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Liao J, Wei X, Tao K, Deng G, Shu J, Qiao Q, Chen G, Wei Z, Fan M, Saud S, Fahad S, Chen S. Phenoloxidases: catechol oxidase - the temporary employer and laccase - the rising star of vascular plants. HORTICULTURE RESEARCH 2023; 10:uhad102. [PMID: 37786731 PMCID: PMC10541563 DOI: 10.1093/hr/uhad102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 05/16/2023] [Accepted: 05/05/2023] [Indexed: 10/04/2023]
Abstract
Phenolics are vital for the adaptation of plants to terrestrial habitats and for species diversity. Phenoloxidases (catechol oxidases, COs, and laccases, LACs) are responsible for the oxidation and polymerization of phenolics. However, their origin, evolution, and differential roles during plant development and land colonization are unclear. We performed the phylogeny, domain, amino acids, compositional biases, and intron analyses to clarify the origin and evolution of COs and LACs, and analysed the structure, selective pressure, and chloroplast targeting to understand the species-dependent distribution of COs. We found that Streptophyta COs were not homologous to the Chlorophyta tyrosinases (TYRs), and might have been acquired by horizontal gene transfer from bacteria. COs expanded in bryophytes. Structural-functionality and selective pressure were partially responsible for the species-dependent retention of COs in embryophytes. LACs emerged in Zygnemaphyceae, having evolved from ascorbate oxidases (AAOs), and prevailed in the vascular plants and strongly expanded in seed plants. COs and LACs coevolved with the phenolic metabolism pathway genes. These results suggested that TYRs and AAOs were the first-stage phenoloxidases in Chlorophyta. COs might be the second key for the early land colonization. LACs were the third one (dominating in the vascular plants) and might be advantageous for diversified phenol substrates and the erect growth of plants. This work provided new insights into how phenoloxidases evolved and were devoted to plant evolution.
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Affiliation(s)
- Jugou Liao
- School of Ecology and Environmental Sciences, Yunnan University; Biocontrol Engineering Research Center of Crop Diseases & Pests, Yunnan Province, Kunming 650091, China
| | - Xuemei Wei
- School of Engineering, Dali University, Dali, Yunnan Province, 671003, China
| | - Keliang Tao
- School of Life Science, Yunnan University, Yunnan Province, Kunming 650091, China
| | - Gang Deng
- College of Horticulture and Landscape, Yunnan Agricultural University, Yunnan Province, Kunming 650091, China
| | - Jie Shu
- School of Life Science, Yunnan University, Yunnan Province, Kunming 650091, China
| | - Qin Qiao
- College of Horticulture and Landscape, Yunnan Agricultural University, Yunnan Province, Kunming 650091, China
| | - Gonglin Chen
- School of Ecology and Environmental Sciences, Yunnan University; Biocontrol Engineering Research Center of Crop Diseases & Pests, Yunnan Province, Kunming 650091, China
| | - Zhuo Wei
- School of Ecology and Environmental Sciences, Yunnan University; Biocontrol Engineering Research Center of Crop Diseases & Pests, Yunnan Province, Kunming 650091, China
| | - Meihui Fan
- School of Ecology and Environmental Sciences, Yunnan University; Biocontrol Engineering Research Center of Crop Diseases & Pests, Yunnan Province, Kunming 650091, China
| | - Shah Saud
- College of Life Science, Linyi University, Linyi, Shandong 276000, China
| | - Shah Fahad
- Department of Agronomy, Abdul Wali Khan University Mardan, Khyber Pakhtunkhwa 23200, Pakistan
| | - Suiyun Chen
- School of Ecology and Environmental Sciences, Yunnan University; Biocontrol Engineering Research Center of Crop Diseases & Pests, Yunnan Province, Kunming 650091, China
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Cote-L’Heureux A, Maurer-Alcalá XX, Katz LA. Old genes in new places: A taxon-rich analysis of interdomain lateral gene transfer events. PLoS Genet 2022; 18:e1010239. [PMID: 35731825 PMCID: PMC9255765 DOI: 10.1371/journal.pgen.1010239] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 07/05/2022] [Accepted: 05/06/2022] [Indexed: 11/26/2022] Open
Abstract
Vertical inheritance is foundational to Darwinian evolution, but fails to explain major innovations such as the rapid spread of antibiotic resistance among bacteria and the origin of photosynthesis in eukaryotes. While lateral gene transfer (LGT) is recognized as an evolutionary force in prokaryotes, the role of LGT in eukaryotic evolution is less clear. With the exception of the transfer of genes from organelles to the nucleus, a process termed endosymbiotic gene transfer (EGT), the extent of interdomain transfer from prokaryotes to eukaryotes is highly debated. A common critique of studies of interdomain LGT is the reliance on the topology of single-gene trees that attempt to estimate more than one billion years of evolution. We take a more conservative approach by identifying cases in which a single clade of eukaryotes is found in an otherwise prokaryotic gene tree (i.e. exclusive presence). Starting with a taxon-rich dataset of over 13,600 gene families and passing data through several rounds of curation, we identify and categorize the function of 306 interdomain LGT events into diverse eukaryotes, including 189 putative EGTs, 52 LGTs into Opisthokonta (i.e. animals, fungi and their microbial relatives), and 42 LGTs nearly exclusive to anaerobic eukaryotes. To assess differential gene loss as an explanation for exclusive presence, we compare branch lengths within each LGT tree to a set of vertically-inherited genes subsampled to mimic gene loss (i.e. with the same taxonomic sampling) and consistently find shorter relative distance between eukaryotes and prokaryotes in LGT trees, a pattern inconsistent with gene loss. Our methods provide a framework for future studies of interdomain LGT and move the field closer to an understanding of how best to model the evolutionary history of eukaryotes.
