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Garcia S, Kovarik A, Maiwald S, Mann L, Schmidt N, Pascual-Díaz JP, Vitales D, Weber B, Heitkam T. The Dynamic Interplay Between Ribosomal DNA and Transposable Elements: A Perspective From Genomics and Cytogenetics. Mol Biol Evol 2024; 41:msae025. [PMID: 38306580 PMCID: PMC10946416 DOI: 10.1093/molbev/msae025] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 12/06/2023] [Accepted: 01/29/2024] [Indexed: 02/04/2024] Open
Abstract
Although both are salient features of genomes, at first glance ribosomal DNAs and transposable elements are genetic elements with not much in common: whereas ribosomal DNAs are mainly viewed as housekeeping genes that uphold all prime genome functions, transposable elements are generally portrayed as selfish and disruptive. These opposing characteristics are also mirrored in other attributes: organization in tandem (ribosomal DNAs) versus organization in a dispersed manner (transposable elements); evolution in a concerted manner (ribosomal DNAs) versus evolution by diversification (transposable elements); and activity that prolongs genomic stability (ribosomal DNAs) versus activity that shortens it (transposable elements). Re-visiting relevant instances in which ribosomal DNA-transposable element interactions have been reported, we note that both repeat types share at least four structural and functional hallmarks: (1) they are repetitive DNAs that shape genomes in evolutionary timescales, (2) they exchange structural motifs and can enter co-evolution processes, (3) they are tightly controlled genomic stress sensors playing key roles in senescence/aging, and (4) they share common epigenetic marks such as DNA methylation and histone modification. Here, we give an overview of the structural, functional, and evolutionary characteristics of both ribosomal DNAs and transposable elements, discuss their roles and interactions, and highlight trends and future directions as we move forward in understanding ribosomal DNA-transposable element associations.
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Affiliation(s)
- Sònia Garcia
- Institut Botànic de Barcelona (IBB), CSIC-CMCNB, 08038 Barcelona, Catalonia, Spain
| | - Ales Kovarik
- Institute of Biophysics, Academy of Sciences of the Czech Republic, 61265 Brno, Czech Republic
| | - Sophie Maiwald
- Faculty of Biology, Technische Universität Dresden, D-01069 Dresden, Germany
| | - Ludwig Mann
- Faculty of Biology, Technische Universität Dresden, D-01069 Dresden, Germany
| | - Nicola Schmidt
- Faculty of Biology, Technische Universität Dresden, D-01069 Dresden, Germany
| | | | - Daniel Vitales
- Institut Botànic de Barcelona (IBB), CSIC-CMCNB, 08038 Barcelona, Catalonia, Spain
- Laboratori de Botànica–Unitat Associada CSIC, Facultat de Farmàcia i Ciències de l’Alimentació, Universitat de Barcelona, 08028 Barcelona, Catalonia, Spain
| | - Beatrice Weber
- Faculty of Biology, Technische Universität Dresden, D-01069 Dresden, Germany
| | - Tony Heitkam
- Faculty of Biology, Technische Universität Dresden, D-01069 Dresden, Germany
- Institute of Biology, NAWI Graz, Karl-Franzens-Universität, A-8010 Graz, Austria
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Genome Evolution and the Future of Phylogenomics of Non-Avian Reptiles. Animals (Basel) 2023; 13:ani13030471. [PMID: 36766360 PMCID: PMC9913427 DOI: 10.3390/ani13030471] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 01/13/2023] [Accepted: 01/15/2023] [Indexed: 02/01/2023] Open
Abstract
Non-avian reptiles comprise a large proportion of amniote vertebrate diversity, with squamate reptiles-lizards and snakes-recently overtaking birds as the most species-rich tetrapod radiation. Despite displaying an extraordinary diversity of phenotypic and genomic traits, genomic resources in non-avian reptiles have accumulated more slowly than they have in mammals and birds, the remaining amniotes. Here we review the remarkable natural history of non-avian reptiles, with a focus on the physical traits, genomic characteristics, and sequence compositional patterns that comprise key axes of variation across amniotes. We argue that the high evolutionary diversity of non-avian reptiles can fuel a new generation of whole-genome phylogenomic analyses. A survey of phylogenetic investigations in non-avian reptiles shows that sequence capture-based approaches are the most commonly used, with studies of markers known as ultraconserved elements (UCEs) especially well represented. However, many other types of markers exist and are increasingly being mined from genome assemblies in silico, including some with greater information potential than UCEs for certain investigations. We discuss the importance of high-quality genomic resources and methods for bioinformatically extracting a range of marker sets from genome assemblies. Finally, we encourage herpetologists working in genomics, genetics, evolutionary biology, and other fields to work collectively towards building genomic resources for non-avian reptiles, especially squamates, that rival those already in place for mammals and birds. Overall, the development of this cross-amniote phylogenomic tree of life will contribute to illuminate interesting dimensions of biodiversity across non-avian reptiles and broader amniotes.
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Ahmad SF, Singchat W, Jehangir M, Panthum T, Srikulnath K. Consequence of Paradigm Shift with Repeat Landscapes in Reptiles: Powerful Facilitators of Chromosomal Rearrangements for Diversity and Evolution. Genes (Basel) 2020; 11:E827. [PMID: 32708239 PMCID: PMC7397244 DOI: 10.3390/genes11070827] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 07/16/2020] [Accepted: 07/17/2020] [Indexed: 12/24/2022] Open
Abstract
Reptiles are notable for the extensive genomic diversity and species richness among amniote classes, but there is nevertheless a need for detailed genome-scale studies. Although the monophyletic amniotes have recently been a focus of attention through an increasing number of genome sequencing projects, the abundant repetitive portion of the genome, termed the "repeatome", remains poorly understood across different lineages. Consisting predominantly of transposable elements or mobile and satellite sequences, these repeat elements are considered crucial in causing chromosomal rearrangements that lead to genomic diversity and evolution. Here, we propose major repeat landscapes in representative reptilian species, highlighting their evolutionary dynamics and role in mediating chromosomal rearrangements. Distinct karyotype variability, which is typically a conspicuous feature of reptile genomes, is discussed, with a particular focus on rearrangements correlated with evolutionary reorganization of micro- and macrochromosomes and sex chromosomes. The exceptional karyotype variation and extreme genomic diversity of reptiles are used to test several hypotheses concerning genomic structure, function, and evolution.
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Affiliation(s)
- Syed Farhan Ahmad
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (S.F.A.); (W.S.); (M.J.); (T.P.)
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Worapong Singchat
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (S.F.A.); (W.S.); (M.J.); (T.P.)
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Maryam Jehangir
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (S.F.A.); (W.S.); (M.J.); (T.P.)
- Integrative Genomics Lab-LGI, Department of Structural and Functional Biology, Institute of Bioscience at Botucatu, São Paulo State University (UNESP), Botucatu 18618-689, Brazil
| | - Thitipong Panthum
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (S.F.A.); (W.S.); (M.J.); (T.P.)
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Kornsorn Srikulnath
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (S.F.A.); (W.S.); (M.J.); (T.P.)
