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Piccoli C, Muñoz-Mérida A, Crottini A. Correction: PARSID: a Python script for automatic analysis of local BLAST results for a rapid molecular taxonomic identification. BMC Res Notes 2024; 17:116. [PMID: 38654349 DOI: 10.1186/s13104-024-06771-2] [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: 04/25/2024] Open
Affiliation(s)
- Costanza Piccoli
- CIBIO, Centro de Investigação em Bioaffiliationersidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Campus de Vairão, 4485-661, Vairão, Portugal.
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169- 007, Porto, Portugal.
- BIOPOLIS Program in Genomics, Bioaffiliationersity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal.
| | - Antonio Muñoz-Mérida
- CIBIO, Centro de Investigação em Bioaffiliationersidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Campus de Vairão, 4485-661, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169- 007, Porto, Portugal
- BIOPOLIS Program in Genomics, Bioaffiliationersity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal
| | - Angelica Crottini
- CIBIO, Centro de Investigação em Bioaffiliationersidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Campus de Vairão, 4485-661, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169- 007, Porto, Portugal
- BIOPOLIS Program in Genomics, Bioaffiliationersity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal
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Piccoli C, Muñoz-Mérida A, Crottini A. PARSID: a Python script for automatic analysis of local BLAST results for a rapid molecular taxonomic identification. BMC Res Notes 2024; 17:35. [PMID: 38268047 PMCID: PMC10807118 DOI: 10.1186/s13104-024-06686-y] [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: 08/05/2023] [Accepted: 01/05/2024] [Indexed: 01/26/2024] Open
Abstract
OBJECTIVE A reliable taxonomic identification of species from molecular samples is the first step for many studies. For researchers unfamiliar with programming, running a BLAST analysis, filtering, and organizing results for hundreds of sequences through the BLAST web interface can be difficult. Additionally, sequences deposited in GenBank can have outdated taxonomic identification. The use of reliable Reference Sequences Library (RSL) containing accurate taxonomically-identified sequences facilitates this task. Pending the availability of a RSL with the user, we developed a tool that automates the molecular taxonomic identification of sequences. RESULTS We developed PARSID, a Python script running through the command-line that automates the routine workflow of blasting an input sequence file against the user's RSL, and retrieves the matches with the highest percentage of identity in five steps. PARSID accepts cut-off parameters and supplementary information in a.csv file for filtering the results. The final output is visualized in a spreadsheet. We tested its functioning using 10 input sequences simulating different situations of the molecular taxonomic identification of sequences against an example RSL containing 25 sequences. Step-by-step instructions and test files are publicly available at https://github.com/kokinide/PARSID.git .
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Affiliation(s)
- Costanza Piccoli
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Campus de Vairão, 4485-661, Vairão, Portugal.
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169- 007, Porto, Portugal.
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal.
| | - Antonio Muñoz-Mérida
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Campus de Vairão, 4485-661, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169- 007, Porto, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal
| | - Angelica Crottini
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Campus de Vairão, 4485-661, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169- 007, Porto, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal
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Veríssimo A, Castro LFC, Muñoz-Mérida A, Almeida T, Gaigher A, Neves F, Flajnik MF, Ohta Y. An Ancestral Major Histocompatibility Complex Organization in Cartilaginous Fish: Reconstructing MHC Origin and Evolution. Mol Biol Evol 2023; 40:msad262. [PMID: 38059517 PMCID: PMC10751288 DOI: 10.1093/molbev/msad262] [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: 09/11/2023] [Revised: 11/06/2023] [Accepted: 11/27/2023] [Indexed: 12/08/2023] Open
Abstract
Cartilaginous fish (sharks, rays, and chimeras) comprise the oldest living jawed vertebrates with a mammalian-like adaptive immune system based on immunoglobulins (Ig), T-cell receptors (TCRs), and the major histocompatibility complex (MHC). Here, we show that the cartilaginous fish "adaptive MHC" is highly regimented and compact, containing (i) a classical MHC class Ia (MHC-Ia) region containing antigen processing (antigen peptide transporters and immunoproteasome) and presenting (MHC-Ia) genes, (ii) an MHC class II (MHC-II) region (with alpha and beta genes) with linkage to beta-2-microglobulin (β2m) and bromodomain-containing 2, (iii) nonclassical MHC class Ib (MHC-Ib) regions with 450 million-year-old lineages, and (iv) a complement C4 associated with the MHC-Ia region. No MHC-Ib genes were found outside of the elasmobranch MHC. Our data suggest that both MHC-I and MHC-II genes arose after the second round of whole-genome duplication (2R) on a human chromosome (huchr) 6 precursor. Further analysis of MHC paralogous regions across early branching taxa from all jawed vertebrate lineages revealed that Ig/TCR genes likely arose on a precursor of the huchr9/12/14 MHC paralog. The β2m gene is linked to the Ig/TCR genes in some vertebrates suggesting that it was present at 1R, perhaps as the donor of C1 domain to the primordial MHC gene. In sum, extant cartilaginous fish exhibit a conserved and prototypical MHC genomic organization with features found in various vertebrates, reflecting the ancestral arrangement for the jawed vertebrates.
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Affiliation(s)
- Ana Veríssimo
- CIBIO-InBIO, Research Center in Biodiversity and Genetic Resources, University of Porto, Vairão 4485-661, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão 4485-661, Portugal
| | - L Filipe C Castro
- Department of Biology, Faculty of Sciences, University of Porto, Porto 4169-007, Portugal
- CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Matosinhos, Portugal
| | - Antonio Muñoz-Mérida
- CIBIO-InBIO, Research Center in Biodiversity and Genetic Resources, University of Porto, Vairão 4485-661, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão 4485-661, Portugal
| | - Tereza Almeida
- CIBIO-InBIO, Research Center in Biodiversity and Genetic Resources, University of Porto, Vairão 4485-661, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão 4485-661, Portugal
| | - Arnaud Gaigher
- CIBIO-InBIO, Research Center in Biodiversity and Genetic Resources, University of Porto, Vairão 4485-661, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão 4485-661, Portugal
- Research Group for Evolutionary Immunogenomics, Max Planck Institute for Evolutionary Biology, Plön, Germany
- Research Unit for Evolutionary Immunogenomics, Department of Biology, University of Hamburg, Hamburg, Germany
| | - Fabiana Neves
- CIBIO-InBIO, Research Center in Biodiversity and Genetic Resources, University of Porto, Vairão 4485-661, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão 4485-661, Portugal
| | - Martin F Flajnik
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Yuko Ohta
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
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Garcia-Raventós A, Muñoz-Mérida A, Lapiedra O, Unzeta M, Ferrandiz-Rovira M, Sol D. Identification of sex-linked SNP markers in wild populations of monomorphic birds. Mol Ecol Resour 2023; 23:1905-1913. [PMID: 37675830 DOI: 10.1111/1755-0998.13862] [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: 02/01/2023] [Revised: 07/28/2023] [Accepted: 08/21/2023] [Indexed: 09/08/2023]
Abstract
Single-nucleotide polymorphism (SNP) analysis is a powerful tool for population genetics, pedigree reconstruction and phenotypic trait mapping. However, the untapped potential of SNP markers to discriminate the sex of individuals in species with reduced sexual dimorphism or of individuals during immature stages remains a largely unexplored avenue. Here, we developed a novel protocol for molecular sexing of birds based on the detection of unique Z- and W-linked SNP markers. Our method is based on the identification of two unique loci, one in each sexual chromosome. Individuals are considered males when they show no calls for the W-linked SNP and are heterozygous or homozygous for the Z-linked SNP, while females exhibit both Z- and W-linked SNP calls. We validated the method in the Jackdaw (Corvus monedula). The reduced sexual dimorphism in this species makes it difficult to identify the sex of individuals in the wild. We assessed the reliability of the method using 36 individuals of known sex and found that their sex was correctly assigned in 100% of cases. The sex-linked markers also proved to be widely applicable for discriminating males and females from a sample of 927 genotyped individuals at different maturity stages, with an accuracy of 99.5%. Since SNP markers are increasingly used in quantitative genetic analyses of wild populations, the approach we propose has great potential to be integrated into broader genetic research programmes without the need for additional sexing techniques.
