Fernandes M, Brustolini OJB, de Avelar Carpinetti P, Ferreira A, da Silva Ferreira MF. Effects of trimer repeats on Psidium guajava L. gene expression and prospection of functional microsatellite markers. Sci Rep 2024; 14:9811. [PMID: 38684872 PMCID: PMC11059378 DOI: 10.1038/s41598-024-60417-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Accepted: 04/23/2024] [Indexed: 05/02/2024] Open
Abstract
Most research on trinucleotide repeats (TRs) focuses on human diseases, with few on the impact of TR expansions on plant gene expression. This work investigates TRs' effect on global gene expression in Psidium guajava L., a plant species with widespread distribution and significant relevance in the food, pharmacology, and economics sectors. We analyzed TR-containing coding sequences in 1,107 transcripts from 2,256 genes across root, shoot, young leaf, old leaf, and flower bud tissues of the Brazilian guava cultivars Cortibel RM and Paluma. Structural analysis revealed TR sequences with small repeat numbers (5-9) starting with cytosine or guanine or containing these bases. Functional annotation indicated TR-containing genes' involvement in cellular structures and processes (especially cell membranes and signal recognition), stress response, and resistance. Gene expression analysis showed significant variation, with a subset of highly expressed genes in both cultivars. Differential expression highlighted numerous down-regulated genes in Cortibel RM tissues, but not in Paluma, suggesting interplay between tissues and cultivars. Among 72 differentially expressed genes with TRs, 24 form miRNAs, 13 encode transcription factors, and 11 are associated with transposable elements. In addition, a set of 20 SSR-annotated, transcribed, and differentially expressed genes with TRs was selected as phenotypic markers for Psidium guajava and, potentially for closely related species as well.
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Affiliation(s)
- Giovanna Pinto Pires
- Centro de Ciências Agrárias e Engenharias, Departamento de Agronomia, Universidade Federal Do Espírito Santo, Alto Universitário, s/n, Alegre, ES, 29500-000, Brazil
| | - Vinicius Sartori Fioresi
- Centro de Ciências Agrárias e Engenharias, Departamento de Agronomia, Universidade Federal Do Espírito Santo, Alto Universitário, s/n, Alegre, ES, 29500-000, Brazil
| | - Drielli Canal
- Centro de Ciências Agrárias e Engenharias, Departamento de Agronomia, Universidade Federal Do Espírito Santo, Alto Universitário, s/n, Alegre, ES, 29500-000, Brazil
| | - Dener Cezati Canal
- Centro de Ciências Agrárias e Engenharias, Departamento de Agronomia, Universidade Federal Do Espírito Santo, Alto Universitário, s/n, Alegre, ES, 29500-000, Brazil
| | - Miquéias Fernandes
- Centro de Ciências Agrárias e Engenharias, Departamento de Agronomia, Universidade Federal Do Espírito Santo, Alto Universitário, s/n, Alegre, ES, 29500-000, Brazil
| | - Otávio José Bernardes Brustolini
- Laboratório Nacional de Computação Científica (LNCC). Av. Getulio Vargas, 333, Petrópolis, Rio de Janeiro, Quitandinha, 25651-076, Brazil
| | - Paola de Avelar Carpinetti
- Centro de Ciências Agrárias e Engenharias, Departamento de Agronomia, Universidade Federal Do Espírito Santo, Alto Universitário, s/n, Alegre, ES, 29500-000, Brazil
| | - Adésio Ferreira
- Centro de Ciências Agrárias e Engenharias, Departamento de Agronomia, Universidade Federal Do Espírito Santo, Alto Universitário, s/n, Alegre, ES, 29500-000, Brazil
| | - Marcia Flores da Silva Ferreira
- Centro de Ciências Agrárias e Engenharias, Departamento de Agronomia, Universidade Federal Do Espírito Santo, Alto Universitário, s/n, Alegre, ES, 29500-000, Brazil.