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Affiliation(s)
- Auden Cote-L’Heureux
- Department of Biological Sciences, Smith College, Northampton, Massachusetts, United States of America
| | | | - Laura A. Katz
- Department of Biological Sciences, Smith College, Northampton, Massachusetts, United States of America
- Program in Organismic Biology and Evolution, University of Massachusetts Amherst, Amherst, Massachusetts, United States of America
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Tan LY, Yeo XY, Bae HG, Lee DPS, Ho RC, Kim JE, Jo DG, Jung S. Association of Gut Microbiome Dysbiosis with Neurodegeneration: Can Gut Microbe-Modifying Diet Prevent or Alleviate the Symptoms of Neurodegenerative Diseases? Life (Basel) 2021; 11:698. [PMID: 34357070 PMCID: PMC8305650 DOI: 10.3390/life11070698] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 07/09/2021] [Accepted: 07/12/2021] [Indexed: 12/11/2022] Open
Abstract
The central nervous system was classically perceived as anatomically and functionally independent from the other visceral organs. But in recent decades, compelling evidence has led the scientific community to place a greater emphasis on the role of gut microbes on the brain. Pathological observations and early gastrointestinal symptoms highlighted that gut dysbiosis likely precedes the onset of cognitive deficits in Alzheimer's disease (AD) and Parkinson's disease (PD) patients. The delicate balance in the number and functions of pathogenic microbes and alternative probiotic populations is critical in the modulation of systemic inflammation and neuronal health. However, there is limited success in restoring healthy microbial biodiversity in AD and PD patients with general probiotics interventions and fecal microbial therapies. Fortunately, the gut microflora is susceptible to long-term extrinsic influences such as lifestyle and dietary choices, providing opportunities for treatment through comparatively individual-specific control of human behavior. In this review, we examine the impact of restrictive diets on the gut microbiome populations associated with AD and PD. The overall evidence presented supports that gut dysbiosis is a plausible prelude to disease onset, and early dietary interventions are likely beneficial for the prevention and treatment of progressive neurodegenerative diseases.
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Affiliation(s)
- Li Yang Tan
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore 138667, Singapore; (L.Y.T.); (X.Y.Y.)
- Department of Psychological Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore;
| | - Xin Yi Yeo
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore 138667, Singapore; (L.Y.T.); (X.Y.Y.)
- Department of Psychological Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore;
| | - Han-Gyu Bae
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Korea;
| | - Delia Pei Shan Lee
- Department of Food Science and Technology, Faculty of Science, National University of Singapore, Singapore 117542, Singapore;
| | - Roger C. Ho
- Department of Psychological Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore;
- Institute for Health Innovation & Technology (iHealthtech), National University of Singapore, Singapore 117599, Singapore
| | - Jung Eun Kim
- Department of Food Science and Technology, Faculty of Science, National University of Singapore, Singapore 117542, Singapore;
| | - Dong-Gyu Jo
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Korea;
| | - Sangyong Jung
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore 138667, Singapore; (L.Y.T.); (X.Y.Y.)