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Affiliation(s)
| | - Antonio Muñoz-Mérida
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus Agrário de Vairão, Universidade do Porto, Vairão, Portugal
| | | | | | | | - Daniel Sol
- CREAF, Catalonia, Spain
- CSIC, Catalonia, Spain
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Jowers MJ, Smart U, Sánchez-Ramírez S, Murphy JC, Gómez A, Bosque RJ, Sarker GC, Noonan BP, Faria JF, Harris DJ, da Silva NJ, Prudente ALC, Weber J, Kok PJR, Rivas GA, Jadin RC, Sasa M, Muñoz-Mérida A, Moreno-Rueda G, Smith EN. Unveiling underestimated species diversity within the Central American Coralsnake, a medically important complex of venomous taxa. Sci Rep 2023; 13:11674. [PMID: 37468518 DOI: 10.1038/s41598-023-37734-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 06/27/2023] [Indexed: 07/21/2023] Open
Abstract
Coralsnakes of the genus Micrurus are a diverse group of venomous snakes ranging from the southern United States to southern South America. Much uncertainty remains over the genus diversity, and understanding Micrurus systematics is of medical importance. In particular, the widespread Micrurus nigrocinctus spans from Mexico throughout Central America and into Colombia, with a number of described subspecies. This study provides new insights into the phylogenetic relationships within M. nigrocinctus by examining sequence data from a broad sampling of specimens from Mexico, Guatemala, Honduras, Nicaragua, Costa Rica, and Panama. The recovered phylogenetic relationships suggest that M. nigrocinctus is a species complex originating in the Pliocene and composed of at least three distinct species-level lineages. In addition, recovery of highly divergent clades supports the elevation of some currently recognized subspecies to the full species rank while others may require synonymization.
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Affiliation(s)
- Michael J Jowers
- CIBIO/InBIO (Centro de Investigação em Biodiversidade e Recursos Genéticos), Universidade do Porto, Campus Agrario De Vairão, 4485-661, Vairão, Portugal.
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal.
- Departamento de Zoología, Facultad de Ciencias, Universidad de Granada, 18071, Granada, Spain.
| | - Utpal Smart
- Department of Biology, Texas State University, 601 University Dr., San Marcos, TX, 78666, USA
| | - Santiago Sánchez-Ramírez
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks, Toronto, ON, M5S 3B2, Canada
| | - John C Murphy
- Science and Education, Field Museum, 1400 S. Lake Shore Drive, Chicago, IL, 60605, USA
| | - Aarón Gómez
- Facultad de Microbiología, Instituto Clodomiro Picado, Universidad de Costa Rica, San José, Costa Rica
| | - Renan J Bosque
- Department of Biological Sciences, Southwestern Oklahoma State University, Weatherford, OK, 73096, USA
| | - Goutam C Sarker
- Department of Biology and Amphibian and Reptile Diversity Research Center, University of Texas at Arlington, Arlington, TX, 76019, USA
- Department of Biology, Cottey College, 1000 W. Austin Blvd, Nevada, MO, 64772, USA
| | - Brice P Noonan
- Department of Biology, The University of Mississippi, Oxford, MS, 38677, USA
| | - J Filipe Faria
- CIBIO/InBIO (Centro de Investigação em Biodiversidade e Recursos Genéticos), Universidade do Porto, Campus Agrario De Vairão, 4485-661, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, 4099-002, Porto, Portugal
| | - D James Harris
- CIBIO/InBIO (Centro de Investigação em Biodiversidade e Recursos Genéticos), Universidade do Porto, Campus Agrario De Vairão, 4485-661, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal
| | - Nelson Jorge da Silva
- Pontifícia Universidade Católica de Goiás - Programa de Pós-Graduação em Ciências Ambientais e Saúde, Goiânia, Goiás, 74605140, Brazil
| | - Ana L C Prudente
- Laboratório de Herpetologia, Coordenação de Zoologia, Museu Paraense Emílio Goeldi (MPEG), Belém, Pará, Brazil
- Programa de Pós-Graduação em Zoologia (UFPA/MPEG) and Biodiversidade e Evolução (MPEG), Belém, Pará, Brazil
| | - John Weber
- Department of Geology, Grand Valley State University, Allendale, MI, 49401, USA
| | - Philippe J R Kok
- Department of Ecology and Vertebrate Zoology, Faculty of Biology and Environmental Protection, University of Łódź, 12/16 Banacha Str, 90-237, Lodz, Poland
- Department of Life Sciences, The Natural History Museum, London, SW7 5BD, UK
| | - Gilson A Rivas
- Museo de Biología, Facultad Experimental de Ciencias, Universidad del Zulia, Maracaibo, Venezuela
| | - Robert C Jadin
- Department of Biology and Museum of Natural History, University of Wisconsin Stevens Point, Stevens Point, WI, 54481, USA
| | - Mahmood Sasa
- Facultad de Microbiología, Instituto Clodomiro Picado, Universidad de Costa Rica, San José, Costa Rica
- Museo de Zoología, Centro de Investigación en Biodiversidad y Ecología Tropical, Universidad de Costa Rica, San José, Costa Rica
| | - Antonio Muñoz-Mérida
- CIBIO/InBIO (Centro de Investigação em Biodiversidade e Recursos Genéticos), Universidade do Porto, Campus Agrario De Vairão, 4485-661, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal
| | - Gregorio Moreno-Rueda
- Departamento de Zoología, Facultad de Ciencias, Universidad de Granada, 18071, Granada, Spain
| | - Eric N Smith
- Department of Biology and Amphibian and Reptile Diversity Research Center, University of Texas at Arlington, Arlington, TX, 76019, USA
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Neves F, Muñoz-Mérida A, Machado AM, Almeida T, Gaigher A, Esteves PJ, Castro LFC, Veríssimo A. Corrigendum: Uncovering a 500 million year old history and evidence of pseudogenization for TLR15. Front Immunol 2023; 14:1216338. [PMID: 37234170 PMCID: PMC10206515 DOI: 10.3389/fimmu.2023.1216338] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 05/04/2023] [Indexed: 05/27/2023] Open
Abstract
[This corrects the article DOI: 10.3389/fimmu.2022.1020601.].
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Affiliation(s)
- Fabiana Neves
- CIBIO‐InBIO, Research Center in Biodiversity and Genetic Resources, University of Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
| | - Antonio Muñoz-Mérida
- CIBIO‐InBIO, Research Center in Biodiversity and Genetic Resources, University of Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
- Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
| | - André M. Machado
- Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
- CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Matosinhos, Portugal
| | - Tereza Almeida
- CIBIO‐InBIO, Research Center in Biodiversity and Genetic Resources, University of Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
| | - Arnaud Gaigher
- CIBIO‐InBIO, Research Center in Biodiversity and Genetic Resources, University of Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
- Research Group for Evolutionary Immunogenomics, Max Planck Institute for Evolutionary Biology, Plön, Germany
- Research Unit for Evolutionary Immunogenomics, Department of Biology, University of Hamburg, Hamburg, Germany
| | - Pedro J. Esteves
- CIBIO‐InBIO, Research Center in Biodiversity and Genetic Resources, University of Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
- Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
- CITS - Center of Investigation in Health Technologies, CESPU, Gandra, Portugal
| | - L. Filipe C. Castro
- Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
- CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Matosinhos, Portugal
| | - Ana Veríssimo
- CIBIO‐InBIO, Research Center in Biodiversity and Genetic Resources, University of Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
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Neves F, Muñoz-Mérida A, Machado AM, Almeida T, Gaigher A, Esteves PJ, Castro LFC, Veríssimo A. Uncovering a 500 million year old history and evidence of pseudogenization for TLR15. Front Immunol 2022; 13:1020601. [PMID: 36605191 PMCID: PMC9808068 DOI: 10.3389/fimmu.2022.1020601] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 11/23/2022] [Indexed: 12/24/2022] Open
Abstract
Introduction Toll like receptors (TLRs) are at the front line of pathogen recognition and host immune response. Many TLR genes have been described to date with some being found across metazoans while others are restricted to specific lineages. A cryptic member of the TLR gene family, TLR15, has a unique phylogenetic distribution. Initially described in extant species of birds and reptiles, an ortholog has been reported for cartilaginous fish. Methods Here, we significantly expanded the evolutionary analysis of TLR15 gene evolution, taking advantage of large genomic and transcriptomic resources available from different lineages of vertebrates. Additionally, we objectively search for TLR15 in lobe-finned and ray-finned fish, as well as in cartilaginous fish and jawless vertebrates. Results and discussion We confirm the presence of TLR15 in early branching jawed vertebrates - the cartilaginous fish, as well as in basal Sarcopterygii - in lungfish. However, within cartilaginous fish, the gene is present in Holocephalans (all three families) but not in Elasmobranchs (its sister-lineage). Holocephalans have long TLR15 protein sequences that disrupt the typical TLR structure, and some species display a pseudogene sequence due to the presence of frameshift mutations and early stop codons. Additionally, TLR15 has low expression levels in holocephalans when compared with other TLR genes. In turn, lungfish also have long TLR15 protein sequences but the protein structure is not compromised. Finally, TLR15 presents several sites under negative selection. Overall, these results suggest that TLR15 is an ancient TLR gene and is experiencing ongoing pseudogenization in early-branching vertebrates.
