1,720,983 research outputs found
TaxMan: a taxonomic database manager
Get PDFAbstract Background Phylogenetic analysis of large, multiple-gene datasets, assembled from public sequence databases, is rapidly becoming a popular way to approach difficult phylogenetic problems. Supermatrices (concatenated multiple sequence alignments of multiple genes) can yield more phylogenetic signal than individual genes. However, manually assembling such datasets for a large taxonomic group is time-consuming and error-prone. Additionally, sequence curation, alignment and assessment of the results of phylogenetic analysis are made particularly difficult by the potential for a given gene in a given species to be unrepresented, or to be represented by multiple or partial sequences. We have developed a software package, TaxMan, that largely automates the processes of sequence acquisition, consensus building, alignment and taxon selection to facilitate this type of phylogenetic study. Results TaxMan uses freely available tools to allow rapid assembly, storage and analysis of large, aligned DNA and protein sequence datasets for user-defined sets of species and genes. The user provides GenBank format files and a list of gene names and synonyms for the loci to analyse. Sequences are extracted from the GenBank files on the basis of annotation and sequence similarity. Consensus sequences are built automatically. Alignment is carried out (where possible, at the protein level) and aligned sequences are stored in a database. TaxMan can automatically determine the best subset of taxa to examine phylogeny at a given taxonomic level. By using the stored aligned sequences, large concatenated multiple sequence alignments can be generated rapidly for a subset and output in analysis-ready file formats. Trees resulting from phylogenetic analysis can be stored and compared with a reference taxonomy. Conclusion TaxMan allows rapid automated assembly of a multigene datasets of aligned sequences for large taxonomic groups. By extracting sequences on the basis of both annotation and BLAST similarity, it ensures that all available sequence data can be brought to bear on a phylogenetic problem, but remains fast enough to cope with many thousands of records. By automatically assisting in the selection of the best subset of taxa to address a particular phylogenetic problem, TaxMan greatly speeds up the process of generating multiple sequence alignments for phylogenetic analysis. Our results indicate that an automated phylogenetic workbench can be a useful tool when correctly guided by user knowledge.</p
AMiGA: the arthropodan mitochondrial genomes accessible database
No full textFeijão P, Neiva LS, Azeredo-Espin AML d., Lessinger AC. AMiGA: the arthropodan mitochondrial genomes accessible database. Bioinformatics. 2006;22(7):902-903
The mitochondrial DNA control region of muscidae flies: Evolution and structural conservation in a dipteran context
No full textThe structure and evolution of the mtDNA control region (CR) and its flanking genes in economically important dipterans from the family Muscidae (Brachycera: Calyptratae), Haematobia irritans, Musca domestica, Atherigona orientalis, and Stomoxys calcitrans are presented in this paper, along with the description of short noncoding intergenic regions possibly related to CR flanking sequences in Stomoxys calcitrans and Ophyra aenescens mtDNAs (ScIR and OaIR, respectively). S. calcitrans showed a large CR with an similar to 550-bp element tandemly repeated and a duplicated tRNA(Ile) stop gene. The characterization of H. irritans, M. domestica, A. orientalis, and S. calcitrans CR sequences led to the identification of seven conserved sequence blocks homologous to the elements previously described for Calliphoridae and Oestridae species (Brachycera: Calyptratae). Comparative analysis with Drosophila species (Brachycera: Acalyptratae) revealed four conserved regions. The putative functional roles of the conserved elements in the regulation of replication and transcription processes are addressed. The characterization of the structural organization of the mitochondrial genome CR demonstrates the plasticity of the mtDNA molecule in family Muscidae.64551952
Characterization of polymorphic microsatellite markers for the blowfly Chrysomya albiceps (Diptera : Calliphoridae)
No full textChrysomya albiceps is a blowfly of great medical, sanitary and forensic importance widely distributed in the Afrotropical, southern Palaearctic, northern Oriental regions and, recently, in Central and South Americas. Here, we report the characterization of 13 polymorphic microsatellite markers for C. albiceps. The number of alleles ranged from three to 13 alleles with expected heterozygosities ranging from 0.4668 to 0.8408. These markers will be extremely useful for investigating many important aspects of this species such as population structure, dispersal and colonization dynamics.8120821
The Phylogeographic History of the New World Screwworm Fly, Inferred by Approximate Bayesian Computation Analysis
No full textCoordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Insect pest phylogeography might be shaped both by biogeographic events and by human influence. Here, we conducted an approximate Bayesian computation (ABC) analysis to investigate the phylogeography of the New World screwworm fly, Cochliomyia hominivorax, with the aim of understanding its population history and its order and time of divergence. Our ABC analysis supports that populations spread from North to South in the Americas, in at least two different moments. The first split occurred between the North/Central American and South American populations in the end of the Last Glacial Maximum (15,300-19,000 YBP). The second split occurred between the North and South Amazonian populations in the transition between the Pleistocene and the Holocene eras (9,100-11,000 YBP). The species also experienced population expansion. Phylogenetic analysis likewise suggests this north to