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117593, Singapore
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Assessment of Genetic Diversity and Symbiotic Efficiency of Selected Rhizobia Strains Nodulating Lentil ( Lens culinaris Medik.). PLANTS 2020; 10:plants10010015. [PMID: 33374129 PMCID: PMC7823456 DOI: 10.3390/plants10010015] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 12/13/2020] [Accepted: 12/14/2020] [Indexed: 11/30/2022]
Abstract
A total of 14 Rhizobium strains were isolated from lentil accessions grown at the ICARDA experimental research station at Marchouch in Morocco and used for molecular characterization and symbiotic efficiency assessment. Individual phylogenetic analysis using the 16S rRNA gene, house-keeping genes rpoB, recA, and gyrB, and symbiotic genes nodD and nodA along with Multilocus Sequence Analysis (MLSA) of the concatenated genes (16S rRNA-rpoB-recA-gyrB) was carried out for the identification and clustering of the isolates. The symbiotic efficiency of the strains was assessed on three Moroccan lentil cultivars (Bakria, Chakkouf, and Zaria) based on the number of nodules, plant height, plant dry weight, and total nitrogen content in leaves. The results showed that the individual phylogenetic analysis clustered all the strains into Rhizobium laguerreae and Rhizobium leguminosarum with sequence similarity ranging from 94 to 100%, except one strain which clustered with Mesorhizobium huakuii with sequence similarity of 100%. The MLSA of the concatenated genes and the related percentages of similarity clustered these strains into two groups of Rhizobium species, with one strain as a new genospecies when applying the threshold of 96%. For symbiotic efficiency, the Bakria variety showed the best association with 10 strains compared to its non-inoculated control (p-value ≤ 0.05), followed by Chakkouf and Zaria. The present study concluded that the genetic diversity and the symbiotic efficiency of Rhizobium strains appeared to be mainly under the control of the lentil genotypes.
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Dunn CD, Paavilainen VO. Wherever I may roam: organellar protein targeting and evolvability. Curr Opin Genet Dev 2019; 58-59:9-16. [DOI: 10.1016/j.gde.2019.07.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 06/26/2019] [Accepted: 07/20/2019] [Indexed: 02/08/2023]
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Chizhevskaya EP, Naidenova EA, Onishchuk OP, Andronov EE, Simarov BV. The Melanin Biosynthesis Gene from the CA15-1 Strain of Alfalfa Nodule Bacteria: Molecular Analysis and Phylogeny. RUSS J GENET+ 2018. [DOI: 10.1134/s1022795418080045] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Berruezo F, de Souza FSJ, Picca PI, Nemirovsky SI, Martínez Tosar L, Rivero M, Mentaberry AN, Zelada AM. Sequencing of small RNAs of the fern Pleopeltis minima (Polypodiaceae) offers insight into the evolution of the microrna repertoire in land plants. PLoS One 2017; 12:e0177573. [PMID: 28494025 PMCID: PMC5426797 DOI: 10.1371/journal.pone.0177573] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 04/28/2017] [Indexed: 12/22/2022] Open
Abstract
MicroRNAs (miRNAs) are short, single stranded RNA molecules that regulate the stability and translation of messenger RNAs in diverse eukaryotic groups. Several miRNA genes are of ancient origin and have been maintained in the genomes of animal and plant taxa for hundreds of millions of years, playing key roles in development and physiology. In the last decade, genome and small RNA (sRNA) sequencing of several plant species have helped unveil the evolutionary history of land plants. Among these, the fern group (monilophytes) occupies a key phylogenetic position, as it represents the closest extant cousin taxon of seed plants, i.e. gymno- and angiosperms. However, in spite of their evolutionary, economic and ecological importance, no fern genome has been sequenced yet and few genomic resources are available for this group. Here, we sequenced the small RNA fraction of an epiphytic South American fern, Pleopeltis minima (Polypodiaceae), and compared it to plant miRNA databases, allowing for the identification of miRNA families that are shared by all land plants, shared by all vascular plants (tracheophytes) or shared by euphyllophytes (ferns and seed plants) only. Using the recently described transcriptome of another fern, Lygodium japonicum, we also estimated the degree of conservation of fern miRNA targets in relation to other plant groups. Our results pinpoint the origin of several miRNA families in the land plant evolutionary tree with more precision and are a resource for future genomic and functional studies of fern miRNAs.
