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Wittler R. Alignment- and reference-free phylogenomics with colored de Bruijn graphs. Algorithms Mol Biol 2020; 15:4. [PMID: 32280365 PMCID: PMC7137503 DOI: 10.1186/s13015-020-00164-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 03/21/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The increasing amount of available genome sequence data enables large-scale comparative studies. A common task is the inference of phylogenies-a challenging task if close reference sequences are not available, genome sequences are incompletely assembled, or the high number of genomes precludes multiple sequence alignment in reasonable time. RESULTS We present a new whole-genome based approach to infer phylogenies that is alignment- and reference-free. In contrast to other methods, it does not rely on pairwise comparisons to determine distances to infer edges in a tree. Instead, a colored de Bruijn graph is constructed, and information on common subsequences is extracted to infer phylogenetic splits. CONCLUSIONS The introduced new methodology for large-scale phylogenomics shows high potential. Application to different datasets confirms robustness of the approach. A comparison to other state-of-the-art whole-genome based methods indicates comparable or higher accuracy and efficiency.
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Affiliation(s)
- Roland Wittler
- Genome Informatics, Faculty of Technology, Bielefeld University, Bielefeld, Germany
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
- Center for Biotechnology, Bielefeld Institute for Bioinformatics Infrastructure, Bielefeld University, Bielefeld, Germany
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2
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Simão MC, Haudry A, Granzotto A, de Setta N, Carareto CMA. Helena and BS: Two Travellers between the Genera Drosophila and Zaprionus. Genome Biol Evol 2018; 10:2671-2685. [PMID: 30165545 PMCID: PMC6179348 DOI: 10.1093/gbe/evy184] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/22/2018] [Indexed: 12/20/2022] Open
Abstract
The frequency of horizontal transfers of transposable elements (HTTs) varies among the types of elements according to the transposition mode and the geographical and temporal overlap of the species involved in the transfer. The drosophilid species of the genus Zaprionus and those of the melanogaster, obscura, repleta, and virilis groups of the genus Drosophila investigated in this study shared space and time at some point in their evolutionary history. This is particularly true of the subgenus Zaprionus and the melanogaster subgroup, which overlapped both geographically and temporally in Tropical Africa during their period of origin and diversification. Here, we tested the hypothesis that this overlap may have facilitated the transfer of retrotransposons without long terminal repeats (non-LTRs) between these species. We estimated the HTT frequency of the non-LTRs BS and Helena at the genome-wide scale by using a phylogenetic framework and a vertical and horizontal inheritance consistence analysis (VHICA). An excessively low synonymous divergence among distantly related species and incongruities between the transposable element and species phylogenies allowed us to propose at least four relatively recent HTT events of Helena and BS involving ancestors of the subgroup melanogaster and ancestors of the subgenus Zaprionus during their concomitant diversification in Tropical Africa, along with older possible events between species of the subgenera Drosophila and Sophophora. This study provides the first evidence for HTT of non-LTRs retrotransposons between Drosophila and Zaprionus, including an in-depth reconstruction of the time frame and geography of these events.
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Affiliation(s)
- Maryanna C Simão
- Universidade Estadual Paulista (Unesp), Instituto de Biociências Letras e Ciências Exatas (Ibilce), Câmpus São José do Rio Preto, SP, Brazil
| | - Annabelle Haudry
- Univ Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive, Villeurbanne, France
| | - Adriana Granzotto
- Universidade Estadual Paulista (Unesp), Instituto de Biociências Letras e Ciências Exatas (Ibilce), Câmpus São José do Rio Preto, SP, Brazil
| | - Nathalia de Setta
- Universidade Federal do ABC (UFABC), Centro de Ciências Naturais e Humanas (CCNH), São Bernardo do Campo, SP, Brazil
| | - Claudia M A Carareto
- Universidade Estadual Paulista (Unesp), Instituto de Biociências Letras e Ciências Exatas (Ibilce), Câmpus São José do Rio Preto, SP, Brazil
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3
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Wallau GL, Vieira C, Loreto ÉLS. Genetic exchange in eukaryotes through horizontal transfer: connected by the mobilome. Mob DNA 2018; 9:6. [PMID: 29422954 PMCID: PMC5791352 DOI: 10.1186/s13100-018-0112-9] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 01/24/2018] [Indexed: 12/11/2022] Open
Abstract
Background All living species contain genetic information that was once shared by their common ancestor. DNA is being inherited through generations by vertical transmission (VT) from parents to offspring and from ancestor to descendant species. This process was considered the sole pathway by which biological entities exchange inheritable information. However, Horizontal Transfer (HT), the exchange of genetic information by other means than parents to offspring, was discovered in prokaryotes along with strong evidence showing that it is a very important process by which prokaryotes acquire new genes. Main body For some time now, it has been a scientific consensus that HT events were rare and non-relevant for evolution of eukaryotic species, but there is growing evidence supporting that HT is an important and frequent phenomenon in eukaryotes as well. Conclusion Here, we will discuss the latest findings regarding HT among eukaryotes, mainly HT of transposons (HTT), establishing HTT once and for all as an important phenomenon that should be taken into consideration to fully understand eukaryotes genome evolution. In addition, we will discuss the latest development methods to detect such events in a broader scale and highlight the new approaches which should be pursued by researchers to fill the knowledge gaps regarding HTT among eukaryotes.
