Composition and interrelationships of a large Neotropical freshwater fish group, the subfamily Cheirodontinae (Characiformes: Characidae): A case study based on mitochondrial and nuclear DNA sequences

•Relationships of Cheirodontinae based on a broad taxonomic sample.•Results reject the monophyly of Cheirodontinae as previously conceived.•Exclusion of Amazonspinther and Spintherobolus from the subfamily Cheirodontinae.•The removal of Leptagoniates pi of the genus Leptagoniates and inclusion in Cheirodontinae.•Division of Cheirodontinae in three newly defined monophyletic tribes. Characidae is the most species-rich family of freshwater fishes in the order Characiformes, with more than 1000 valid species that correspond to approximately 55% of the order. Few hypotheses about the composition and internal relationships within this family are available and most fail to reach an agreement. Among Characidae, Cheirodontinae is an emblematic group that includes 18 genera (1 fossil) and approximately 60 described species distributed throughout the Neotropical region. The taxonomic and systematic history of Cheirodontinae is complex, and only two hypotheses about the internal relationships in this subfamily have been reported to date. In the present study, we test the composition and relationships of fishes assigned to Cheirodontinae based on a broad taxonomic sample that also includes some characid incertae sedis taxa that were previously considered to be part of Cheirodontinae. We present phylogenetic analyses of a large molecular dataset of mitochondrial and nuclear DNA sequences. Our results reject the monophyly of Cheirodontinae as previously conceived, as well as the tribes Cheirodontini and Compsurini, and the genera Cheirodon, Compsura, Leptagoniates, Macropsobrycon, Odontostilbe, and Serrapinnus. On the basis of these results we propose: (1) the exclusion of Amazonspinther and Spintherobolus from the subfamily Cheirodontinae since they are the sister-group of all remaining Characidae; (2) the removal of Macropsobrycon xinguensis of the genus Macropsobrycon; (3) the removal of Leptagoniates pi of the genus Leptagoniates; (4) the inclusion of Leptagoniates pi in the subfamily Cheirodontinae; (5) the removal of Cheirodon stenodon of the genus Cheirodon and its inclusion in the subfamily Cheirodontinae under a new genus name; (6) the need to revise the polyphyletic genera Compsura, Odontostilbe, and Serrapinnus; and (7) the division of Cheirodontinae in three newly defined monophyletic tribes: Cheirodontini, Compsurini, and Pseudocheirodontini. Our results suggest that our knowledge about the largest Neotropical fish family, Characidae, still is incipient. © 2013 Elsevier Inc..

Tracking the evolution of sex chromosome systems in Melanoplinae grasshoppers through chromosomal mapping of repetitive DNA sequences

Background: The accumulation of repetitive DNA during sex chromosome differentiation is a common feature of many eukaryotes and becomes more evident after recombination has been restricted or abolished. The accumulated repetitive sequences include multigene families, microsatellites, satellite DNAs and mobile elements, all of which are important for the structural remodeling of heterochromatin. In grasshoppers, derived sex chromosome systems, such as neo-XY♂/XX♀ and neo-X1X2Y♂/X 1X1X2X2♀, are frequently observed in the Melanoplinae subfamily. However, no studies concerning the evolution of sex chromosomes in Melanoplinae have addressed the role of the repetitive DNA sequences. To further investigate the evolution of sex chromosomes in grasshoppers, we used classical cytogenetic and FISH analyses to examine the repetitive DNA sequences in six phylogenetically related Melanoplinae species with X0♂/XX♀, neo-XY♂/XX♀ and neo-X1X2Y♂/X1X1X 2X2♀ sex chromosome systems. Results: Our data indicate a non-spreading of heterochromatic blocks and pool of repetitive DNAs (C 0 t-1 DNA) in the sex chromosomes; however, the spreading of multigene families among the neo-sex chromosomes of Eurotettix and Dichromatos was remarkable, particularly for 5S rDNA. In autosomes, FISH mapping of multigene families revealed distinct patterns of chromosomal organization at the intra- and intergenomic levels. Conclusions: These results suggest a common origin and subsequent differential accumulation of repetitive DNAs in the sex chromosomes of Dichromatos and an independent origin of the sex chromosomes of the neo-XY and neo-X1X2Y systems. Our data indicate a possible role for repetitive DNAs in the diversification of sex chromosome systems in grasshoppers. © 2013Palacios-Gimenez et al.; licensee BioMed Central Ltd.

Orthogonal polynomials on the unit circle and chain sequences

Szego{double acute} has shown that real orthogonal polynomials on the unit circle can be mapped to orthogonal polynomials on the interval [-1,1] by the transformation 2x=z+z-1. In the 80's and 90's Delsarte and Genin showed that real orthogonal polynomials on the unit circle can be mapped to symmetric orthogonal polynomials on the interval [-1,1] using the transformation 2x=z1/2+z-1/2. We extend the results of Delsarte and Genin to all orthogonal polynomials on the unit circle. The transformation maps to functions on [-1,1] that can be seen as extensions of symmetric orthogonal polynomials on [-1,1] satisfying a three-term recurrence formula with real coefficients {cn} and {dn}, where {dn} is also a positive chain sequence. Via the results established, we obtain a characterization for a point w(|w|=1) to be a pure point of the measure involved. We also give a characterization for orthogonal polynomials on the unit circle in terms of the two sequences {cn} and {dn}. © 2013 Elsevier Inc.