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Affiliation(s)
- Fabiana Neves
- CIBIO‐InBIO, Research Center in Biodiversity and Genetic Resources, University of Porto, Vairão, Portugal,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal,*Correspondence: Fabiana Neves,
| | - Antonio Muñoz-Mérida
- CIBIO‐InBIO, Research Center in Biodiversity and Genetic Resources, University of Porto, Vairão, Portugal,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal,Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
| | - André M. Machado
- Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal,CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Matosinhos, Portugal
| | - Tereza Almeida
- CIBIO‐InBIO, Research Center in Biodiversity and Genetic Resources, University of Porto, Vairão, Portugal,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
| | - Arnaud Gaigher
- CIBIO‐InBIO, Research Center in Biodiversity and Genetic Resources, University of Porto, Vairão, Portugal,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal,Research Group for Evolutionary Immunogenomics, Max Planck Institute for Evolutionary Biology, Plön, Germany,Research Unit for Evolutionary Immunogenomics, Department of Biology, University of Hamburg, Hamburg, Germany
| | - Pedro J. Esteves
- CIBIO‐InBIO, Research Center in Biodiversity and Genetic Resources, University of Porto, Vairão, Portugal,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal,Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal,CITS - Center of Investigation in Health Technologies, CESPU, Gandra, Portugal
| | - L. Filipe C. Castro
- Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal,CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Matosinhos, Portugal
| | - Ana Veríssimo
- CIBIO‐InBIO, Research Center in Biodiversity and Genetic Resources, University of Porto, Vairão, Portugal,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
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8
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Gomes-de-Sá S, Barradas P, Queirós-Reis L, Matas IM, Amorim I, Cardoso L, Muñoz-Mérida A, Mesquita JR. De Novo Assembly of the Dirofilaria immitis Genome by Long-Read Nanopore-Based Sequencing Technology on an Adult Worm from a Canine Cardiopulmonary Dirofilariosis Case. Animals (Basel) 2022; 12:ani12111342. [PMID: 35681811 PMCID: PMC9179477 DOI: 10.3390/ani12111342] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 05/13/2022] [Accepted: 05/24/2022] [Indexed: 11/29/2022] Open
Abstract
Simple Summary Dirofilaria immitis is a zoonotic parasite that infects canids and other vertebrates. We expanded the use of long-read nanopore-based sequencing technology by performing genomic de novo assembly of a D. immitis specimen retrieved from a canine cardiopulmonary dirofilariasis case by using the ONT MinION platform. We also identified loci previously characterized as being associated to macrocyclic lactone resistance selection pressure. The identification of a resistant zoonotic parasite alerts for the overuse of macrocyclic lactone in the region. Abstract Dirofilaria immitis is a zoonotic parasitic nematode that infects domestic and wild canids, among its vertebrate hosts. The genetic analysis of D. immitis nowadays transcends the need for genetic taxonomy of nematodes, such as the study of resistance to macrocyclic lactone. We expanded the use of long-read nanopore-based sequencing technology on nematodes by performing genomic de novo assembly of a D. immitis specimen retrieved from a canine cardiopulmonary dirofilariasis case using the ONT MinION platform, followed by the study of macrocyclic lactone resistance. The assembled genome of D. immitis consists of 110 contigs with an N50 of 3687191. The genome size is 87899012 and contains a total of 9741 proteins; 6 ribosomal RNAs, with three belonging to the small subunit (18S) and three to the large subunit (28S); and 73 tRNAs. Subsequent analysis of six loci previously characterized as being associated to macrocyclic lactone resistance selection pressure showed that four have a genotype associated with either some loss of efficacy or the resistance phenotype. Considering the zoonotic potential of D. immitis, the identification of a resistant parasite alerts for the overuse of macrocyclic lactone in the region, which poses a potential risk to both veterinary and human public health.
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Affiliation(s)
- Sónia Gomes-de-Sá
- ICBAS—School of Medicine and Biomedical Sciences, Porto University, 4050-313 Porto, Portugal; (S.G.-d.-S.); (L.Q.-R.); (I.A.)
| | - Patrícia Barradas
- Epidemiology Research Unit (EPIUnit), Instituto de Saúde Pública da Universidade do Porto, 4050-600 Porto, Portugal;
- Laboratório para a Investigação Integrativa e Translacional em Saúde Populacional (ITR), 4050-600 Porto, Portugal
- Department of Sciences, University Institute of Health Sciences (IUCS), CESPU, CRL, 4585-116 Gandra, Portugal
| | - Luís Queirós-Reis
- ICBAS—School of Medicine and Biomedical Sciences, Porto University, 4050-313 Porto, Portugal; (S.G.-d.-S.); (L.Q.-R.); (I.A.)
- Epidemiology Research Unit (EPIUnit), Instituto de Saúde Pública da Universidade do Porto, 4050-600 Porto, Portugal;
- Laboratório para a Investigação Integrativa e Translacional em Saúde Populacional (ITR), 4050-600 Porto, Portugal
| | - Isabel M. Matas
- Centro de Investigação em Biodiversidade e Recursos Genéticos (CIBIO/InBIO), Universidade do Porto, Vairão, 4485-661 Porto, Portugal; (I.M.M.); (A.M.-M.)
| | - Irina Amorim
- ICBAS—School of Medicine and Biomedical Sciences, Porto University, 4050-313 Porto, Portugal; (S.G.-d.-S.); (L.Q.-R.); (I.A.)
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), 4220-135 Porto, Portugal
- Institute for Research and Innovation in Health (i3S), University of Porto, 4200-135 Porto, Portugal
| | - Luís Cardoso
- Department of Veterinary Sciences, School of Agrarian and Veterinary Sciences, University of Trás-os-Montes e Alto Douro (UTAD), 5000-801 Vila Real, Portugal;
- Animal and Veterinary Research Centre (CECAV), UTAD, 5000-801 Vila Real, Portugal
| | - Antonio Muñoz-Mérida
- Centro de Investigação em Biodiversidade e Recursos Genéticos (CIBIO/InBIO), Universidade do Porto, Vairão, 4485-661 Porto, Portugal; (I.M.M.); (A.M.-M.)
| | - João R. Mesquita
- ICBAS—School of Medicine and Biomedical Sciences, Porto University, 4050-313 Porto, Portugal; (S.G.-d.-S.); (L.Q.-R.); (I.A.)
- Epidemiology Research Unit (EPIUnit), Instituto de Saúde Pública da Universidade do Porto, 4050-600 Porto, Portugal;
- Laboratório para a Investigação Integrativa e Translacional em Saúde Populacional (ITR), 4050-600 Porto, Portugal
- Correspondence:
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9
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Freitas S, Gazda MA, Rebelo MÂ, Muñoz-Pajares AJ, Vila-Viçosa C, Muñoz-Mérida A, Gonçalves LM, Azevedo-Silva D, Afonso S, Castro I, Castro PH, Sottomayor M, Beja-Pereira A, Tereso J, Ferrand N, Gonçalves E, Martins A, Carneiro M, Azevedo H. Pervasive hybridization with local wild relatives in Western European grapevine varieties. Sci Adv 2021; 7:eabi8584. [PMID: 34797710 PMCID: PMC8604406 DOI: 10.1126/sciadv.abi8584] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Grapevine (Vitis vinifera L.) diversity richness results from a complex domestication history over multiple historical periods. Here, we used whole-genome resequencing to elucidate different aspects of its recent evolutionary history. Our results support a model in which a central domestication event in grapevine was followed by postdomestication hybridization with local wild genotypes, leading to the presence of an introgression signature in modern wine varieties across Western Europe. The strongest signal was associated with a subset of Iberian grapevine varieties showing large introgression tracts. We targeted this study group for further analysis, demonstrating how regions under selection in wild populations from the Iberian Peninsula were preferentially passed on to the cultivated varieties by gene flow. Examination of underlying genes suggests that environmental adaptation played a fundamental role in both the evolution of wild genotypes and the outcome of hybridization with cultivated varieties, supporting a case of adaptive introgression in grapevine.