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Liu H, Zhang Y, Chen J. Whole-genome sequencing and functional annotation of pathogenic Paraconiothyrium brasiliense causing human cellulitis. Hum Genomics 2023; 17:65. [PMID: 37461066 DOI: 10.1186/s40246-023-00512-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 07/11/2023] [Indexed: 07/20/2023] Open
Abstract
BACKGROUND A pathogenic filamentous fungus causing eyelid cellulitis was isolated from the secretion from a patient's left eyelid, and a phylogenetic analysis based on the rDNA internal transcribed spacer region (ITS) and single-copy gene families identified the isolated strain as Paraconiothyrium brasiliense. The genus Paraconiothyrium contains the major plant pathogenic fungi, and in our study, P. brasiliense was identified for the first time as causing human infection. To comprehensively analyze the pathogenicity, and proteomics of the isolated strain from a genetic perspective, whole-genome sequencing was performed with the Illumina NovaSeq and Oxford Nanopore Technologies platforms, and a bioinformatics analysis was performed with BLAST against genome sequences in various publicly available databases. RESULTS The genome of P. brasiliense GGX 413 is 39.49 Mb in length, with a 51.2% GC content, and encodes 13,057 protein-coding genes and 181 noncoding RNAs. Functional annotation showed that 592 genes encode virulence factors that are involved in human disease, including 61 lethal virulence factors and 30 hypervirulence factors. Fifty-four of these 592 virulence genes are related to carbohydrate-active enzymes, including 46 genes encoding secretory CAZymes, and 119 associated with peptidases, including 70 genes encoding secretory peptidases, and 27 are involved in secondary metabolite synthesis, including four that are associated with terpenoid metabolism. CONCLUSIONS This study establishes the genomic resources of P. brasiliense and provides a theoretical basis for future studies of the pathogenic mechanism of its infection of humans, the treatment of the diseases caused, and related research.
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Affiliation(s)
- Haibing Liu
- Department of Clinical Laboratory, The Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
| | - Yue Zhang
- Department of Clinical Laboratory, The Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
| | - Jianguo Chen
- Department of Clinical Laboratory, The Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu, China.
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Silva MA, Soares FAF, Clarindo WR, Mendes LA, Alves LB, Ferreira A, da Silva Ferreira MF. Genomic and epigenomic variation in Psidium species and their outcome under the yield and composition of essential oils. Sci Rep 2023; 13:1385. [PMID: 36697447 PMCID: PMC9876884 DOI: 10.1038/s41598-023-27912-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 01/10/2023] [Indexed: 01/26/2023] Open
Abstract
Diploid and polyploid species derived from the euploid series x = 11 occur in the genus Psidium, as well as intraspecific cytotypes. Euploidy in the genus can alter the gene copy number, resulting in several "omics" variations. We revisited the euploidy, reported genomic (nuclear 2C value, GC%, and copy number of secondary metabolism genes) and epigenomic (5-mC%) differences in Psidium, and related them to essential oil yield and composition. Mean 2C values ranged from 0.90 pg (P. guajava) to 7.40 pg (P. gaudichaudianum). 2C value is intraspecifically varied in P. cattleyanum and P. gaudichaudianum, evidencing cytotypes that can be formed from euploid (non-reduced) and/or aneuploid reproductive cells. GC% ranged from 34.33% (P. guineense) to 48.95% (P. myrtoides), and intraspecific variations occurred even for species without 2C value intraspecific variation. Essential oil yield increased in relation to 2C value and to GC%. We showed that P. guajava (diploid) possesses two and P. guineense (tetraploid) four copies of the one specific TPS gene, as well as eight and sixteen copies respectively of the conserved regions that occur in eight TPS genes. We provide a wide "omics'' characterization of Psidium and show the outcome of the genome and epigenome variation in secondary metabolism.
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Affiliation(s)
- Matheus Alves Silva
- Departamento de Agronomia, Centro de Ciências Agrárias e Engenharias, Universidade Federal do Espírito Santo, Alto Universitário, s/n, Guararema, Alegre, ES, 29500-000, Brazil
| | - Fernanda Aparecida Ferrari Soares
- Departamento de Biologia Geral, Universidade Federal de Viçosa, Av. Peter Henry Rolfs, s/n, Campus Universitário, Viçosa, MG, 36570-900, Brazil
| | - Wellington Ronildo Clarindo
- Departamento de Biologia Geral, Universidade Federal de Viçosa, Av. Peter Henry Rolfs, s/n, Campus Universitário, Viçosa, MG, 36570-900, Brazil
| | - Luiza Alves Mendes
- Departamento de Química, Universidade Federal de Viçosa, Av. Peter Henry Rolfs, s/n, Campus Universitário, Viçosa, MG, 36570-900, Brazil
| | - Luziane Brandão Alves
- Departamento de Agronomia, Centro de Ciências Agrárias e Engenharias, Universidade Federal do Espírito Santo, Alto Universitário, s/n, Guararema, Alegre, ES, 29500-000, Brazil
| | - Adésio Ferreira
- Departamento de Agronomia, Centro de Ciências Agrárias e Engenharias, Universidade Federal do Espírito Santo, Alto Universitário, s/n, Guararema, Alegre, ES, 29500-000, Brazil
| | - Marcia Flores da Silva Ferreira
- Departamento de Agronomia, Centro de Ciências Agrárias e Engenharias, Universidade Federal do Espírito Santo, Alto Universitário, s/n, Guararema, Alegre, ES, 29500-000, Brazil.
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