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Affiliation(s)
- Gabriel Luz Wallau
- 1Entomology Department, Aggeu Magalhães Institute, Oswaldo Cruz Foundation, Recife, PE Brazil
| | - Cristina Vieira
- 2Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive, UMR5558, F-69622 Villeurbanne, France
| | - Élgion Lúcio Silva Loreto
- 3Department of Biochemistry and Molecular Biology, Federal University of Santa Maria, Santa Maria, RS Brazil
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4
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Wallau GL, Capy P, Loreto E, Le Rouzic A, Hua-Van A. VHICA, a New Method to Discriminate between Vertical and Horizontal Transposon Transfer: Application to the Mariner Family within Drosophila. Mol Biol Evol 2015; 33:1094-109. [PMID: 26685176 PMCID: PMC4776708 DOI: 10.1093/molbev/msv341] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Transposable elements (TEs) are genomic repeated sequences that display complex evolutionary patterns. They are usually inherited vertically, but can occasionally be transmitted between sexually independent species, through so-called horizontal transposon transfers (HTTs). Recurrent HTTs are supposed to be essential in life cycle of TEs, which are otherwise destined for eventual decay. HTTs also impact the host genome evolution. However, the extent of HTTs in eukaryotes is largely unknown, due to the lack of efficient, statistically supported methods that can be applied to multiple species sequence data sets. Here, we developed a new automated method available as a R package "vhica" that discriminates whether a given TE family was vertically or horizontally transferred, and potentially infers donor and receptor species. The method is well suited for TE sequences extracted from complete genomes, and applicable to multiple TEs and species at the same time. We first validated our method using Drosophila TE families with well-known evolutionary histories, displaying both HTTs and vertical transmission. We then tested 26 different lineages of mariner elements recently characterized in 20 Drosophila genomes, and found HTTs in 24 of them. Furthermore, several independent HTT events could often be detected within the same mariner lineage. The VHICA (Vertical and Horizontal Inheritance Consistence Analysis) method thus appears as a valuable tool to analyze the evolutionary history of TEs across a large range of species.
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Affiliation(s)
- Gabriel Luz Wallau
- Pós Graduação em Biodiversidade Animal, Universidade Federal de Santa Maria, Santa Maria, Rio Grande do Sul, Brazil Departamento de Entomologia, Centro de Pesquisas Aggeu Magalhães-FIOCRUZ-CPqAM, Recife, PE, Brazil
| | - Pierre Capy
- Laboratoire Évolution, Génomes, Comportement, Écologie; CNRS, IRD, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Elgion Loreto
- Pós Graduação em Biodiversidade Animal, Universidade Federal de Santa Maria, Santa Maria, Rio Grande do Sul, Brazil Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Santa Maria, Rio Grande do Sul, Brazil
| | - Arnaud Le Rouzic
- Laboratoire Évolution, Génomes, Comportement, Écologie; CNRS, IRD, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Aurélie Hua-Van
- Laboratoire Évolution, Génomes, Comportement, Écologie; CNRS, IRD, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
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Abstract
Retroelements with long-terminal repeats (LTRs) inhabit nearly all eukaryotic genomes. During the time of their rich evolutionary history they have developed highly diverse forms, ranging from ordinary retrotransposons to complex pathogenic retroviruses such as HIV-I. Errantiviruses are a group of insect endogenous LTR elements that share structural and functional features with vertebrate endogenous retroviruses. The errantiviruses illustrate one of the evolutionary strategies of retrotransposons to become infective, which together with their similarities to vertebrate retroviruses make them an attractive object of research promising to shed more light on the evolution of retroviruses.