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Affiliation(s)
- Sara Freitas
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4099-002 Porto, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal
| | - Małgorzata A. Gazda
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4099-002 Porto, Portugal
| | - Miguel Â. Rebelo
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
| | - Antonio J. Muñoz-Pajares
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal
- Departamento de Genética, Facultad de Ciencias, Universidad de Granada, Campus Fuentenueva, 18071 Granada, Spain
| | - Carlos Vila-Viçosa
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4099-002 Porto, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal
- MHNC-UP, Museum of Natural History and Science of the University of Porto–PO Herbarium, University of Porto, Praça Gomes Teixeira, 4099-002 Porto, Portugal
| | - Antonio Muñoz-Mérida
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
| | - Luís M. Gonçalves
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
| | - David Azevedo-Silva
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4099-002 Porto, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal
| | - Sandra Afonso
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal
| | - Isaura Castro
- CITAB, Centre for the Research and Technology of Agro-Environmental and Biological Sciences, Universidade de Trás-os-Montes e Alto Douro, Quinta de Prados, 5000-801 Vila Real, Portugal
| | - Pedro H. Castro
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal
| | - Mariana Sottomayor
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4099-002 Porto, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal
| | - Albano Beja-Pereira
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal
- DGAOT, Faculty of Sciences, Universidade do Porto, Rua Campo Alegre 687, 4169-007 Porto, Portugal
- Sustainable Agrifood Production Research Centre (GreenUPorto), Universidade do Porto, Rua da Agrária 747, 4485-646 Vairão, Portugal
| | - João Tereso
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal
- MHNC-UP, Museum of Natural History and Science of the University of Porto–PO Herbarium, University of Porto, Praça Gomes Teixeira, 4099-002 Porto, Portugal
- Centre for Archaeology, UNIARQ, School of Arts and Humanities, University of Lisbon, 1600-214 Lisbon, Portugal
| | - Nuno Ferrand
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4099-002 Porto, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal
- Department of Zoology, Centre for Ecological Genomics and Wildlife Conservation, University of Johannesburg, 2006 Johannesburg, South Africa
| | - Elsa Gonçalves
- LEAF, Linking Landscape, Environment, Agriculture, and Food, Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, 1349-017 Lisboa, Portugal
- Portuguese Association for Grapevine Diversity-PORVID, Tapada da Ajuda, 1349-017 Lisboa, Portugal
| | - Antero Martins
- LEAF, Linking Landscape, Environment, Agriculture, and Food, Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, 1349-017 Lisboa, Portugal
- Portuguese Association for Grapevine Diversity-PORVID, Tapada da Ajuda, 1349-017 Lisboa, Portugal
| | - Miguel Carneiro
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4099-002 Porto, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal
| | - Herlander Azevedo
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4099-002 Porto, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal
- Corresponding author.
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10
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Almeida T, Ohta Y, Gaigher A, Muñoz-Mérida A, Neves F, Castro LFC, Machado AM, Esteves PJ, Veríssimo A, Flajnik MF. A Highly Complex, MHC-Linked, 350 Million-Year-Old Shark Nonclassical Class I Lineage. J Immunol 2021; 207:824-836. [PMID: 34301841 DOI: 10.4049/jimmunol.2000851] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 05/09/2021] [Indexed: 11/19/2022]
Abstract
Cartilaginous fish, or Chondrichthyes, are the oldest extant vertebrates to possess the MHC and the Ig superfamily-based Ag receptors, the defining genes of the gnathostome adaptive immune system. In this work, we have identified a novel MHC lineage, UEA, a complex multigene nonclassical class I family found in sharks (division Selachii) but not detected in chimaeras (subclass Holocephali) or rays (division Batoidea). This new lineage is distantly related to the previously reported nonclassical class I lineage UCA, which appears to be present only in dogfish sharks (order Squaliformes). UEA lacks conservation of the nine invariant residues in the peptide (ligand)-binding regions (PBR) that bind to the N and C termini of bound peptide in most vertebrate classical class I proteins, which are replaced by relatively hydrophobic residues compared with the classical UAA. In fact, UEA and UCA proteins have the most hydrophobic-predicted PBR of all identified chondrichthyan class I molecules. UEA genes detected in the whale shark and bamboo shark genome projects are MHC linked. Consistent with UEA comprising a very large gene family, we detected weak expression in different tissues of the nurse shark via Northern blotting and RNA sequencing. UEA genes fall into three sublineages with unique characteristics in the PBR. UEA shares structural and genetic features with certain nonclassical class I genes in other vertebrates, such as the highly complex XNC nonclassical class I genes in Xenopus, and we anticipate that each shark gene, or at least each sublineage, will have a unique function, perhaps in bacterial defense.
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Affiliation(s)
- Tereza Almeida
- CIBIO-InBIO, Centro de Investigacão em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Universidade do Porto, Vairão, Porto, Portugal.,Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal.,Department of Microbiology and Immunology, University of Maryland Baltimore, Baltimore, MD; and
| | - Yuko Ohta
- Department of Microbiology and Immunology, University of Maryland Baltimore, Baltimore, MD; and
| | - Arnaud Gaigher
- CIBIO-InBIO, Centro de Investigacão em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Universidade do Porto, Vairão, Porto, Portugal
| | - Antonio Muñoz-Mérida
- CIBIO-InBIO, Centro de Investigacão em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Universidade do Porto, Vairão, Porto, Portugal
| | - Fabiana Neves
- CIBIO-InBIO, Centro de Investigacão em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Universidade do Porto, Vairão, Porto, Portugal
| | - L Filipe C Castro
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal.,Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Porto, Portugal
| | - André M Machado
- Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Porto, Portugal
| | - Pedro J Esteves
- CIBIO-InBIO, Centro de Investigacão em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Universidade do Porto, Vairão, Porto, Portugal.,Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal
| | - Ana Veríssimo
- CIBIO-InBIO, Centro de Investigacão em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Universidade do Porto, Vairão, Porto, Portugal
| | - Martin F Flajnik
- Department of Microbiology and Immunology, University of Maryland Baltimore, Baltimore, MD; and
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11
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Almeida T, Gaigher A, Muñoz-Mérida A, Neves F, Castro LFC, Flajnik MF, Ohta Y, Esteves PJ, Veríssimo A. Cartilaginous fish class II genes reveal unprecedented old allelic lineages and confirm the late evolutionary emergence of DM. Mol Immunol 2020; 128:125-138. [PMID: 33126081 PMCID: PMC8010645 DOI: 10.1016/j.molimm.2020.10.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [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: 08/14/2020] [Revised: 09/22/2020] [Accepted: 10/03/2020] [Indexed: 12/16/2022]
Abstract
Cartilaginous fish (chimaeras, rays and sharks) are the most basal extant jawed vertebrates with an adaptive immune system based on the Major Histocompatibility Complex (MHC). Despite being a key taxon in the evolution of vertebrate adaptive immunity, no comprehensive characterization of MHC class II genes has been undertaken for the group. We performed extensive bioinformatic searches on a taxonomically diverse dataset of transcriptomes and genomes of cartilaginous fish targeting MHC class II sequences. Class IIα and IIβ sequences were retrieved from all taxa analyzed and showed typical features of classical class II genes. Phylogenetic trees of the immunoglobulin superfamily domain showed two divergent and remarkably ancient lineages of class II genes in Selachians (sharks), originating >350 million years ago. Close linkage of lineage-specific pairs of IIα and IIβ genes was found, confirming previous results, with genes from distinct lineages segregating as alleles. Nonclassical class II DM sequences were not retrieved from these data and classical class II sequences lacked the conserved residues shown to interact with DM molecules, supporting claims that the DM system arose only in the lobe-finned fish lineage leading to tetrapods. Based on our search methods, other divergent class II genes are unlikely in cartilaginous fish.