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
- Center for Advanced Studies in Tropical Natural Resources, National Research University-Kasetsart University, Kasetsart University, Bangkok 10900, Thailand
- Center of Excellence on Agricultural Biotechnology (AG-BIO/PERDO-CHE), Bangkok 10900, Thailand
- Omics Center for Agriculture, Bioresources, Food and Health, Kasetsart University (OmiKU), Bangkok 10900, Thailand
- Amphibian Research Center, Hiroshima University, 1-3-1, Kagamiyama, Higashihiroshima 739-8526, Japan
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Nishiyama E, Ohshima K. Cross-Kingdom Commonality of a Novel Insertion Signature of RTE-Related Short Retroposons. Genome Biol Evol 2018; 10:1471-1483. [PMID: 29850801 PMCID: PMC6007223 DOI: 10.1093/gbe/evy098] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/18/2018] [Indexed: 12/15/2022] Open
Abstract
In multicellular organisms, such as vertebrates and flowering plants, horizontal transfer (HT) of genetic information is thought to be a rare event. However, recent findings unveiled unexpectedly frequent HT of RTE-clade LINEs. To elucidate the molecular footprints of the genomic integration machinery of RTE-related retroposons, the sequence patterns surrounding the insertion sites of plant Au-like SINE families were analyzed in the genomes of a wide variety of flowering plants. A novel and remarkable finding regarding target site duplications (TSDs) for SINEs was they start with thymine approximately one helical pitch (ten nucleotides) downstream of a thymine stretch. This TSD pattern was found in RTE-clade LINEs, which share the 3'-end sequence of these SINEs, in the genome of leguminous plants. These results demonstrably show that Au-like SINEs were mobilized by the enzymatic machinery of RTE-clade LINEs. Further, we discovered the same TSD pattern in animal SINEs from lizard and mammals, in which the RTE-clade LINEs sharing the 3'-end sequence with these animal SINEs showed a distinct TSD pattern. Moreover, a significant correlation was observed between the first nucleotide of TSDs and microsatellite-like sequences found at the 3'-ends of SINEs and LINEs. We propose that RTE-encoded protein could preferentially bind to a DNA region that contains a thymine stretch to cleave a phosphodiester bond downstream of the stretch. Further, determination of cleavage sites and/or efficiency of primer sites for reverse transcription may depend on microsatellite-like repeats in the RNA template. Such a unique mechanism may have enabled retroposons to successfully expand in frontier genomes after HT.
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Affiliation(s)
- Eri Nishiyama
- Graduate School of Bioscience, Nagahama Institute of Bio-Science and Technology, Shiga, Japan
| | - Kazuhiko Ohshima
- Graduate School of Bioscience, Nagahama Institute of Bio-Science and Technology, Shiga, Japan
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Ishijima J, Uno Y, Nunome M, Nishida C, Kuraku S, Matsuda Y. Molecular cytogenetic characterization of chromosome site-specific repetitive sequences in the Arctic lamprey (Lethenteron camtschaticum, Petromyzontidae). DNA Res 2017; 24:93-101. [PMID: 28025319 PMCID: PMC5381345 DOI: 10.1093/dnares/dsw053] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2016] [Accepted: 11/02/2016] [Indexed: 12/19/2022] Open
Abstract
All extant lamprey karyotypes are characterized by almost all dot-shaped microchromosomes. To understand the molecular basis of chromosome structure in lampreys, we performed chromosome C-banding and silver staining and chromosome mapping of the 18S–28S and 5S ribosomal RNA (rRNA) genes and telomeric TTAGGG repeats in the Arctic lamprey (Lethenteron camtschaticum). In addition, we cloned chromosome site-specific repetitive DNA sequences and characterized them by nucleotide sequencing, chromosome in situ hybridization, and filter hybridization. Three types of repetitive sequences were detected; a 200-bp AT-rich repetitive sequence, LCA-EcoRIa that co-localized with the 18S–28S rRNA gene clusters of 3 chromosomal pairs; a 364-bp AT-rich LCA-EcoRIb sequence that showed homology to the EcoRI sequence family from the sea lamprey (Petromyzon marinus), which contains short repeats as centromeric motifs; and a GC-rich 702-bp LCA-ApaI sequence that was distributed on nearly all chromosomes and showed significant homology with the integrase-coding region of a Ty3/Gypsy family long terminal repeat (LTR) retrotransposon. All three repetitive sequences are highly conserved within the Petromyzontidae or within Petromyzontidae and Mordaciidae. Molecular cytogenetic characterization of these site-specific repeats showed that they may be correlated with programed genome rearrangement (LCA-EcoRIa), centromere structure and function (LCA-EcoRIb), and site-specific amplification of LTR retroelements through homogenization between non-homologous chromosomes (LCA-ApaI).
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Affiliation(s)
- Junko Ishijima
- Laboratory of Animal Cytogenetics, Department of Biological Sciences, Graduate School of Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
| | - Yoshinobu Uno
- Laboratory of Animal Genetics, Department of Applied Molecular Biosciences, Nagoya University, Nagoya, Aichi 464-8601, Japan
| | - Mitsuo Nunome
- Avian Bioscience Research Center, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi 464-8601, Japan
| | - Chizuko Nishida
- Department of Natural History Sciences, Faculty of Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
| | - Shigehiro Kuraku
- Phyloinformatics Unit, RIKEN Center for Life Science Technologies, Kobe 650-0047, Japan
| | - Yoichi Matsuda
- Laboratory of Animal Genetics, Department of Applied Molecular Biosciences, Nagoya University, Nagoya, Aichi 464-8601, Japan
- Avian Bioscience Research Center, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi 464-8601, Japan
- To whom correspondence should be addressed. Tel. +81 52 789 4100. Fax. +81 52 789 4099.
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Ruggiero RP, Bourgeois Y, Boissinot S. LINE Insertion Polymorphisms are Abundant but at Low Frequencies across Populations of Anolis carolinensis. Front Genet 2017; 8:44. [PMID: 28450881 PMCID: PMC5389967 DOI: 10.3389/fgene.2017.00044] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 03/29/2017] [Indexed: 12/30/2022] Open
Abstract
Vertebrate genomes differ considerably in size and structure. Among the features that show the most variation is the abundance of Long Interspersed Nuclear Elements (LINEs). Mammalian genomes contain 100,000s LINEs that belong to a single clade, L1, and in most species a single family is usually active at a time. In contrast, non-mammalian vertebrates (fish, amphibians and reptiles) contain multiple active families, belonging to several clades, but each of them is represented by a small number of recently inserted copies. It is unclear why vertebrate genomes harbor such drastic differences in LINE composition. To address this issue, we conducted whole genome resequencing to investigate the population genomics of LINEs across 13 genomes of the lizard Anolis carolinensis sampled from two geographically and genetically distinct populations in the Eastern Florida and the Gulf Atlantic regions of the United States. We used the Mobile Element Locator Tool to identify and genotype polymorphic insertions from five major clades of LINEs (CR1, L1, L2, RTE and R4) and the 41 subfamilies that constitute them. Across these groups we found large variation in the frequency of polymorphic insertions and the observed length distributions of these insertions, suggesting these groups vary in their activity and how frequently they successfully generate full-length, potentially active copies. Though we found an abundance of polymorphic insertions (over 45,000) most of these were observed at low frequencies and typically appeared as singletons. Site frequency spectra for most LINEs showed a significant shift toward low frequency alleles compared to the spectra observed for total genomic single nucleotide polymorphisms. Using Tajima's D, FST and the mean number of pairwise differences in LINE insertion polymorphisms, we found evidence that negative selection is acting on LINE families in a length-dependent manner, its effects being stronger in the larger Eastern Florida population. Our results suggest that a large effective population size and negative selection limit the expansion of polymorphic LINE insertions across these populations and that the probability of LINE polymorphisms reaching fixation is extremely low.