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Affiliation(s)
- Yury Stefanov
- Engelhardt Institute of Molecular Biology; Russian Academy of Sciences; Moscow, Russia
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6
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Dias ES, Carareto CMA. Ancestral polymorphism and recent invasion of transposable elements in Drosophila species. BMC Evol Biol 2012; 12:119. [PMID: 22823479 PMCID: PMC3499218 DOI: 10.1186/1471-2148-12-119] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2011] [Accepted: 07/10/2012] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND During the evolution of transposable elements, some processes, such as ancestral polymorphisms and horizontal transfer of sequences between species, can produce incongruences in phylogenies. We investigated the evolutionary history of the transposable elements Bari and 412 in the sequenced genomes of the Drosophila melanogaster group and in the sibling species D. melanogaster and D. simulans using traditional phylogenetic and network approaches. RESULTS Maximum likelihood (ML) phylogenetic analyses revealed incongruences and unresolved relationships for both the Bari and 412 elements. The DNA transposon Bari within the D. ananassae genome is more closely related to the element of the melanogaster complex than to the sequence in D. erecta, which is inconsistent with the species phylogeny. Divergence analysis and the comparison of the rate of synonymous substitutions per synonymous site of the Bari and host gene sequences explain the incongruence as an ancestral polymorphism that was inherited stochastically by the derived species. Unresolved relationships were observed in the ML phylogeny of both elements involving D. melanogaster, D. simulans and D. sechellia. A network approach was used to attempt to resolve these relationships. The resulting tree suggests recent transfers of both elements between D. melanogaster and D. simulans. The divergence values of the elements between these species support this conclusion. CONCLUSIONS We showed that ancestral polymorphism and recent invasion of genomes due to introgression or horizontal transfer between species occurred during the evolutionary history of the Bari and 412 elements in the melanogaster group. These invasions likely occurred in Africa during the Pleistocene, before the worldwide expansion of D. melanogaster and D. simulans.
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Affiliation(s)
- Elaine Silva Dias
- Department of Biology, São José do Rio Preto, UNESP-São Paulo State University, São Paulo, Brazil
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7
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Wallau GL, Ortiz MF, Loreto ELS. Horizontal transposon transfer in eukarya: detection, bias, and perspectives. Genome Biol Evol 2012; 4:689-99. [PMID: 22798449 PMCID: PMC3516303 DOI: 10.1093/gbe/evs055] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The genetic similarity observed among species is normally attributed to the existence of
a common ancestor. However, a growing body of evidence suggests that the exchange of
genetic material is not limited to the transfer from parent to offspring but can also
occur through horizontal transfer (HT). Transposable elements (TEs) are DNA fragments with
an innate propensity for HT; they are mobile and possess parasitic characteristics that
allow them to exist and proliferate within host genomes. However, horizontal transposon
transfer (HTT) is not easily detected, primarily because the complex TE life cycle can
generate phylogenetic patterns similar to those expected for HTT events. The increasingly
large number of new genome projects, in all branches of life, has provided an
unprecedented opportunity to evaluate the TE content and HTT events in these species,
although a standardized method of HTT detection is required before trends in the HTT rates
can be evaluated in a wide range of eukaryotic taxa and predictions about these events can
be made. Thus, we propose a straightforward hypothesis test that can be used by TE
specialists and nonspecialists alike to discriminate between HTT events and natural TE
life cycle patterns. We also discuss several plausible explanations and predictions for
the distribution and frequency of HTT and for the inherent biases of HTT detection.
Finally, we discuss some of the methodological concerns for HTT detection that may result
in the underestimation and overestimation of HTT rates during eukaryotic genome
evolution.
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Affiliation(s)
- Gabriel Luz Wallau
- Programa de Pós-Graduação em Biodiversidade Animal, Universidade Federal de Santa Maria, Brazil.
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8
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Commar LS, Galego LGDC, Ceron CR, Carareto CMA. Taxonomic and evolutionary analysis of Zaprionus indianus and its colonization of Palearctic and Neotropical regions. Genet Mol Biol 2012; 35:395-406. [PMID: 22888286 PMCID: PMC3389525 DOI: 10.1590/s1415-47572012000300003] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2011] [Accepted: 02/28/2012] [Indexed: 11/21/2022] Open
Abstract
Zaprionus indianus is a dipteran (Drosophilidae) with a wide distribution throughout the tropics and temperate Palearctic and Nearctic regions. There have been proposals to reclassify the genus Zaprionus as a subgenus or group of the genus Drosophila because various molecular markers have indicated a close relationship between Zaprionus species and the immigrans-Hirtodrosophila radiation within Drosophila. These markers, together with alloenzymes and quantitative traits, have been used to describe the probable scenario for the expansion of Zaprionus indianus from its center of dispersal (Africa) to regions of Asia (ancient dispersal) and the Americas (recent dispersal). The introduction of Z. indianus into Brazil was first reported in 1999 and the current consensus is that the introduced flies came from high-latitude African populations through the importation of fruit. Once in Brazil, Z. indianus spread rapidly throughout the Southeast and then to the rest of the country, in association with highway-based fruit commerce. These and other aspects of the evolutionary biology of Z. indianus are addressed in this review, including a description of a probable route for this species’ dispersal during its recent expansion.