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Affiliation(s)
- Tereza Almeida
- CIBIO-InBIO, Centro de Investigacão em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, 4485-661 Vairão, Portugal; Department of Biology, Faculty of Sciences - University of Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal; Department of Microbiology and Immunology, University of Maryland, Baltimore, MD 21201, USA
| | - Arnaud Gaigher
- CIBIO-InBIO, Centro de Investigacão em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, 4485-661 Vairão, Portugal
| | - Antonio Muñoz-Mérida
- CIBIO-InBIO, Centro de Investigacão em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, 4485-661 Vairão, Portugal
| | - Fabiana Neves
- CIBIO-InBIO, Centro de Investigacão em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, 4485-661 Vairão, Portugal
| | - L Filipe C Castro
- Department of Biology, Faculty of Sciences - University of Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal; CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, 4450-208 Matosinhos, Portugal
| | - Martin F Flajnik
- Department of Microbiology and Immunology, University of Maryland, Baltimore, MD 21201, USA
| | - Yuko Ohta
- Department of Microbiology and Immunology, University of Maryland, Baltimore, MD 21201, USA
| | - Pedro J Esteves
- CIBIO-InBIO, Centro de Investigacão em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, 4485-661 Vairão, Portugal; Department of Biology, Faculty of Sciences - University of Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal
| | - Ana Veríssimo
- CIBIO-InBIO, Centro de Investigacão em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, 4485-661 Vairão, Portugal.
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12
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Estrella-González MJ, Suárez-Estrella F, Jurado MM, López MJ, López-González JA, Siles-Castellano AB, Muñoz-Mérida A, Moreno J. Uncovering new indicators to predict stability, maturity and biodiversity of compost on an industrial scale. Bioresour Technol 2020; 313:123557. [PMID: 32512428 DOI: 10.1016/j.biortech.2020.123557] [Citation(s) in RCA: 5] [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: 03/17/2020] [Revised: 05/15/2020] [Accepted: 05/17/2020] [Indexed: 06/11/2023]
Abstract
Currently, the metagenomic study of the composting process has gained great importance since it has allowed the identification of the existence of microorganisms that, until now, had not been isolated during the process by traditional techniques. However, it is still complex to determine which bioindicators could reveal the degree of maturity and stability of a particular compost. Thereby, the main objective of this work was to demonstrate the possible correlation between traditional parameters of maturity and stability of compost, with other indicators of biodiversity in products highly heterogeneous from composting processes on an industrial scale. The results demonstrated the enormous influence of the raw materials in characterizing the products obtained. Even so, important relationships were established between the Chao1 and Shannon indexes, and certain parameters related to the maturity, stability and toxicity of the samples, such as nitrification index, humification rate, phenolic content, germination index or oxygen consumption.
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Affiliation(s)
- M J Estrella-González
- Department of Biology and Geology, CITE II-B, University of Almería, Agrifood Campus of International Excellence, ceiA3, 04120, CIAIMBITAL, Almería, Spain
| | - F Suárez-Estrella
- Department of Biology and Geology, CITE II-B, University of Almería, Agrifood Campus of International Excellence, ceiA3, 04120, CIAIMBITAL, Almería, Spain.
| | - M M Jurado
- Department of Biology and Geology, CITE II-B, University of Almería, Agrifood Campus of International Excellence, ceiA3, 04120, CIAIMBITAL, Almería, Spain
| | - M J López
- Department of Biology and Geology, CITE II-B, University of Almería, Agrifood Campus of International Excellence, ceiA3, 04120, CIAIMBITAL, Almería, Spain
| | - J A López-González
- Department of Biology and Geology, CITE II-B, University of Almería, Agrifood Campus of International Excellence, ceiA3, 04120, CIAIMBITAL, Almería, Spain
| | - A B Siles-Castellano
- Department of Biology and Geology, CITE II-B, University of Almería, Agrifood Campus of International Excellence, ceiA3, 04120, CIAIMBITAL, Almería, Spain
| | - A Muñoz-Mérida
- CIBIO-InBIO, Universidade do Porto, Campus de Vairão, Rua Padre Armando Quintas, 4485-661 Vairão, Portugal
| | - J Moreno
- Department of Biology and Geology, CITE II-B, University of Almería, Agrifood Campus of International Excellence, ceiA3, 04120, CIAIMBITAL, Almería, Spain
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13
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Belaj A, de la Rosa R, Lorite IJ, Mariotti R, Cultrera NGM, Beuzón CR, González-Plaza JJ, Muñoz-Mérida A, Trelles O, Baldoni L. Usefulness of a New Large Set of High Throughput EST-SNP Markers as a Tool for Olive Germplasm Collection Management. Front Plant Sci 2018; 9:1320. [PMID: 30298075 PMCID: PMC6160578 DOI: 10.3389/fpls.2018.01320] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 08/22/2018] [Indexed: 05/08/2023]
Abstract
Germplasm collections are basic tools for conservation, characterization, and efficient use of olive genetic resources. The identification of the olive cultivars maintained in the collections is an important ongoing task which has been performed by both, morphological and molecular markers. In the present study, based on the sequencing results of previous genomic projects, a new set of 1,043 EST-SNP markers has been identified. In order to evaluate its discrimination capacity and utility in diversity studies, this set of markers was used in a representative number of accessions from 20 different olive growing countries and maintained at the World Olive Germplasm Collection of IFAPA Centre 'Alameda del Obispo' (Córdoba, Spain), one of the world's largest olive germplasm bank. Thus, the cultivated material included: cultivars belonging to previously defined core collections by means of SSR markers and agronomical traits, well known homonymy cases, possible redundancies previously identified in the collection, and recently introduced accessions. Marker stability was tested in repeated analyses of a selected number of accessions, as well as in different trees and accessions belonging to the same cultivar. In addition, 15 genotypes from a cross 'Picual' × 'Arbequina' cultivars from the IFAPA olive breeding program and a set of 89 wild genotypes were also included in the study. Our results indicate that, despite their relatively wide variability, the new set of EST-SNPs displayed lower levels of genetic diversity than SSRs in the set of olive core collections tested. However, the EST-SNP markers displayed consistent and reliable results from different plant material sources and plant propagation events. The EST-SNPs revealed a clear cut off between inter- and intra-cultivar variation in olive. Besides, they were able to reliably discriminate among different accessions, to detect possible homonymy cases as well as efficiently ascertain the presence of redundant germplasm in the collection. Additionally, these markers were highly transferable to the wild genotypes. These results, together with the low genotyping error rates and the easy and fully automated procedure used to get the genotyping data, validate the new set of EST-SNPs as possible markers of choice for olive cultivar identification.
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Affiliation(s)
- Angjelina Belaj
- IFAPA Centro Alameda del Obispo, Córdoba, Spain
- *Correspondence: Angjelina Belaj,
| | | | | | | | | | - Carmen R. Beuzón
- Instituto de Hortofruticultura Subtropical y Mediterranea, Universidad de Málaga-Consejo Superior de Investigaciones Científicas, Málaga, Spain
| | - J. J. González-Plaza
- Instituto de Hortofruticultura Subtropical y Mediterranea, Universidad de Málaga-Consejo Superior de Investigaciones Científicas, Málaga, Spain
- Present address: J. J. González-Plaza, Faculty of Forestry and Wood Sciences, Czech University of Life Sciences, Prague, Czechia
| | - A. Muñoz-Mérida
- CIBIO, InBIO – Research Network in Biodiversity and Evolutionary Biology, University of Porto, Porto, Portugal
| | - O. Trelles
- Department of Integrated Bioinformatics, National Institute for Bioinformatics, Universidad de Málaga, Málaga, Spain
| | - Luciana Baldoni
- CNR – Institute of Biosciences and Bioresources, Perugia, Italy
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14
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Casimiro-Soriguer CS, Muñoz-Mérida A, Pérez-Pulido AJ. Sma3s: A universal tool for easy functional annotation of proteomes and transcriptomes. Proteomics 2017; 17. [PMID: 28544705 DOI: 10.1002/pmic.201700071] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [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: 02/18/2017] [Revised: 04/23/2017] [Accepted: 05/16/2017] [Indexed: 11/10/2022]
Abstract
The current cheapening of next-generation sequencing has led to an enormous growth in the number of sequenced genomes and transcriptomes, allowing wet labs to get the sequences from their organisms of study. To make the most of these data, one of the first things that should be done is the functional annotation of the protein-coding genes. But it used to be a slow and tedious step that can involve the characterization of thousands of sequences. Sma3s is an accurate computational tool for annotating proteins in an unattended way. Now, we have developed a completely new version, which includes functionalities that will be of utility for fundamental and applied science. Currently, the results provide functional categories such as biological processes, which become useful for both characterizing particular sequence datasets and comparing results from different projects. But one of the most important implemented innovations is that it has now low computational requirements, and the complete annotation of a simple proteome or transcriptome usually takes around 24 hours in a personal computer. Sma3s has been tested with a large amount of complete proteomes and transcriptomes, and it has demonstrated its potential in health science and other specific projects.