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Mezzasalma M, Visone V, Petraccioli A, Odierna G, Capriglione T, Guarino FM. Non-random accumulation of LINE1-like sequences on differentiated snake W chromosomes. J Zool (1987) 2016. [DOI: 10.1111/jzo.12355] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- M. Mezzasalma
- Department of Biology; University of Naples Federico II; Naples Italy
| | - V. Visone
- Department of Biology; University of Naples Federico II; Naples Italy
| | - A. Petraccioli
- Department of Biology; University of Naples Federico II; Naples Italy
| | - G. Odierna
- Department of Biology; University of Naples Federico II; Naples Italy
| | - T. Capriglione
- Department of Biology; University of Naples Federico II; Naples Italy
| | - F. M. Guarino
- Department of Biology; University of Naples Federico II; Naples Italy
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Sanz-Soler R, Sanz L, Calvete JJ. Distribution ofRPTLNGenes Across Reptilia: Hypothesized Role for RPTLN in the Evolution of SVMPs. Integr Comp Biol 2016; 56:989-1003. [DOI: 10.1093/icb/icw031] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
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Carvalho NDM, Pinheiro VSS, Carmo EJ, Goll LG, Schneider CH, Gross MC. The Organization of Repetitive DNA in the Genomes of Amazonian Lizard Species in the Family Teiidae. Cytogenet Genome Res 2016; 147:161-8. [PMID: 26867142 DOI: 10.1159/000443714] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/05/2015] [Indexed: 11/19/2022] Open
Abstract
Repetitive DNA is the largest fraction of the eukaryote genome and comprises tandem and dispersed sequences. It presents variations in relation to its composition, number of copies, distribution, dynamics, and genome organization, and participates in the evolutionary diversification of different vertebrate species. Repetitive sequences are usually located in the heterochromatin of centromeric and telomeric regions of chromosomes, contributing to chromosomal structures. Therefore, the aim of this study was to physically map repetitive DNA sequences (5S rDNA, telomeric sequences, tropomyosin gene 1, and retroelements Rex1 and SINE) of mitotic chromosomes of Amazonian species of teiids (Ameiva ameiva, Cnemidophorus sp. 1, Kentropyx calcarata, Kentropyx pelviceps, and Tupinambis teguixin) to understand their genome organization and karyotype evolution. The mapping of repetitive sequences revealed a distinct pattern in Cnemidophorus sp. 1, whereas the other species showed all sequences interspersed in the heterochromatic region. Physical mapping of the tropomyosin 1 gene was performed for the first time in lizards and showed that in addition to being functional, this gene has a structural function similar to the mapped repetitive elements as it is located preferentially in centromeric regions and termini of chromosomes.
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Affiliation(s)
- Natalia D M Carvalho
- Laboratx00F3;rio de Citogenx00F4;mica Animal, Instituto de Cix00EA;ncias Biolx00F3;gicas, Universidade Federal do Amazonas, Manaus, Brazil
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Traldi JB, Vicari MR, Martinez JDF, Blanco DR, Lui RL, Moreira-Filho O. Chromosome Analyses of Apareiodon argenteus and Apareiodon davisi (Characiformes, Parodontidae): An Extensive Chromosomal Polymorphism of 45S and 5S Ribosomal DNAs. Zebrafish 2016; 13:19-25. [DOI: 10.1089/zeb.2015.1124] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Affiliation(s)
- Josiane Baccarin Traldi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos-SP, Brazil
| | - Marcelo Ricardo Vicari
- Departamento de Biologia Estrutural, Molecular e Genética, Universidade Estadual de Ponta Grossa, Ponta Grossa-PR, Brazil
| | | | | | - Roberto Laridondo Lui
- Centro de Ciências Biológicas e da Saúde, Universidade Estadual do Oeste do Paraná, Cascavel-PR, Brazil
| | - Orlando Moreira-Filho
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos-SP, Brazil
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Godakova SA, Korchagin VI, Semeynova SK, Chernyavskaya MM, Sevast’yanova GA, Ryskov AP. Characterization of retrotransposon Bov-B LINE reverse transcriptase gene sequences in parthenogenetic lizards Darevskia unisexualis and bisexual species D. nairensis and D. valentini. Mol Biol 2015. [DOI: 10.1134/s002689331503005x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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12
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Doucet AJ, Droc G, Siol O, Audoux J, Gilbert N. U6 snRNA Pseudogenes: Markers of Retrotransposition Dynamics in Mammals. Mol Biol Evol 2015; 32:1815-32. [PMID: 25761766 PMCID: PMC4476161 DOI: 10.1093/molbev/msv062] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Transposable elements comprise more than 45% of the human genome and long interspersed nuclear element 1 (LINE-1 or L1) is the only autonomous mobile element remaining active. Since its identification, it has been proposed that L1 contributes to the mobilization and amplification of other cellular RNAs and more recently, experimental demonstrations of this function has been described for many transcripts such as Alu, a nonautonomous mobile element, cellular mRNAs, or small noncoding RNAs. Detailed examination of the mobilization of various cellular RNAs revealed distinct pathways by which they could be recruited during retrotransposition; template choice or template switching. Here, by analyzing genomic structures and retrotransposition signatures associated with small nuclear RNA (snRNA) sequences, we identified distinct recruiting steps during the L1 retrotransposition cycle for the formation of snRNA-processed pseudogenes. Interestingly, some of the identified recruiting steps take place in the nucleus. Moreover, after comparison to other vertebrate genomes, we established that snRNA amplification by template switching is common to many LINE families from several LINE clades. Finally, we suggest that U6 snRNA copies can serve as markers of L1 retrotransposition dynamics in mammalian genomes.
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Affiliation(s)
- Aurélien J Doucet
- Institut de Génétique Humaine, CNRS, UPR 1142, Montpellier, France Institute for Research on Cancer and Aging, Nice (IRCAN), INSERM, U1081, CNRS UMR 7284, Nice, France
| | - Gaëtan Droc
- Institut de Génétique Humaine, CNRS, UPR 1142, Montpellier, France Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), UMR AGAP, Montpellier, France
| | - Oliver Siol
- Institut de Génétique Humaine, CNRS, UPR 1142, Montpellier, France Institut de Génétique Humaine, CNRS, UPR 1142, Montpellier, France
| | - Jérôme Audoux
- Institute for Regenerative Medicine and Biotherapy, INSERM, U1183, Montpellier, France
| | - Nicolas Gilbert
- Institut de Génétique Humaine, CNRS, UPR 1142, Montpellier, France Institute for Regenerative Medicine and Biotherapy, INSERM, U1183, Montpellier, France
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Novel X-linked genes revealed by quantitative polymerase chain reaction in the green anole, Anolis carolinensis. G3-GENES GENOMES GENETICS 2014; 4:2107-13. [PMID: 25172916 PMCID: PMC4232536 DOI: 10.1534/g3.114.014084] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The green anole, Anolis carolinensis (ACA), is the model reptile for a vast array of biological disciplines. It was the first nonavian reptile to have its genome fully sequenced. During the genome project, the XX/XY system of sex chromosomes homologous to chicken chromosome 15 (GGA15) was revealed, and 106 X-linked genes were identified. We selected 38 genes located on eight scaffolds in ACA and having orthologs located on GGA15, then tested their linkage to ACA X chromosome by using comparative quantitative fluorescent real-time polymerase chain reaction applied to male and female genomic DNA. All tested genes appeared to be X-specific and not present on the Y chromosome. Assuming that all genes located on these scaffolds should be localized to the ACA X chromosome, we more than doubled the number of known X-linked genes in ACA, from 106 to 250. While demonstrating that the gene content of chromosome X in ACA and GGA15 is largely conserved, we nevertheless showed that numerous interchromosomal rearrangements had occurred since the splitting of the chicken and anole evolutionary lineages. The presence of many ACA X-specific genes localized to distinct contigs indicates that the ACA Y chromosome should be highly degenerated, having lost a large amount of its original gene content during evolution. The identification of novel genes linked to the X chromosome and absent on the Y chromosome in the model lizard species contributes to ongoing research as to the evolution of sex determination in reptiles and provides important information for future comparative and functional genomics.