south colonization and Maxent models suggest an increase in the number of suitable areas in South America from the past to present. We found that the phylogeographic patterns observed in C. hominivorax cannot be explained only by climatic oscillations and can be connected to host population histories. Interestingly we found these patterns are very coincident with general patterns of ancient human movements in the Americas, suggesting that humans might have played a crucial role in shaping the distribution and population structure of this insect pest. This work presents the first hypothesis test regarding the processes that shaped the current phylogeographic structure of C. hominivorax and represents an alternate perspective on investigating the problem of insect pests.810Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)FAO/IAEA [11822/RO]Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)FAPESP [03/13598-0]FAO/IAEA [11822/RO
Methods for the recovery of mitochondrial DNA sequences from museum specimens of myiasis-causing flies
No full textMitochondrial DNA (mtDNA) sequences from eight species of myiasis-causing flies, stored for up to 50 years, were amplified successfully. Universal primers were used to amplify six specific regions from total genomic DNA, including five mtDNA genes. The comparison of phenol/chloroform, DNAzol(R) and Chelex techniques for DNA extraction showed that the DNAzol(R) reagent was the most efficient in retrieving DNA from museum specimens, although the Chelex extraction procedure is currently the most frequently reported method. Comparison of the universal primer sequences with the homologous sequences of Cochliomyia hominivorax Coquerel and Chrysomya putoria Wiedemann (Diptera: Calliphoridae) revealed mismatches that could contribute to the low recovery of a short sequence from subunit II of cytochrome oxidase. The ability to characterize mtDNA markers from museum specimens should be useful in comparative studies of contemporary samples and should help in elucidating species introduction, colonization and dispersal.161394
Microsatellite markers for population genetic studies of the blowfly Chrysomya putoria (Diptera: Calliphoridae)
Get PDFFundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)The investigation of the genetic variation and population structure of Chrysomya species is of great interest for both basic and applied research. However, very limited genetic information is available for this genus across its geographical distribution. Here, we describe 12 polymorphic microsatellite loci isolated from Chrysomya putoria with expected heterozygosities ranging from 0.1402-0.8312. These markers are of potential applied interest for forensic entomologists and for the characterisation of the genetic structure of C. putoria from recently colonised regions, with great promise for understanding the colonisation dynamics and spread of the genus Chrysomya in the New World.104710471050Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)FAPESP [03/01458-9]CNPq [471132/01-2
Conservation and versatility of a new set of primers for long-PCR amplification of complete insect mitochondrial genomes based on Haematobia irritans mtDNA sequences
No full textThe amplification of complete mitochondrial genomes by long PCR (polymerase chain reaction) has been a major contribution to the large-scale sequencing of arthropodan mitochondrial genomes. In this work, we designed six conserved long-PCR primers to successfully recover the entire mitochondrial genome of the horn fly Haematobia irritans (Diptera: Muscidae) in two overlapping fragments. The conservation and versatility of these primers were tested for 17 other species from four major insect orders: Diptera (14), Coleoptera (1), Lepidoptera (1) and Hymenoptera (1). The amplification of complete mitochondrial genomes in orders other than Diptera suggested an even broader application of these primers, especially within the Hexapoda.5488588
Isolation and characterization of microsatellite markers in the new world screw-worm Cochliomyia hominivorax (Diptera : Calliphoridae)
No full textThe new world screw-worm, Cochliomyia hominivorax, is one of the most important parasitic insect pests. This species causes myiasis and, consequently, significant losses to livestock industries in neotropical regions. As part of an investigation into the genetic variability and population structure of the new world screw-worm, a set of 10 polymorphic microsatellite markers was isolated from an AC-enriched genomic library. Amplification of the reported loci in 30 screw-worms revealed an average of 6.9 alleles per locus with expected heterozygosities ranging from 0.3831 to 0.8022. Cross-species amplifications suggested that these loci may be useful in other Calliphoridae species.4218218
Mitochondrial DNA diversity in wild and cultured populations of Brycon opalinus (Cuvier, 1819) (Characiformes, Characidae, Bryconinae) from the Paraiba do Sul Basin, Brazil
No full textRFLP analysis of mitochondrial DNA was carried out to investigate the population genetic structure of cultured and wild populations of Pirapitinga-do-sul-Brycon opalinus (Cuvier, 1819) (Characiformes, Characidae, Bryconinae) from the Paraiba do sul basin, Brazil. mtDNA samples were collected from 257 specimens sampled in seven rivers of the Paraiba basin and in a hatchery used for restocking. An initial screening with 24 restriction enzymes revealed six informative enzymes, which generated 27 haplotypes, Haplotype diversities were high both in the hatchery broodstock (h = 0.75) and in the samples from the wild (h = 0.60). Nucleotide diversity among the 27 B. opalinus haplotypes was 0.825%. Analysis of molecular variance (AMOVA) showed the highest variance within populations (70.48%) while 28.16% of the total diversity was due to interpopulation variance, suggesting the existence of genetic differentiation among B. opalinus populations. (C) 2002 Elsevier Science B.V. All rights reserved.21441730819
- …