Chromosomal organization of repetitive DNA sequences in Astyanax bockmanni (Teleostei, Characiformes): dispersive location, association and co-localization in the genome

Repetitive DNA sequences constitute a great portion of the genome of eukaryotes and are considered key components to comprehend evolutionary mechanisms and karyotypic differentiation. Aiming to contribute to the knowledge of chromosome structure and organization of some repetitive DNA classes in the fish genome, chromosomes of two allopatric populations of Astyanax bockmanni were analyzed using classic cytogenetics techniques and fluorescent in situ hybridization, with probes for ribosomal DNA sequences, histone DNA and transposable elements. These Astyanax populations showed the same diploid number (2n = 50), however with differences in chromosome morphology, distribution of constitutive heterochromatin, and location of 18S rDNA and retroelement Rex3 sites. In contrast, sites for 5S rDNA and H1, H3 and H4 histones showed to be co-located and highly conserved. Our results indicate that dispersion and variability of 18S rDNA and heterochromatin sites are not associated with macro rearrangements in the chromosome structure of these populations. Similarly, distinct evolutionary mechanisms would act upon histone genes and 5S rDNA, contributing to chromosomal association and co-location of these sequences. Data obtained indicate that distinct mechanisms drive the spreading of repetitive DNAs in the genome of A. bockmanni. Also, mobile elements may account for the polymorphism of the major rDNA sites and heterochromatin in this genus. © 2013 Springer Science+Business Media Dordrecht.

Triplet entropy analysis of hemagglutinin and neuraminidase sequences measures influenza virus phylodynamics

The influenza virus has been a challenge to science due to its ability to withstand new environmental conditions. Taking into account the development of virus sequence databases, computational approaches can be helpful to understand virus behavior over time. Furthermore, they can suggest new directions to deal with influenza. This work presents triplet entropy analysis as a potential phylodynamic tool to quantify nucleotide organization of viral sequences. The application of this measure to segments of hemagglutinin (HA) and neuraminidase (NA) of H1N1 and H3N2 virus subtypes has shown some variability effects along timeline, inferring about virus evolution. Sequences were divided by year and compared for virus subtype (H1N1 and H3N2). The nonparametric Mann-Whitney test was used for comparison between groups. Results show that differentiation in entropy precedes differentiation in GC content for both groups. Considering the HA fragment, both triplet entropy as well as GC concentration show intersection in 2009, year of the recent pandemic. Some conclusions about possible flu evolutionary lines were drawn. © 2013 Elsevier B.V.

New insights on the occurrence of peperites and sedimentary deposits within the silicic volcanic sequences of the Parana Magmatic Province, Brazil

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Patterns of rDNA and telomeric sequences diversification: contribution to repetitive DNA organization in Phyllostomidae bats

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

The first assess of the haplotypes from COI gene sequences in species of spittlebugs (Cicadomorpha: Hemiptera) and aquatic true bugs (Gerromorpha and Nepomorpha: Hemiptera) in Brazil

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Selective DMSO-induced conformational changes in proteins from Raman optical activity

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Evolutionary Relationships of the Triatoma matogrossensis Subcomplex, the Endemic Triatoma in Central-Western Brazil, Based on Mitochondrial DNA Sequences

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Genetic Variability and Geographical Diversity of the Main Chagas' Disease Vector Panstrongylus megistus (Hemiptera: Triatominae) in Brazil Based on Ribosomal DNA Intergenic Sequences

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Easy Bioinformatics Analysis (EBiAn): a package for manipulating and analysis of short biological sequences

The work of biochemists and molecular biologists often is dependent or extremely favored by a preliminary computer analysis. Thus, the development of an efficient and friendly computational tool is very important. In this work, we developed a package of programs in Javascript language which can be used online or locally. The programs depend exclusively of Web browsers and are compatible with Internet Explorer, Opera, Mozilla Firefox and Google Chrome. With the EBiAn package it is can perform the main analysis and manipulation of DNA, RNA, proteins and peptides sequences. The programs can be freely accessed and adapted or modified to generate new programs.

Síntese, estrutura e atividade de peptídeos derivados de ParD, o antídoto do módulo toxina-antitoxina ParDE

Pós-graduação em Biotecnologia - IQ

An intriguing model for 5S rDNA sequences dispersion in the genome of freshwater stingray Potamotrygon motoro (Chondrichthyes: Potamotrygonidae)

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Learning HMMs for nucleotide sequences from amino acid alignments

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)