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Accelerated Evolution of Fetuin Family Proteins inProtobothrops flavoviridis(Habu Snake) Serum and the Discovery of an L1-Like Genomic Element in the Intronic Sequence of a Fetuin-Encoding Gene. Biosci Biotechnol Biochem 2014; 77:582-90. [DOI: 10.1271/bbb.120829] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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15
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Yang G, Fattash I, Lee CN, Liu K, Cavinder B. Birth of three stowaway-like MITE families via microhomology-mediated miniaturization of a Tc1/Mariner element in the yellow fever mosquito. Genome Biol Evol 2014; 5:1937-48. [PMID: 24068652 PMCID: PMC3814204 DOI: 10.1093/gbe/evt146] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Eukaryotic genomes contain numerous DNA transposons that move by a cut-and-paste mechanism. The majority of these elements are self-insufficient and dependent on their autonomous relatives to transpose. Miniature inverted repeat transposable elements (MITEs) are often the most numerous nonautonomous DNA elements in a higher eukaryotic genome. Little is known about the origin of these MITE families as few of them are accompanied by their direct ancestral elements in a genome. Analyses of MITEs in the yellow fever mosquito identified its youngest MITE family, designated as Gnome, that contains at least 116 identical copies. Genome-wide search for direct ancestral autonomous elements of Gnome revealed an elusive single copy Tc1/Mariner-like element, named as Ozma, that encodes a transposase with a DD37E triad motif. Strikingly, Ozma also gave rise to two additional MITE families, designated as Elf and Goblin. These three MITE families were derived at different times during evolution and bear internal sequences originated from different regions of Ozma. Upon close inspection of the sequence junctions, the internal deletions during the formation of these three MITE families always occurred between two microhomologous sites (6–8 bp). These results suggest that multiple MITE families may originate from a single ancestral autonomous element, and formation of MITEs can be mediated by sequence microhomology. Ozma and its related MITEs are exceptional candidates for the long sought-after endogenous active transposon tool in genetic control of mosquitoes.
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Affiliation(s)
- Guojun Yang
- Department of Biology, University of Toronto Mississauga, Ontario, Canada
- *Corresponding author: E-mail:
| | - Isam Fattash
- Department of Biology, University of Toronto Mississauga, Ontario, Canada
| | - Chia-Ni Lee
- Department of Biology, University of Toronto Mississauga, Ontario, Canada
| | - Kun Liu
- Department of Botany and Plant Sciences, University of California Riverside
| | - Brad Cavinder
- Department of Plant Pathology and Microbiology, University of California Riverside
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16
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Lindič N, Budič M, Petan T, Knisbacher BA, Levanon EY, Lovšin N. Differential inhibition of LINE1 and LINE2 retrotransposition by vertebrate AID/APOBEC proteins. Retrovirology 2013; 10:156. [PMID: 24344916 PMCID: PMC3880073 DOI: 10.1186/1742-4690-10-156] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2013] [Accepted: 12/02/2013] [Indexed: 01/06/2023] Open
Abstract
Background The role of AID/APOBEC proteins in the mammalian immune response against retroviruses and retrotransposons is well established. G to A hypermutations, the hallmark of their cytidine deaminase activity, are present in several mammalian retrotransposons. However, the role of AID/APOBEC proteins in non-mammalian retroelement restriction is not completely understood. Results Here we provide the first evidence of anti-retroelement activity of a reptilian APOBEC protein. The green anole lizard A1 protein displayed potent DNA mutator activity and inhibited ex vivo retrotransposition of LINE1 and LINE2 ORF1 protein encoding elements, displaying a mechanism of action similar to that of the human A1 protein. In contrast, the human A3 proteins did not require ORF1 protein to inhibit LINE retrotransposition, suggesting a differential mechanism of anti-LINE action of A1 proteins, which emerged in amniotes, and A3 proteins, exclusive to placental mammals. In accordance, genomic analyses demonstrate differential G to A DNA editing of LINE retrotransposons in the lizard genome, which is also the first evidence for G to A DNA editing in non-mammalian genomes. Conclusion Our data suggest that vertebrate APOBEC proteins differentially inhibit the retrotransposition of LINE elements and that the anti-retroelement activity of APOBEC proteins predates mammals.
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Affiliation(s)
| | | | | | | | | | - Nika Lovšin
- Department of Chemistry and Biochemistry, Chair of Biochemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, SI-1000, Ljubljana, Slovenia.
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17
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Jiang J, Zhao L, Yan L, Zhang L, Cao Y, Wang Y, Jiang Y, Yan T, Cao Y. Structural features and mechanism of translocation of non-LTR retrotransposons in Candida albicans. Virulence 2013; 5:245-52. [PMID: 24317340 PMCID: PMC3956500 DOI: 10.4161/viru.27278] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
A number of abundant mobile genetic elements called retrotransposons reverse transcribe RNA to generate DNA for insertion into eukaryotic genomes. Non-long-terminal repeat (non-LTR) retrotransposons represent a major class of retrotransposons, and transposons that move by target-primed reverse transcription lack LTRs characteristic of retroviruses and retroviral-like transposons. Yeast model systems in Candida albicans and Saccharomyces cerevisiae have been developed for the study of non-LTR retrotransposons. Non-LTR retrotransposons are divided into LINEs (long interspersed nuclear elements), SINEs (short interspersed nuclear elements), and SVA (SINE, VNTR, and Alu). LINE-1 elements have been described in fungi, and several families called Zorro elements have been detected from C. albicans. They are all members of L1 clades. Through a mechanism named target-primed reverse transcription (TPRT), LINEs translocate the new copy into the target site to initiate DNA synthesis primed by the 3′ OH of the broken strand. In this article, we describe some advances in the research on structural features and origin of non-LTR retrotransposons in C. albicans, and discuss mechanisms underlying their reverse transcription and integration of the donor copy into the target site.