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Affiliation(s)
- Leliane Silva Commar
- Departamento de Biologia, Universidade Estadual Paulista "Júlio de Mesquita Filho", São José do Rio Preto, SP, Brazil
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9
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New Drosophila P-like elements and reclassification of Drosophila P-elements subfamilies. Mol Genet Genomics 2012; 287:531-40. [PMID: 22610468 DOI: 10.1007/s00438-012-0691-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2011] [Accepted: 04/12/2012] [Indexed: 10/28/2022]
Abstract
Genomic searches for P-like transposable elements were performed (1) in silico in the 12 available Drosophila genomes and (2) by PCR using degenerate primers in 21 Neotropical Drosophila species. In silico searches revealed P-like sequences only in Drosophila persimilis and Drosophila willistoni. Sixteen new P-like elements were obtained by PCR. These sequences were added to sequences of previously described P-like elements, and a phylogenetic analysis was performed. The subfamilies of P-elements described in the literature (Canonical, M, O, T, and K) were included in the reconstructed tree, and all were monophyletic. However, we suggest that some subfamilies can be enlarged, other subdivided, and some new subfamilies may be proposed, totalizing eleven subfamilies, most of which contain new P-like sequences. Our analyses support the monophyly of P-like elements in Drosophilidae. We suggest that, once these elements need host-specific factors to be mobilizable, the horizontal transfer (HT) of P-like elements may be inhibited among more distant taxa. Nevertheless, HT among Drosophilidae species appears to be a common phenomenon.
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10
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Carareto CM. Tropical Africa as a cradle for horizontal transfers of transposable elements between species of the genera Drosophila and Zaprionus. Mob Genet Elements 2011; 1:179-186. [PMID: 22312591 DOI: 10.4161/mge.1.3.18052] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2011] [Accepted: 09/12/2011] [Indexed: 11/19/2022] Open
Abstract
We have recently reported numerous cases of horizontal transfers of transposable elements between species of drosophilids. These studies revealed a substantial number of horizontal transfers between species of the subgroup melanogaster of the genus Drosophila and between these species and species of the genus Zaprionus. In this review, these transfers and similar, previously reported events are discussed and reanalysed to portray the interrelationships between the species that allowed the occurrence of so many horizontal transfers. The paper also addresses problems that may arise in drawing inferences about the time period during which the horizontal transfers occurred and the factors that may be associated with these transfers are discussed.
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Affiliation(s)
- Claudia Ma Carareto
- Laboratory of Molecular Evolution; Department of Biology; UNESP-São Paulo State University; São Paulo, Brazil
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11
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de Setta N, Van Sluys MA, Capy P, Carareto CMA. Copia retrotransposon in the Zaprionus genus: another case of transposable element sharing with the Drosophila melanogaster subgroup. J Mol Evol 2011; 72:326-38. [PMID: 21347850 DOI: 10.1007/s00239-011-9435-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2010] [Accepted: 02/07/2011] [Indexed: 11/24/2022]
Abstract
Copia is a retrotransposon that appears to be distributed widely among the Drosophilidae subfamily. Evolutionary analyses of regulatory regions have indicated that the Copia retrotransposon evolved through both positive and purifying selection, and that horizontal transfer (HT) could also explain its patchy distribution of the among the subfamilies of the melanogaster subgroup. Additionally, Copia elements could also have transferred between melanogaster subgroup and other species of Drosophilidae-D. willistoni and Z. tuberculatus. In this study, we surveyed seven species of the Zaprionus genus by sequencing the LTR-ULR and reverse transcriptase regions, and by using RT-PCR in order to understand the distribution and evolutionary history of Copia in the Zaprionus genus. The Copia element was detected, and was transcriptionally active, in all species investigated. Structural and selection analysis revealed Zaprionus elements to be closely related to the most ancient subfamily of the melanogaster subgroup, and they seem to be evolving mainly under relaxed purifying selection. Taken together, these results allowed us to classify the Zaprionus sequences as a new subfamily-ZapCopia, a member of the Copia retrotransposon family of the melanogaster subgroup. These findings indicate that the Copia retrotransposon is an ancient component of the genomes of the Zaprionus species and broaden our understanding of the diversity of retrotransposons in the Zaprionus genus.