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Affiliation(s)
| | - Antonio Muñoz-Mérida
- CIBIO-InBIO, Research Network in Biodiversity and Evolutionary Biology, Universidade do Porto, Vairão, Portugal
| | - Antonio J Pérez-Pulido
- Centro Andaluz de Biología del Desarrollo (CABD-CSIC-JA), Universidad Pablo de Olavide, Sevilla, Spain
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15
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Castro PH, Lilay GH, Muñoz-Mérida A, Schjoerring JK, Azevedo H, Assunção AGL. Phylogenetic analysis of F-bZIP transcription factors indicates conservation of the zinc deficiency response across land plants. Sci Rep 2017. [PMID: 28630437 PMCID: PMC5476651 DOI: 10.1038/s41598-017-03903-6] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [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] [Indexed: 11/20/2022] Open
Abstract
Basic leucine zipper (bZIP) transcription factors control important developmental and physiological processes in plants. In Arabidopsis thaliana, the three gene F-bZIP subfamily has been associated with zinc deficiency and salt stress response. Benefiting from the present abundance of plant genomic data, we performed an evolutionary and structural characterization of plant F-bZIPs. We observed divergence during seed plant evolution, into two groups and inferred different selective pressures for each. Group 1 contains AtbZIP19 and AtbZIP23 and appears more conserved, whereas Group 2, containing AtbZIP24, is more prone to gene loss and expansion events. Transcriptomic and experimental data reinforced AtbZIP19/23 as pivotal regulators of the zinc deficiency response, mostly via the activation of genes from the ZIP metal transporter family, and revealed that they are the main regulatory switch of AtZIP4. A survey of AtZIP4 orthologs promoters across different plant taxa revealed an enrichment of the Zinc Deficiency Response Element (ZDRE) to which both AtbZIP19/23 bind. Overall, our results indicate that while the AtbZIP24 function in the regulation of the salt stress response may be the result of neo-functionalization, the AtbZIP19/23 function in the regulation of the zinc deficiency response may be conserved in land plants (Embryophytes).
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Affiliation(s)
- Pedro Humberto Castro
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871, Copenhagen, Denmark
| | - Grmay H Lilay
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871, Copenhagen, Denmark
| | - Antonio Muñoz-Mérida
- CIBIO, InBIO - Research Network in Biodiversity and Evolutionary Biology, University of Porto, Campus Agrário de Vairão, 4485-661, Vairão, Portugal
| | - Jan K Schjoerring
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871, Copenhagen, Denmark
| | - Herlânder Azevedo
- CIBIO, InBIO - Research Network in Biodiversity and Evolutionary Biology, University of Porto, Campus Agrário de Vairão, 4485-661, Vairão, Portugal.,Department of Biology, Faculty of Sciences, University of Porto, Rua Campo Alegre, 4169-007, Porto, Portugal
| | - Ana G L Assunção
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871, Copenhagen, Denmark. .,CIBIO, InBIO - Research Network in Biodiversity and Evolutionary Biology, University of Porto, Campus Agrário de Vairão, 4485-661, Vairão, Portugal.
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16
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Amil-Ruiz F, Garrido-Gala J, Gadea J, Blanco-Portales R, Muñoz-Mérida A, Trelles O, de los Santos B, Arroyo FT, Aguado-Puig A, Romero F, Mercado JÁ, Pliego-Alfaro F, Muñoz-Blanco J, Caballero JL. Partial Activation of SA- and JA-Defensive Pathways in Strawberry upon Colletotrichum acutatum Interaction. Front Plant Sci 2016; 7:1036. [PMID: 27471515 PMCID: PMC4945649 DOI: 10.3389/fpls.2016.01036] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 07/01/2016] [Indexed: 05/04/2023]
Abstract
Understanding the nature of pathogen host interaction may help improve strawberry (Fragaria × ananassa) cultivars. Plant resistance to pathogenic agents usually operates through a complex network of defense mechanisms mediated by a diverse array of signaling molecules. In strawberry, resistance to a variety of pathogens has been reported to be mostly polygenic and quantitatively inherited, making it difficult to associate molecular markers with disease resistance genes. Colletotrichum acutatum spp. is a major strawberry pathogen, and completely resistant cultivars have not been reported. Moreover, strawberry defense network components and mechanisms remain largely unknown and poorly understood. Assessment of the strawberry response to C. acutatum included a global transcript analysis, and acidic hormones SA and JA measurements were analyzed after challenge with the pathogen. Induction of transcripts corresponding to the SA and JA signaling pathways and key genes controlling major steps within these defense pathways was detected. Accordingly, SA and JA accumulated in strawberry after infection. Contrastingly, induction of several important SA, JA, and oxidative stress-responsive defense genes, including FaPR1-1, FaLOX2, FaJAR1, FaPDF1, and FaGST1, was not detected, which suggests that specific branches in these defense pathways (those leading to FaPR1-2, FaPR2-1, FaPR2-2, FaAOS, FaPR5, and FaPR10) were activated. Our results reveal that specific aspects in SA and JA dependent signaling pathways are activated in strawberry upon interaction with C. acutatum. Certain described defense-associated transcripts related to these two known signaling pathways do not increase in abundance following infection. This finding suggests new insight into a specific putative molecular strategy for defense against this pathogen.
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Affiliation(s)
- Francisco Amil-Ruiz
- Departamento de Bioquímica y Biología Molecular e Instituto Andaluz de Biotecnología, Edificio Severo Ochoa (C6), Universidad de CórdobaCórdoba, Spain
| | - José Garrido-Gala
- Departamento de Bioquímica y Biología Molecular e Instituto Andaluz de Biotecnología, Edificio Severo Ochoa (C6), Universidad de CórdobaCórdoba, Spain
| | - José Gadea
- Instituto de Biología Molecular y Celular de Plantas, Universidad Politécnica de Valencia–Consejo Superior de Investigaciones CientíficasValencia, Spain
| | - Rosario Blanco-Portales
- Departamento de Bioquímica y Biología Molecular e Instituto Andaluz de Biotecnología, Edificio Severo Ochoa (C6), Universidad de CórdobaCórdoba, Spain
| | - Antonio Muñoz-Mérida
- Departamento de Arquitectura de Computación, Universidad de Málaga, Campus de TeatinosMálaga, Spain
| | - Oswaldo Trelles
- Departamento de Arquitectura de Computación, Universidad de Málaga, Campus de TeatinosMálaga, Spain
| | - Berta de los Santos
- Centro Andalusian Institute of Agricultural and Fishering Research and Training (IFAPA) Las Torres-Tomejil, CAPMA–Junta de AndalucíaSevilla, Spain
| | - Francisco T. Arroyo
- Centro Andalusian Institute of Agricultural and Fishering Research and Training (IFAPA) Las Torres-Tomejil, CAPMA–Junta de AndalucíaSevilla, Spain
| | - Ana Aguado-Puig
- Centro Andalusian Institute of Agricultural and Fishering Research and Training (IFAPA) Las Torres-Tomejil, CAPMA–Junta de AndalucíaSevilla, Spain
| | - Fernando Romero
- Centro Andalusian Institute of Agricultural and Fishering Research and Training (IFAPA) Las Torres-Tomejil, CAPMA–Junta de AndalucíaSevilla, Spain
| | - José-Ángel Mercado
- Departamento de Biología Vegetal, Facultad de Ciencias, Universidad de Málaga, Campus de TeatinosMálaga, Spain
| | - Fernando Pliego-Alfaro
- Departamento de Biología Vegetal, Facultad de Ciencias, Universidad de Málaga, Campus de TeatinosMálaga, Spain
| | - Juan Muñoz-Blanco
- Departamento de Bioquímica y Biología Molecular e Instituto Andaluz de Biotecnología, Edificio Severo Ochoa (C6), Universidad de CórdobaCórdoba, Spain
| | - José L. Caballero
- Departamento de Bioquímica y Biología Molecular e Instituto Andaluz de Biotecnología, Edificio Severo Ochoa (C6), Universidad de CórdobaCórdoba, Spain
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17
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Azevedo H, Azinheiro SG, Muñoz-Mérida A, Castro PH, Huettel B, Aarts MG, Assunção AG. Transcriptomic profiling of Arabidopsis gene expression in response to varying micronutrient zinc supply. Genom Data 2016; 7:256-8. [PMID: 26981422 PMCID: PMC4778672 DOI: 10.1016/j.gdata.2016.01.021] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 01/30/2016] [Indexed: 12/31/2022]
Abstract
Deficiency of the micronutrient zinc is a widespread condition in agricultural soils, causing a negative impact on crop quality and yield. Nevertheless, there is an insufficient knowledge on the regulatory and molecular mechanisms underlying the plant response to inadequate zinc nutrition [1]. This information should contribute to the development of plant-based solutions with improved nutrient-use-efficiency traits in crops. Previously, the transcription factors bZIP19 and bZIP23 were identified as essential regulators of the response to zinc deficiency in Arabidopsis thaliana [2]. A microarray experiment comparing gene expression between roots of wild-type and the mutant bzip19 bzip23, exposed to zinc deficiency, led to the identification of differentially expressed genes related with zinc homeostasis, namely its transport and plant internal translocation [2]. Here, we provide the detailed methodology, bioinformatics analysis and quality controls related to the microarray gene expression profiling published by Assunção and co-workers [2]. Most significantly, the present dataset comprises new experimental variables, including analysis of shoot tissue, and zinc sufficiency and excess supply. Thus, it expands from 8 to 42 microarrays hybridizations, which have been deposited at the Gene Expression Omnibus (GEO) under the accession number GSE77286. Overall, it provides a resource for research on the molecular basis and regulatory events of the plant response to zinc supply, emphasizing the importance of Arabidopsis bZIP19 and bZIP23 transcription factors.