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Affiliation(s)
- Jingchen Jiang
- Department of Pharmacology; School of Pharmacy; China Pharmaceutical University; Nanjing, PR China
| | - Liuya Zhao
- R & D Center of New Drug; School of Pharmacy; Second Military Medical University; Shanghai, PR China
| | - Lan Yan
- R & D Center of New Drug; School of Pharmacy; Second Military Medical University; Shanghai, PR China
| | - Lulu Zhang
- R & D Center of New Drug; School of Pharmacy; Second Military Medical University; Shanghai, PR China
| | - Yingying Cao
- R & D Center of New Drug; School of Pharmacy; Second Military Medical University; Shanghai, PR China
| | - Yan Wang
- R & D Center of New Drug; School of Pharmacy; Second Military Medical University; Shanghai, PR China
| | - Yuanying Jiang
- R & D Center of New Drug; School of Pharmacy; Second Military Medical University; Shanghai, PR China
| | - Tianhua Yan
- Department of Pharmacology; School of Pharmacy; China Pharmaceutical University; Nanjing, PR China
| | - Yongbing Cao
- R & D Center of New Drug; School of Pharmacy; Second Military Medical University; Shanghai, PR China
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18
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RNA-Mediated Gene Duplication and Retroposons: Retrogenes, LINEs, SINEs, and Sequence Specificity. INTERNATIONAL JOURNAL OF EVOLUTIONARY BIOLOGY 2013; 2013:424726. [PMID: 23984183 PMCID: PMC3747384 DOI: 10.1155/2013/424726] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Accepted: 07/01/2013] [Indexed: 11/18/2022]
Abstract
A substantial number of “retrogenes” that are derived from the mRNA of various intron-containing genes have been reported. A class of mammalian retroposons, long interspersed element-1 (LINE1, L1), has been shown to be involved in the reverse transcription of retrogenes (or processed pseudogenes) and non-autonomous short interspersed elements (SINEs). The 3′-end sequences of various SINEs originated from a corresponding LINE. As the 3′-untranslated regions of several LINEs are essential for retroposition, these LINEs presumably require “stringent” recognition of the 3′-end sequence of the RNA template. However, the 3′-ends of mammalian L1s do not exhibit any similarity to SINEs, except for the presence of 3′-poly(A) repeats. Since the 3′-poly(A) repeats of L1 and Alu SINE are critical for their retroposition, L1 probably recognizes the poly(A) repeats, thereby mobilizing not only Alu SINE but also cytosolic mRNA. Many flowering plants only harbor L1-clade LINEs and a significant number of SINEs with poly(A) repeats, but no homology to the LINEs. Moreover, processed pseudogenes have also been found in flowering plants. I propose that the ancestral L1-clade LINE in the common ancestor of green plants may have recognized a specific RNA template, with stringent recognition then becoming relaxed during the course of plant evolution.
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Nikaido M, Noguchi H, Nishihara H, Toyoda A, Suzuki Y, Kajitani R, Suzuki H, Okuno M, Aibara M, Ngatunga BP, Mzighani SI, Kalombo HWJ, Masengi KWA, Tuda J, Nogami S, Maeda R, Iwata M, Abe Y, Fujimura K, Okabe M, Amano T, Maeno A, Shiroishi T, Itoh T, Sugano S, Kohara Y, Fujiyama A, Okada N. Coelacanth genomes reveal signatures for evolutionary transition from water to land. Genome Res 2013; 23:1740-8. [PMID: 23878157 PMCID: PMC3787270 DOI: 10.1101/gr.158105.113] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Coelacanths are known as “living fossils,” as they show remarkable morphological resemblance to the fossil record and belong to the most primitive lineage of living Sarcopterygii (lobe-finned fishes and tetrapods). Coelacanths may be key to elucidating the tempo and mode of evolution from fish to tetrapods. Here, we report the genome sequences of five coelacanths, including four Latimeria chalumnae individuals (three specimens from Tanzania and one from Comoros) and one L. menadoensis individual from Indonesia. These sequences cover two African breeding populations and two known extant coelacanth species. The genome is ∼2.74 Gbp and contains a high proportion (∼60%) of repetitive elements. The genetic diversity among the individuals was extremely low, suggesting a small population size and/or a slow rate of evolution. We found a substantial number of genes that encode olfactory and pheromone receptors with features characteristic of tetrapod receptors for the detection of airborne ligands. We also found that limb enhancers of bmp7 and gli3, both of which are essential for limb formation, are conserved between coelacanth and tetrapods, but not ray-finned fishes. We expect that some tetrapod-like genes may have existed early in the evolution of primitive Sarcopterygii and were later co-opted to adapt to terrestrial environments. These coelacanth genomes will provide a cornerstone for studies to elucidate how ancestral aquatic vertebrates evolved into terrestrial animals.
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Affiliation(s)
- Masato Nikaido
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, Kanagawa 226-8501, Japan
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20
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Durban J, Pérez A, Sanz L, Gómez A, Bonilla F, Rodríguez S, Chacón D, Sasa M, Angulo Y, Gutiérrez JM, Calvete JJ. Integrated "omics" profiling indicates that miRNAs are modulators of the ontogenetic venom composition shift in the Central American rattlesnake, Crotalus simus simus. BMC Genomics 2013; 14:234. [PMID: 23575160 PMCID: PMC3660174 DOI: 10.1186/1471-2164-14-234] [Citation(s) in RCA: 136] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2012] [Accepted: 03/14/2013] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Understanding the processes that drive the evolution of snake venom is a topic of great research interest in molecular and evolutionary toxinology. Recent studies suggest that ontogenetic changes in venom composition are genetically controlled rather than environmentally induced. However, the molecular mechanisms underlying these changes remain elusive. Here we have explored the basis and level of regulation of the ontogenetic shift in the venom composition of the Central American rattlesnake, Crotalus s. simus using a combined proteomics and transcriptomics approach. RESULTS Proteomic analysis showed that the ontogenetic shift in the venom composition of C. s. simus is essentially characterized by a gradual reduction in the expression of serine proteinases and PLA2 molecules, particularly crotoxin, a β-neurotoxic heterodimeric PLA2, concominantly with an increment of PI and PIII metalloproteinases at age 9-18 months. Comparison of the transcriptional activity of the venom glands of neonate and adult C. s. simus specimens indicated that their transcriptomes exhibit indistinguisable toxin family profiles, suggesting that the elusive mechanism by which shared transcriptomes generate divergent venom phenotypes may operate post-transcriptionally. Specifically, miRNAs with frequency count of 1000 or greater exhibited an uneven distribution between the newborn and adult datasets. Of note, 590 copies of a miRNA targeting crotoxin B-subunit was exclusively found in the transcriptome of the adult snake, whereas 1185 copies of a miRNA complementary to a PIII-SVMP mRNA was uniquely present in the newborn dataset. These results support the view that age-dependent changes in the concentration of miRNA modulating the transition from a crotoxin-rich to a SVMP-rich venom from birth through adulthood can potentially explain what is observed in the proteomic analysis of the ontogenetic changes in the venom composition of C. s. simus. CONCLUSIONS Existing snake venom toxins are the result of early recruitment events in the Toxicofera clade of reptiles by which ordinary genes were duplicated, and the new genes selectively expressed in the venom gland and amplified to multigene families with extensive neofunctionalization throughout the approximately 112-125 million years of ophidian evolution. Our findings support the view that understanding the phenotypic diversity of snake venoms requires a deep knowledge of the mechanisms regulating the transcriptional and translational activity of the venom gland. Our results suggest a functional role for miRNAs. The impact of specific miRNAs in the modulation of venom composition, and the integration of the mechanisms responsible for the generation of these miRNAs in the evolutionary landscape of the snake's venom gland, are further challenges for future research.