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Affiliation(s)
- Florencia Berruezo
- Laboratorio de Agrobiotecnología, Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Flávio S. J. de Souza
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr Héctor N. Torres" (INGEBI-CONICET), Buenos Aires, Argentina
- Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Pablo I. Picca
- Departamento de Biodiversidad y Biología Experimental, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Sergio I. Nemirovsky
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN, CONICET-UBA), Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Leandro Martínez Tosar
- Laboratorio de Agrobiotecnología, Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
- Instituto de Biodiversidad y Biología Experimental y Aplicada, Consejo Nacional de Investigaciones Científicas y Técnicas-Universidad de Buenos Aires (IBBEA, CONICET-UBA), Buenos Aires, Argentina
| | - Mercedes Rivero
- Instituto de Agrobiotecnología de Rosario (INDEAR), Rosario, Santa Fe, Argentina
| | - Alejandro N. Mentaberry
- Laboratorio de Agrobiotecnología, Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
- Instituto de Biodiversidad y Biología Experimental y Aplicada, Consejo Nacional de Investigaciones Científicas y Técnicas-Universidad de Buenos Aires (IBBEA, CONICET-UBA), Buenos Aires, Argentina
| | - Alicia M. Zelada
- Laboratorio de Agrobiotecnología, Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
- Instituto de Biodiversidad y Biología Experimental y Aplicada, Consejo Nacional de Investigaciones Científicas y Técnicas-Universidad de Buenos Aires (IBBEA, CONICET-UBA), Buenos Aires, Argentina
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Li C, Li D, Li J, Shao F, Lu S. Characterization of the polyphenol oxidase gene family reveals a novel microRNA involved in posttranscriptional regulation of PPOs in Salvia miltiorrhiza. Sci Rep 2017; 7:44622. [PMID: 28304398 PMCID: PMC5356337 DOI: 10.1038/srep44622] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 02/10/2017] [Indexed: 12/11/2022] Open
Abstract
Salvia miltiorrhiza is a well-known material of traditional Chinese medicine. Understanding the regulatory mechanisms of phenolic acid biosynthesis and metabolism are important for S. miltiorrhiza quality improvement. We report here that S. miltiorrhiza contains 19 polyphenol oxidases (PPOs), forming the largest PPO gene family in plant species to our knowledge. Analysis of gene structures and sequence features revealed the conservation and divergence of SmPPOs. SmPPOs were differentially expressed in plant tissues and eight of them were predominantly expressed in phloem and xylem, indicating that some SmPPOs are functionally redundant, whereas the others are associated with different physiological processes. Expression patterns of eighteen SmPPOs were significantly altered under MeJA treatment, and twelve were yeast extract and Ag+-responsive, suggesting the majority of SmPPOs are stress-responsive. Analysis of high-throughput small RNA sequences and degradome data showed that miR1444-mediated regulation of PPOs existing in P. trichocarpa is absent from S. miltiorrhiza. Instead, a subset of SmPPOs was posttranscriptionally regulated by a novel miRNA, termed Smi-miR12112. It indicates the specificity and significance of miRNA-mediated regulation of PPOs. The results shed light on the regulation of SmPPO expression and suggest the complexity of SmPPO-associated phenolic acid biosynthesis and metabolism.
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Affiliation(s)
- Caili Li
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences &Peking Union Medical College, No. 151, Malianwa North Road, Haidian District, Beijing 100193, China
| | - Dongqiao Li
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences &Peking Union Medical College, No. 151, Malianwa North Road, Haidian District, Beijing 100193, China
| | - Jiang Li
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences &Peking Union Medical College, No. 151, Malianwa North Road, Haidian District, Beijing 100193, China
| | - Fenjuan Shao
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences &Peking Union Medical College, No. 151, Malianwa North Road, Haidian District, Beijing 100193, China
| | - Shanfa Lu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences &Peking Union Medical College, No. 151, Malianwa North Road, Haidian District, Beijing 100193, China
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Wang M, Li C, Lu S. Origin and evolution of MIR1444 genes in Salicaceae. Sci Rep 2017; 7:39740. [PMID: 28071760 PMCID: PMC5223194 DOI: 10.1038/srep39740] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 11/25/2016] [Indexed: 11/30/2022] Open
Abstract
miR1444s are functionally significant miRNAs targeting polyphenol oxidase (PPO) genes for cleavage. MIR1444 genes were reported only in Populus trichocarpa. Through the computational analysis of 215 RNA-seq data, four whole genome sequences of Salicaceae species and deep sequencing of six P. trichocarpa small RNA libraries, we investigated the origin and evolution history of MIR1444s. A total of 23 MIR1444s were identified. Populus and Idesia species contain two MIR1444 genes, while Salix includes only one. Populus and Idesia MIR1444b genes and Salix MIR1444s were phylogenetically separated from Populus and Idesia MIR1444a genes. Ptr-miR1444a and ptr-miR1444b showed sequence divergence. Compared with ptr-miR1444b, ptr-miR1444a started 2 nt upstream of precursor, resulting in differential regulation of PPO targets. Sequence alignments showed that MIR1444 genes exhibited extensive similarity to their PPO targets, the characteristics of MIRs originated from targets through an inverted gene duplication event. Genome sequence comparison showed that MIR1444 genes in Populus and Idesia were expanded through the Salicoid genome duplication event. A copy of MIR1444 gene was lost in Salix through DNA segment deletion during chromosome rearrangements. The results provide significant information for the origin of plant miRNAs and the mechanism of Salicaceae gene evolution and divergence.
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Affiliation(s)
- Meizhen Wang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Caili Li
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Shanfa Lu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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Abstract
Three recent papers underline the importance of the host genomic background in allowing the stable maintenance of horizontally acquired genes. These studies suggest that post-transfer changes in both host genome and acquired genes contribute to the stable integration of foreign genes.
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Affiliation(s)
- Luis Boto
- Dpto. Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales (CSIC), C/José Gutierrez Abascal 2, 28006, Madrid, Spain.
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