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Affiliation(s)
- Herlânder Azevedo
- CIBIO-InBIO, Research Network in Biodiversity and Evolutionary Biology, Universidade do Porto, Campus Agrário de Vairão, 4485-661 Vairão, Portugal
| | - Sarah Gaspar Azinheiro
- CIBIO-InBIO, Research Network in Biodiversity and Evolutionary Biology, Universidade do Porto, Campus Agrário de Vairão, 4485-661 Vairão, Portugal
| | - Antonio Muñoz-Mérida
- CIBIO-InBIO, Research Network in Biodiversity and Evolutionary Biology, Universidade do Porto, Campus Agrário de Vairão, 4485-661 Vairão, Portugal
| | - Pedro Humberto Castro
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871, Denmark
| | - Bruno Huettel
- Max Planck Institute for Plant Breeding ADIS/DNA Core Facility, D-50829 Cologne, Germany
| | - Mark G.M. Aarts
- Laboratory of Genetics, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Ana G.L. Assunção
- CIBIO-InBIO, Research Network in Biodiversity and Evolutionary Biology, Universidade do Porto, Campus Agrário de Vairão, 4485-661 Vairão, Portugal
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871, Denmark
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18
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González-Plaza JJ, Ortiz-Martín I, Muñoz-Mérida A, García-López C, Sánchez-Sevilla JF, Luque F, Trelles O, Bejarano ER, De La Rosa R, Valpuesta V, Beuzón CR. Transcriptomic Analysis Using Olive Varieties and Breeding Progenies Identifies Candidate Genes Involved in Plant Architecture. Front Plant Sci 2016; 7:240. [PMID: 26973682 PMCID: PMC4773642 DOI: 10.3389/fpls.2016.00240] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 02/12/2016] [Indexed: 05/20/2023]
Abstract
Plant architecture is a critical trait in fruit crops that can significantly influence yield, pruning, planting density and harvesting. Little is known about how plant architecture is genetically determined in olive, were most of the existing varieties are traditional with an architecture poorly suited for modern growing and harvesting systems. In the present study, we have carried out microarray analysis of meristematic tissue to compare expression profiles of olive varieties displaying differences in architecture, as well as seedlings from their cross pooled on the basis of their sharing architecture-related phenotypes. The microarray used, previously developed by our group has already been applied to identify candidates genes involved in regulating juvenile to adult transition in the shoot apex of seedlings. Varieties with distinct architecture phenotypes and individuals from segregating progenies displaying opposite architecture features were used to link phenotype to expression. Here, we identify 2252 differentially expressed genes (DEGs) associated to differences in plant architecture. Microarray results were validated by quantitative RT-PCR carried out on genes with functional annotation likely related to plant architecture. Twelve of these genes were further analyzed in individual seedlings of the corresponding pool. We also examined Arabidopsis mutants in putative orthologs of these targeted candidate genes, finding altered architecture for most of them. This supports a functional conservation between species and potential biological relevance of the candidate genes identified. This study is the first to identify genes associated to plant architecture in olive, and the results obtained could be of great help in future programs aimed at selecting phenotypes adapted to modern cultivation practices in this species.
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Affiliation(s)
- Juan J. González-Plaza
- Departamento de Biología Celular, Genética y Fisiología, Facultad de Ciencias, Instituto de Hortofruticultura Subtropical y Mediterránea, Universidad de Málaga - Consejo Superior de Investigaciones CientíficasMálaga, Spain
| | - Inmaculada Ortiz-Martín
- Departamento de Biología Celular, Genética y Fisiología, Facultad de Ciencias, Instituto de Hortofruticultura Subtropical y Mediterránea, Universidad de Málaga - Consejo Superior de Investigaciones CientíficasMálaga, Spain
| | - Antonio Muñoz-Mérida
- Departamento Arquitectura de Computadores, Escuela Técnica Superior de Ingeniería Informática, Universidad de MálagaMálaga, Spain
| | - Carmen García-López
- Center for Advanced Studies in Olive Grove and Olive Oils, University of JaénJaén, Spain
| | | | - Francisco Luque
- Center for Advanced Studies in Olive Grove and Olive Oils, University of JaénJaén, Spain
| | - Oswaldo Trelles
- Departamento Arquitectura de Computadores, Escuela Técnica Superior de Ingeniería Informática, Universidad de MálagaMálaga, Spain
| | - Eduardo R. Bejarano
- Departamento de Biología Celular, Genética y Fisiología, Facultad de Ciencias, Instituto de Hortofruticultura Subtropical y Mediterránea, Universidad de Málaga - Consejo Superior de Investigaciones CientíficasMálaga, Spain
| | | | - Victoriano Valpuesta
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Instituto de Hortofruticultura Subtropical y Mediterránea, Universidad de Málaga - Consejo Superior de Investigaciones CientíficasMálaga, Spain
| | - Carmen R. Beuzón
- Departamento de Biología Celular, Genética y Fisiología, Facultad de Ciencias, Instituto de Hortofruticultura Subtropical y Mediterránea, Universidad de Málaga - Consejo Superior de Investigaciones CientíficasMálaga, Spain
- *Correspondence: Carmen R. Beuzón
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19
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Abstract
Automatic sequence annotation is an essential component of modern 'omics' studies, which aim to extract information from large collections of sequence data. Most existing tools use sequence homology to establish evolutionary relationships and assign putative functions to sequences. However, it can be difficult to define a similarity threshold that achieves sufficient coverage without sacrificing annotation quality. Defining the correct configuration is critical and can be challenging for non-specialist users. Thus, the development of robust automatic annotation techniques that generate high-quality annotations without needing expert knowledge would be very valuable for the research community. We present Sma3s, a tool for automatically annotating very large collections of biological sequences from any kind of gene library or genome. Sma3s is composed of three modules that progressively annotate query sequences using either: (i) very similar homologues, (ii) orthologous sequences or (iii) terms enriched in groups of homologous sequences. We trained the system using several random sets of known sequences, demonstrating average sensitivity and specificity values of ~85%. In conclusion, Sma3s is a versatile tool for high-throughput annotation of a wide variety of sequence datasets that outperforms the accuracy of other well-established annotation algorithms, and it can enrich existing database annotations and uncover previously hidden features. Importantly, Sma3s has already been used in the functional annotation of two published transcriptomes.