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Affiliation(s)
- Jordi Durban
- Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas, Jaime Roig 11, Valencia 46010, Spain
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21
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Fattash I, Rooke R, Wong A, Hui C, Luu T, Bhardwaj P, Yang G. Miniature inverted-repeat transposable elements: discovery, distribution, and activity. Genome 2013; 56:475-86. [PMID: 24168668 DOI: 10.1139/gen-2012-0174] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Eukaryotic organisms have dynamic genomes, with transposable elements (TEs) as a major contributing factor. Although the large autonomous TEs can significantly shape genomic structures during evolution, genomes often harbor more miniature nonautonomous TEs that can infest genomic niches where large TEs are rare. In spite of their cut-and-paste transposition mechanisms that do not inherently favor copy number increase, miniature inverted-repeat transposable elements (MITEs) are abundant in eukaryotic genomes and exist in high copy numbers. Based on the large number of MITE families revealed in previous studies, accurate annotation of MITEs, particularly in newly sequenced genomes, will identify more genomes highly rich in these elements. Novel families identified from these analyses, together with the currently known families, will further deepen our understanding of the origins, transposase sources, and dramatic amplification of these elements.
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Affiliation(s)
- Isam Fattash
- a Department of Biology, University of Toronto at Mississauga, 3359 Mississauga Road, Mississauga, ON L5L 1C6, Canada
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22
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Abstract
SINEBase (http://sines.eimb.ru) integrates the revisited body of knowledge about short interspersed elements (SINEs). A set of formal definitions concerning SINEs was introduced. All available sequence data were screened through these definitions and the genetic elements misidentified as SINEs were discarded. As a result, 175 SINE families have been recognized in animals, flowering plants and green algae. These families were classified by the modular structure of their nucleotide sequences and the frequencies of different patterns were evaluated. These data formed the basis for the database of SINEs. The SINEBase website can be used in two ways: first, to explore the database of SINE families, and second, to analyse candidate SINE sequences using specifically developed tools. This article presents an overview of the database and the process of SINE identification and analysis.
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Affiliation(s)
- Nikita S Vassetzky
- Laboratory of Eukaryotic Genome Evolution, Engelhardt Institute of Molecular Biology, Moscow 119991, Russia
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23
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Piskurek O, Jackson DJ. Transposable elements: from DNA parasites to architects of metazoan evolution. Genes (Basel) 2012; 3:409-22. [PMID: 24704977 PMCID: PMC3899998 DOI: 10.3390/genes3030409] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2012] [Revised: 06/19/2012] [Accepted: 06/25/2012] [Indexed: 01/22/2023] Open
Abstract
One of the most unexpected insights that followed from the completion of the human genome a decade ago was that more than half of our DNA is derived from transposable elements (TEs). Due to advances in high throughput sequencing technologies it is now clear that TEs comprise the largest molecular class within most metazoan genomes. TEs, once categorised as "junk DNA", are now known to influence genomic structure and function by increasing the coding and non-coding genetic repertoire of the host. In this way TEs are key elements that stimulate the evolution of metazoan genomes. This review highlights several lines of TE research including the horizontal transfer of TEs through host-parasite interactions, the vertical maintenance of TEs over long periods of evolutionary time, and the direct role that TEs have played in generating morphological novelty.
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Affiliation(s)
- Oliver Piskurek
- Courant Research Centre Geobiology, Georg-August-University of Göttingen, Goldschmidtstr. 3, Göttingen 37077, Germany.
| | - Daniel J Jackson
- Courant Research Centre Geobiology, Georg-August-University of Göttingen, Goldschmidtstr. 3, Göttingen 37077, Germany.
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24
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Sanz L, Harrison RA, Calvete JJ. First draft of the genomic organization of a PIII-SVMP gene. Toxicon 2012; 60:455-69. [PMID: 22543188 DOI: 10.1016/j.toxicon.2012.04.331] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2012] [Revised: 03/27/2012] [Accepted: 04/04/2012] [Indexed: 11/20/2022]
Abstract
The evolutionary pathway of highly toxic proteins expressed in snake venom glands from proteins without toxic function and expressed in non-parotid tissues remains poorly understood. Here we examine gene structure of a representative of a venom protein with an ADAMs metalloproteinase evolutionary origin. The structure of the 15,652 bp Echis ocellatus pre-pro EOC00089-like PIII-SVMP gene was assembled from PCR-amplified sequences of overlapping genomic fragments. The gene comprises 12 exons interrupted by 11 introns. In a homology model of the EOC00089-like protein, the insertion of introns interrupting coding regions lie just after or between secondary structure elements. Long interspersed nuclear retroelements (LINE) L2/CR1 and RTE/Bov-B, short interspersed nuclear retroelements SINE/Sauria, and a hobo-activator DNA (Charlie, hAT) transposon were identified within introns 1, 3, 7 and 8. Pairwise amino acid sequence comparisons between EOC00089-like PIII-SVMP and its closest orthologs, ADAM28, from a mammal, Homo sapiens, and the lizard, Anolis carolinensis, showed that the ORFs of these three proteins share 42%/59%, 49%/69%, and 48%/65% (identity/similarity), respectively. The protein-coding positions interrupted by each of the 11 introns of the Echis PIII-SVMP gene are entirely conserved in the A. carolinensis and human ADAM28 genes. However, the lizard and the human ADAM28 genes contain 5 introns not present in the E. ocellatus gene. Furthermore, Echis and Anolis introns exhibit quantitatively and qualitatively distinctions in their inserted retroelements. These findings identify introns as possible key elements in the recruitment and amplification process of SVMPs into the venom gland of extant snakes. Ongoing reptile genome sequencing projects may shed light on this intriguing aspect of the emergence and evolution of venom toxin genes. Furthermore, the organization of the PIII-SVMP reported here provides a genomic explanation for the emergence of dimeric disintegrin subunits encoded by short messengers.
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Affiliation(s)
- Libia Sanz
- Consejo Superior de Investigaciones Científicas, Valencia, Spain
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25
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Abstract
Transposons are DNA sequences capable of moving in genomes. Early evidence showed their accumulation in many species and suggested their continued activity in at least isolated organisms. In the past decade, with the development of various genomic technologies, it has become abundantly clear that ongoing activity is the rule rather than the exception. Active transposons of various classes are observed throughout plants and animals, including humans. They continue to create new insertions, have an enormous variety of structural and functional impact on genes and genomes, and play important roles in genome evolution. Transposon activities have been identified and measured by employing various strategies. Here, we summarize evidence of current transposon activity in various plant and animal genomes.