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Affiliation(s)
- Nathalia de Setta
- Laboratory of Molecular Evolution, Department of Biology, UNESP, São Paulo State University, 15054-000 São José do Rio Preto, SP, Brazil
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Deprá M, Panzera Y, Ludwig A, Valente VLS, Loreto ELS. hosimary: a new hAT transposon group involved in horizontal transfer. Mol Genet Genomics 2010; 283:451-9. [DOI: 10.1007/s00438-010-0531-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2009] [Accepted: 03/06/2010] [Indexed: 10/19/2022]
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Robe LJ, Loreto ELS, Valente VLS. Radiation of the ,,Drosophila“ subgenus (Drosophilidae, Diptera) in the Neotropics. J ZOOL SYST EVOL RES 2010. [DOI: 10.1111/j.1439-0469.2009.00563.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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14
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Díaz-González J, Domínguez A, Albornoz J. Genomic distribution of retrotransposons 297, 1731, copia, mdg1 and roo in the Drosophila melanogaster species subgroup. Genetica 2009; 138:579-86. [PMID: 20012466 DOI: 10.1007/s10709-009-9430-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2009] [Accepted: 12/01/2009] [Indexed: 10/20/2022]
Abstract
The intragenomic distribution of five retrotransposon families (297, 1731, copia, mdg1 and roo) in the species of the melanogaster complex was studied by comparing results of the Southern blotting technique in males and females with those of in situ hybridization. The degree of structural polymorphism of each family in the different species was also investigated by restriction enzyme analysis. It was found that genomic distribution is a trait that depends on the family and species. The distribution of roo is mainly euchromatic in the four species and 1731 is heterochromatic, but the distribution of families 297, copia and mdg1 is markedly different in the melanogaster and simulans clades. These families were mainly euchromatic in D. melanogaster but heterochromatic in its sibling species. In the simulans clade most copia and mdg1 elements are located on chromosome Y. Differences in genomic distribution are unrelated with structural conservation. The relation of intragenomic distribution to phylogeny, transpositional activity and the role of the host genome are discussed.
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Affiliation(s)
- Julia Díaz-González
- Area de Genética, Departamento de Biología Funcional, Universidad de Oviedo, 33071, Oviedo, Spain
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15
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de Setta N, Van Sluys MA, Capy P, Carareto CMA. Multiple invasions of Gypsy and Micropia retroelements in genus Zaprionus and melanogaster subgroup of the genus Drosophila. BMC Evol Biol 2009; 9:279. [PMID: 19954522 PMCID: PMC2797524 DOI: 10.1186/1471-2148-9-279] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2009] [Accepted: 12/02/2009] [Indexed: 11/23/2022] Open
Abstract
Background The Zaprionus genus shares evolutionary features with the melanogaster subgroup, such as space and time of origin. Although little information about the transposable element content in the Zaprionus genus had been accumulated, some of their elements appear to be more closely related with those of the melanogaster subgroup, indicating that these two groups of species were involved in horizontal transfer events during their evolution. Among these elements, the Gypsy and the Micropia retroelements were chosen for screening in seven species of the two Zaprionus subgenera, Anaprionus and Zaprionus. Results Screening allowed the identification of diverse Gypsy and Micropia retroelements only in species of the Zaprionus subgenus, showing that they are transcriptionally active in the sampled species. The sequences of each retroelement were closely related to those of the melanogaster species subgroup, and the most parsimonious hypothesis would be that 15 horizontal transfer events shaped their evolution. The Gypsy retroelement of the melanogaster subgroup probably invaded the Zaprionus genomes about 11 MYA. In contrast, the Micropia retroelement may have been introduced into the Zaprionus subgenus and the melanogaster subgroup from an unknown donor more recently (~3 MYA). Conclusion Gypsy and Micropia of Zaprionus and melanogaster species share similar evolutionary patterns. The sharing of evolutionary, ecological and ethological features probably allowed these species to pass through a permissive period of transposable element invasion, explaining the proposed waves of horizontal transfers.
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Affiliation(s)
- Nathalia de Setta
- Department of Biology, UNESP - São Paulo State University, São José do Rio Preto, SP, Brazil.
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