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Affiliation(s)
- Antonio Muñoz-Mérida
- Integrated Bioinformatics, National Institute for Bioinformatics, University of Málaga, Campus de Teatinos, Spain
| | - Enrique Viguera
- Cellular Biology, Genetics and Physiology Department, University of Málaga, Campus de Teatinos, Spain
| | - M Gonzalo Claros
- Molecular Biology and Biochemistry Department, University of Málaga, Campus de Teatinos, Spain
| | - Oswaldo Trelles
- Integrated Bioinformatics, National Institute for Bioinformatics, University of Málaga, Campus de Teatinos, Spain Computer Architecture Department, University of Málaga, Campus de Teatinos, Spain
| | - Antonio J Pérez-Pulido
- Centro Andaluz de Biología del Desarrollo (CABD, UPO-CSIC-JA), Facultad de Ciencias Experimentales (Área de Genética), Universidad Pablo de Olavide, Sevilla 41013, Spain
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20
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Muñoz-Mérida A, González-Plaza JJ, Cañada A, Blanco AM, García-López MDC, Rodríguez JM, Pedrola L, Sicardo MD, Hernández ML, De la Rosa R, Belaj A, Gil-Borja M, Luque F, Martínez-Rivas JM, Pisano DG, Trelles O, Valpuesta V, Beuzón CR. De novo assembly and functional annotation of the olive (Olea europaea) transcriptome. DNA Res 2013; 20:93-108. [PMID: 23297299 PMCID: PMC3576661 DOI: 10.1093/dnares/dss036] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [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] [Indexed: 11/26/2022] Open
Abstract
Olive breeding programmes are focused on selecting for traits as short juvenile period, plant architecture suited for mechanical harvest, or oil characteristics, including fatty acid composition, phenolic, and volatile compounds to suit new markets. Understanding the molecular basis of these characteristics and improving the efficiency of such breeding programmes require the development of genomic information and tools. However, despite its economic relevance, genomic information on olive or closely related species is still scarce. We have applied Sanger and 454 pyrosequencing technologies to generate close to 2 million reads from 12 cDNA libraries obtained from the Picual, Arbequina, and Lechin de Sevilla cultivars and seedlings from a segregating progeny of a Picual × Arbequina cross. The libraries include fruit mesocarp and seeds at three relevant developmental stages, young stems and leaves, active juvenile and adult buds as well as dormant buds, and juvenile and adult roots. The reads were assembled by library or tissue and then assembled together into 81 020 unigenes with an average size of 496 bases. Here, we report their assembly and their functional annotation.
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Affiliation(s)
- Antonio Muñoz-Mérida
- Department of Integrated Bioinformatics, National Institute for Bioinformatics, University of Málaga, Campus de Teatinos, Málaga, Spain
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21
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Lima-Silva V, Rosado A, Amorim-Silva V, Muñoz-Mérida A, Pons C, Bombarely A, Trelles O, Fernández-Muñoz R, Granell A, Valpuesta V, Botella MÁ. Genetic and genome-wide transcriptomic analyses identify co-regulation of oxidative response and hormone transcript abundance with vitamin C content in tomato fruit. BMC Genomics 2012; 13:187. [PMID: 22583865 PMCID: PMC3462723 DOI: 10.1186/1471-2164-13-187] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [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: 12/07/2011] [Accepted: 04/25/2012] [Indexed: 12/02/2022] Open
Abstract
Background L-ascorbic acid (AsA; vitamin C) is essential for all living plants where it functions as the main hydrosoluble antioxidant. It has diverse roles in the regulation of plant cell growth and expansion, photosynthesis, and hormone-regulated processes. AsA is also an essential component of the human diet, being tomato fruit one of the main sources of this vitamin. To identify genes responsible for AsA content in tomato fruit, transcriptomic studies followed by clustering analysis were applied to two groups of fruits with contrasting AsA content. These fruits were identified after AsA profiling of an F8 Recombinant Inbred Line (RIL) population generated from a cross between the domesticated species Solanum lycopersicum and the wild relative Solanum pimpinellifollium. Results We found large variability in AsA content within the RIL population with individual RILs with up to 4-fold difference in AsA content. Transcriptomic analysis identified genes whose expression correlated either positively (PVC genes) or negatively (NVC genes) with the AsA content of the fruits. Cluster analysis using SOTA allowed the identification of subsets of co-regulated genes mainly involved in hormones signaling, such as ethylene, ABA, gibberellin and auxin, rather than any of the known AsA biosynthetic genes. Data mining of the corresponding PVC and NVC orthologs in Arabidopis databases identified flagellin and other ROS-producing processes as cues resulting in differential regulation of a high percentage of the genes from both groups of co-regulated genes; more specifically, 26.6% of the orthologous PVC genes, and 15.5% of the orthologous NVC genes were induced and repressed, respectively, under flagellin22 treatment in Arabidopsis thaliana. Conclusion Results here reported indicate that the content of AsA in red tomato fruit from our selected RILs are not correlated with the expression of genes involved in its biosynthesis. On the contrary, the data presented here supports that AsA content in tomato fruit co-regulates with genes involved in hormone signaling and they are dependent on the oxidative status of the fruit.
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Affiliation(s)
- Viviana Lima-Silva
- Departamento Biología Molecular y Bioquímica, Instituto de Hortofruticultura Subtropical y Mediterránea, Universidad de Málaga-Consejo Superior de Investigaciones Científicas, Universidad de Málaga, 29071, Málaga, Spain
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Muñoz-Mérida A, Perkins JR, Viguera E, Thode G, Bejarano ER, Pérez-Pulido AJ. Semirna: Searching for Plant miRNAs Using Target Sequences. OMICS: A Journal of Integrative Biology 2012; 16:168-77. [DOI: 10.1089/omi.2011.0115] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Antonio Muñoz-Mérida
- Departamento de Arquitectura de Computadores, Universidad de Málaga, Málaga, Spain
| | - James R. Perkins
- Institute of Structural and Molecular Biology, University College London, London, United Kingdom
| | - Enrique Viguera
- Departamento de Biología Cellular, Genética y Fisiología, Universidad de Málaga, Málaga, Spain
| | - Guillermo Thode
- Departamento de Biología Cellular, Genética y Fisiología, Universidad de Málaga, Málaga, Spain
| | - Eduardo R. Bejarano
- Departamento de Biología Cellular, Genética y Fisiología, Universidad de Málaga, Málaga, Spain
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora,” Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Málagna, Spain
| | - Antonio J. Pérez-Pulido
- Centro Andaluz de Biología del Desarrollo (CABD), CSIC-UPO, Facultad de Ciencias Experimentales (Área de Genética), Universidad Pablo de Olavide, Sevilla, Spain
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23
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Ramírez S, Muñoz-Mérida A, Karlsson J, García M, Pérez-Pulido AJ, Claros MG, Trelles O. MOWServ: a web client for integration of bioinformatic resources. Nucleic Acids Res 2010; 38:W671-6. [PMID: 20525794 PMCID: PMC2896175 DOI: 10.1093/nar/gkq497] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [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] [Indexed: 11/12/2022] Open
Abstract
The productivity of any scientist is affected by cumbersome, tedious and time-consuming tasks that try to make the heterogeneous web services compatible so that they can be useful in their research. MOWServ, the bioinformatic platform offered by the Spanish National Institute of Bioinformatics, was released to provide integrated access to databases and analytical tools. Since its release, the number of available services has grown dramatically, and it has become one of the main contributors of registered services in the EMBRACE Biocatalogue. The ontology that enables most of the web-service compatibility has been curated, improved and extended. The service discovery has been greatly enhanced by Magallanes software and biodataSF. User data are securely stored on the main server by an authentication protocol that enables the monitoring of current or already-finished user's tasks, as well as the pipelining of successive data processing services. The BioMoby standard has been greatly extended with the new features included in the MOWServ, such as management of additional information (metadata such as extended descriptions, keywords and datafile examples), a qualified registry, error handling, asynchronous services and service replication. All of them have increased the MOWServ service quality, usability and robustness. MOWServ is available at http://www.inab.org/MOWServ/ and has a mirror at http://www.bitlab-es.com/MOWServ/.
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Affiliation(s)
- Sergio Ramírez
- Departamento Arquitectura de Computadores, Escuela Técnica Superior de Ingeniería Informática, Universidad de Málaga, Málaga, Spain
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