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Affiliation(s)
- Cheng Ran Lisa Huang
- Institute of Genetic Medicine and High Throughput Biology Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Kathleen H. Burns
- Department of Pathology, Department of Oncology, and High Throughput Biology Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Jef D. Boeke
- Molecular Biology and Genetics, Institute of Genetic Medicine, and High Throughput Biology Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
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26
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Nespolo RF, Bacigalupe LD, Figueroa CC, Koteja P, Opazo JC. Using new tools to solve an old problem: the evolution of endothermy in vertebrates. Trends Ecol Evol 2011; 26:414-23. [DOI: 10.1016/j.tree.2011.04.004] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2010] [Revised: 04/05/2011] [Accepted: 04/11/2011] [Indexed: 01/13/2023]
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Castoe TA, Bronikowski AM, Brodie ED, Edwards SV, Pfrender ME, Shapiro MD, Pollock DD, Warren WC. A proposal to sequence the genome of a garter snake (Thamnophis sirtalis). Stand Genomic Sci 2011; 4:257-70. [PMID: 21677863 PMCID: PMC3111982 DOI: 10.4056/sigs.1664145] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Here we develop an argument in support of sequencing a garter snake (Thamnophis sirtalis) genome, and outline a plan to accomplish this. This snake is a common, widespread, nonvenomous North American species that has served as a model for diverse studies in evolutionary biology, physiology, genomics, behavior and coevolution. The anole lizard is currently the only genome sequence available for a non-avian reptile. Thus, the garter snake at this time would be the first available snake genome sequence and as such would provide much needed comparative representation of non-avian reptilian genomes, and would also allow critical new insights for vertebrate comparative genomic studies. We outline the major areas of discovery that the availability of the garter snake genome would enable, and describe a plan for whole-genome sequencing.
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Affiliation(s)
- Todd A. Castoe
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO
- Corresponding Author: Todd A. Castoe,
| | - Anne M. Bronikowski
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA
| | - Edmund D. Brodie
- Department of Biology, University of Virginia, Charlottesville, VA
| | - Scott V. Edwards
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA
| | | | | | - David D. Pollock
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO
| | - Wesley C. Warren
- Genome Sequencing Center, Washington University School of Medicine, St. Louis, MO
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28
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Tollis M, Boissinot S. The transposable element profile of the anolis genome: How a lizard can provide insights into the evolution of vertebrate genome size and structure. Mob Genet Elements 2011; 1:107-111. [PMID: 22016857 DOI: 10.4161/mge.1.2.17733] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2011] [Revised: 07/28/2011] [Accepted: 07/28/2011] [Indexed: 12/20/2022] Open
Abstract
The recent sequencing of the lizard genome provides a unique opportunity to examine the evolution of vertebrate genomes in a phylogenetic context. The lizard genome contains an extraordinary diversity of active transposable elements that far exceeds the diversity reported in extant mammals and birds. Retrotransposons and DNA transposons are represented by multiple active families, contributing to the very diverse repetitive landscape of the lizard. Surprisingly, ancient transposon copies are relatively rare suggesting that the transposon copy number is tightly controlled in lizard. This bias in favor of young copies results from the joint effect of purifying selection acting on novel insertions and a high rate of DNA loss. Recent analyses have revealed that the repetitive landscape of reptiles differ drastically from other extant amniotes by their diversity but also by the dynamics of amplification of their transposons. Thus, from the point of view of mobile elements, reptile genomes show more similarity to fish and amphibians than to other amniotes.
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Affiliation(s)
- Marc Tollis
- Department of Biology; Queens College; The City University of New York; Flushing, NY USA; The Graduate Center; The City University of New York; New York, NY USA
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29
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Llorens C, Futami R, Covelli L, Domínguez-Escribá L, Viu JM, Tamarit D, Aguilar-Rodríguez J, Vicente-Ripolles M, Fuster G, Bernet GP, Maumus F, Munoz-Pomer A, Sempere JM, Latorre A, Moya A. The Gypsy Database (GyDB) of mobile genetic elements: release 2.0. Nucleic Acids Res 2011; 39:D70-4. [PMID: 21036865 PMCID: PMC3013669 DOI: 10.1093/nar/gkq1061] [Citation(s) in RCA: 236] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
This article introduces the second release of the Gypsy Database of Mobile Genetic Elements (GyDB 2.0): a research project devoted to the evolutionary dynamics of viruses and transposable elements based on their phylogenetic classification (per lineage and protein domain). The Gypsy Database (GyDB) is a long-term project that is continuously progressing, and that owing to the high molecular diversity of mobile elements requires to be completed in several stages. GyDB 2.0 has been powered with a wiki to allow other researchers participate in the project. The current database stage and scope are long terminal repeats (LTR) retroelements and relatives. GyDB 2.0 is an update based on the analysis of Ty3/Gypsy, Retroviridae, Ty1/Copia and Bel/Pao LTR retroelements and the Caulimoviridae pararetroviruses of plants. Among other features, in terms of the aforementioned topics, this update adds: (i) a variety of descriptions and reviews distributed in multiple web pages; (ii) protein-based phylogenies, where phylogenetic levels are assigned to distinct classified elements; (iii) a collection of multiple alignments, lineage-specific hidden Markov models and consensus sequences, called GyDB collection; (iv) updated RefSeq databases and BLAST and HMM servers to facilitate sequence characterization of new LTR retroelement and caulimovirus queries; and (v) a bibliographic server. GyDB 2.0 is available at http://gydb.org.
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Affiliation(s)
- Carlos Llorens
- Biotechvana, Parc Científic, Universitat de València, Calle Catedrático José Beltrán 2, 46980 Paterna, València, Spain.
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30
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Grechko VV, Kosushkin SA, Borodulina OR, Butaeva FG, Darevsky IS. Short interspersed elements (SINEs) of squamate reptiles (Squam1 and Squam2): structure and phylogenetic significance. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2010; 316B:212-26. [PMID: 21462315 DOI: 10.1002/jez.b.21391] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2010] [Revised: 11/05/2010] [Accepted: 11/07/2010] [Indexed: 11/08/2022]
Abstract
Short interspersed elements (SINEs) are important nuclear molecular markers of the evolution of many eukaryotes. However, the SINEs of squamate reptile genomes have been little studied. We first identified two families of SINEs, termed Squam1 and Squam2, in the DNA of meadow lizard Darevskia praticola (Lacertidae) by performing DNA hybridization and PCR. Later, the same families of retrotransposons were found using the same methods in members of another 25 lizard families (from Iguania, Scincomorpha, Gekkota, Varanoidea, and Diploglossa infraorders) and two snake families, but their abundances in these taxa varied greatly. Both SINEs were Squamata-specific and were absent from mammals, birds, crocodiles, turtles, amphibians, and fish. Squam1 possessed some characteristics common to tRNA-related SINEs from fish and mammals, while Squam2 belonged to the tRNA(Ala) group of SINEs and had a more unusual and divergent structure. Squam2-related sequences were found in several unannotated GenBank sequences of squamate reptiles. Squam1 abundance in the Polychrotidae, Agamidae, Leiolepididae, Chamaeleonidae, Scincidae, Lacertidae, Gekkonidae, Varanidae, Helodermatidae, and two snake families were 10(2) -10(4) times higher than those in other taxa (Corytophanidae, Iguanidae, Anguidae, Cordylidae, Gerrhosauridae, Pygopodidae, and Eublepharidae). A less dramatic degree of copy number variation was observed for Squam2 in different taxa. Several Squam1 copies from Lacertidae, Chamaeleonidae, Gekkonidae, Varanidae, and Colubridae were sequenced and found to have evident orthologous features, as well as taxa-specific autapomorphies. Squam1 from Lacertidae and Chamaeleonidae could be divided into several subgroups based on sequence differences. Possible applications of these SINEs as Squamata phylogeny markers are discussed.
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Affiliation(s)
- Vernata V Grechko
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.
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Novick PA, Smith JD, Floumanhaft M, Ray DA, Boissinot S. The evolution and diversity of DNA transposons in the genome of the Lizard Anolis carolinensis. Genome Biol Evol 2010; 3:1-14. [PMID: 21127169 PMCID: PMC3014272 DOI: 10.1093/gbe/evq080] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/26/2010] [Indexed: 01/19/2023] Open
Abstract
DNA transposons have considerably affected the size and structure of eukaryotic genomes and have been an important source of evolutionary novelties. In vertebrates, DNA transposons are discontinuously distributed due to the frequent extinction and recolonization of these genomes by active elements. We performed a detailed analysis of the DNA transposons in the genome of the lizard Anolis carolinensis, the first non-avian reptile to have its genome sequenced. Elements belonging to six of the previously recognized superfamilies of elements (hAT, Tc1/Mariner, Helitron, PIF/Harbinger, Polinton/Maverick, and Chapaev) were identified. However, only four (hAT, Tc1/Mariner, Helitron, and Chapaev) of these superfamilies have successfully amplified in the anole genome, producing 67 distinct families. The majority (57/67) are nonautonomous and demonstrate an extraordinary diversity of structure, resulting from frequent interelement recombination and incorporation of extraneous DNA sequences. The age distribution of transposon families differs among superfamilies and reveals different dynamics of amplification. Chapaev is the only superfamily to be extinct and is represented only by old copies. The hAT, Tc1/Mariner, and Helitron superfamilies show different pattern of amplification, yet they are predominantly represented by young families, whereas divergent families are exceedingly rare. Although it is likely that some elements, in particular long ones, are subjected to purifying selection and do not reach fixation, the majority of families are neutral and accumulate in the anole genome in large numbers. We propose that the scarcity of old copies in the anole genome results from the rapid decay of elements, caused by a high rate of DNA loss.
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Affiliation(s)
- Peter A. Novick
- Department of Biology, Queens College, the City University of New York
- Graduate School and University Center, the City University of New York
| | - Jeremy D. Smith
- Department of Biochemistry and Molecular Biology, Mississippi State University
| | - Mark Floumanhaft
- Department of Biology, Queens College, the City University of New York
| | - David A. Ray
- Department of Biochemistry and Molecular Biology, Mississippi State University
| | - Stéphane Boissinot
- Department of Biology, Queens College, the City University of New York
- Graduate School and University Center, the City University of New York
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Janes DE, Organ CL, Fujita MK, Shedlock AM, Edwards SV. Genome evolution in Reptilia, the sister group of mammals. Annu Rev Genomics Hum Genet 2010; 11:239-64. [PMID: 20590429 DOI: 10.1146/annurev-genom-082509-141646] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The genomes of birds and nonavian reptiles (Reptilia) are critical for understanding genome evolution in mammals and amniotes generally. Despite decades of study at the chromosomal and single-gene levels, and the evidence for great diversity in genome size, karyotype, and sex chromosome diversity, reptile genomes are virtually unknown in the comparative genomics era. The recent sequencing of the chicken and zebra finch genomes, in conjunction with genome scans and the online publication of the Anolis lizard genome, has begun to clarify the events leading from an ancestral amniote genome--predicted to be large and to possess a diverse repeat landscape on par with mammals and a birdlike sex chromosome system--to the small and highly streamlined genomes of birds. Reptilia exhibit a wide range of evolutionary rates of different subgenomes and, from isochores to mitochondrial DNA, provide a critical contrast to the genomic paradigms established in mammals.
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Affiliation(s)
- Daniel E Janes
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
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Luchetti A, Mantovani B. Talua SINE Biology in the Genome of the Reticulitermes Subterranean Termites (Isoptera, Rhinotermitidae). J Mol Evol 2009; 69:589-600. [DOI: 10.1007/s00239-009-9285-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2009] [Accepted: 09/21/2009] [Indexed: 10/20/2022]
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Llorens C, Muñoz-Pomer A, Bernad L, Botella H, Moya A. Network dynamics of eukaryotic LTR retroelements beyond phylogenetic trees. Biol Direct 2009; 4:41. [PMID: 19883502 PMCID: PMC2774666 DOI: 10.1186/1745-6150-4-41] [Citation(s) in RCA: 94] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2009] [Accepted: 11/02/2009] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Sequencing projects have allowed diverse retroviruses and LTR retrotransposons from different eukaryotic organisms to be characterized. It is known that retroviruses and other retro-transcribing viruses evolve from LTR retrotransposons and that this whole system clusters into five families: Ty3/Gypsy, Retroviridae, Ty1/Copia, Bel/Pao and Caulimoviridae. Phylogenetic analyses usually show that these split into multiple distinct lineages but what is yet to be understood is how deep evolution occurred in this system. RESULTS We combined phylogenetic and graph analyses to investigate the history of LTR retroelements both as a tree and as a network. We used 268 non-redundant LTR retroelements, many of them introduced for the first time in this work, to elucidate all possible LTR retroelement phylogenetic patterns. These were superimposed over the tree of eukaryotes to investigate the dynamics of the system, at distinct evolutionary times. Next, we investigated phenotypic features such as duplication and variability of amino acid motifs, and several differences in genomic ORF organization. Using this information we characterized eight reticulate evolution markers to construct phenotypic network models. CONCLUSION The evolutionary history of LTR retroelements can be traced as a time-evolving network that depends on phylogenetic patterns, epigenetic host-factors and phenotypic plasticity. The Ty1/Copia and the Ty3/Gypsy families represent the oldest patterns in this network that we found mimics eukaryotic macroevolution. The emergence of the Bel/Pao, Retroviridae and Caulimoviridae families in this network can be related with distinct inflations of the Ty3/Gypsy family, at distinct evolutionary times. This suggests that Ty3/Gypsy ancestors diversified much more than their Ty1/Copia counterparts, at distinct geological eras. Consistent with the principle of preferential attachment, the connectivities among phenotypic markers, taken as network-represented combinations, are power-law distributed. This evidences an inflationary mode of evolution where the system diversity; 1) expands continuously alternating vertical and gradual processes of phylogenetic divergence with episodes of modular, saltatory and reticulate evolution; 2) is governed by the intrinsic capability of distinct LTR retroelement host-communities to self-organize their phenotypes according to emergent laws characteristic of complex systems. REVIEWERS This article was reviewed by Eugene V. Koonin, Eric Bapteste, and Enmanuelle Lerat (nominated by King Jordan).
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Affiliation(s)
- Carlos Llorens
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva (ICBIBE), Universitat de València, Paterna, Valencia, Spain
- Biotechvana, Parc Científic, Universitat de València, Paterna, Valencia, Spain
| | - Alfonso Muñoz-Pomer
- Biotechvana, Parc Científic, Universitat de València, Paterna, Valencia, Spain
- Departamento de Sistemas Informáticos y Computación (DSIC), Universitat Politècnica de València, Valencia, Spain
| | - Lucia Bernad
- Biotechvana, Parc Científic, Universitat de València, Paterna, Valencia, Spain
| | - Hector Botella
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva (ICBIBE), Universitat de València, Paterna, Valencia, Spain
- Área de Paleontología, Dpto. Geología, Universitat de València, Paterna, Valencia, Spain
| | - Andrés Moya
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva (ICBIBE), Universitat de València, Paterna, Valencia, Spain
- Centro Superior de Investigación en Salud Pública (CSISP), Valencia, Spain
- CIBER de Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
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