First report of Y-linked genes in the kissing bug Rhodnius prolixus.

BACKGROUND: Due to an abundance of repetitive DNA, the annotation of heterochromatic regions of the genome such as the Y chromosome is problematic. The Y chromosome is involved in key biological functions such as male-fertility and sex-determination and hence, accurate identification of its sequences is vital. The hemipteran insect Rhodnius prolixus is an important vector of Chagas disease, a trypanosomiasis affecting 6-7 million people worldwide. Here we report the identification of the first Y-linked genes of this species. RESULTS: The R. prolixus genome was recently sequenced using separate libraries for each sex and the sequences assembled only with male reads are candidates for Y linkage. We found 766 such candidates and PCR tests with the ten largest ones, confirmed Y-linkage for all of them, suggesting that "separate libraries" is a reliable method for the identification of Y-linked sequences. BLAST analyses of the 766 candidate scaffolds revealed that 568 scaffolds contained genes or part of putative genes. We tested Y-linkage for 36 candidates and found that nine of them are Y-linked (the PCR results for the other 25 genes were inconclusive or revealed autosomal/X-linkage). Hence, we describe in this study, for the first time, Y-linked genes in the R. prolixus genome: two zinc finger proteins (Znf-Y1 and Znf-Y2), one metalloproteinase (Met-Y), one aconitase/iron regulatory protein (Aco-Y) and five genes devoid of matches in any database (Rpr-Y1 to Rpr-Y5). Expression profile studies revealed that eight genes are expressed mainly in adult testis (some of which presented a weak expression in the initial developmental stages), while Aco-Y has a gut-restricted expression. CONCLUSIONS: In this study we showed that the approach used for the R. prolixus genome project (separate sequencing of male and female DNA) is key to easy and fast identification of sex-specific (e.g. Y chromosome sequences). The nine new R. prolixus Y-linked genes reported here provide unique markers for population and phylogenetic analysis and further functional studies of these genes may answer some questions about sex determination, male fertility and Y chromosome evolution in this important species.

DrosoPhyla: Resources for Drosophilid Phylogeny and Systematics.

The vinegar fly Drosophila melanogaster is a pivotal model for invertebrate development, genetics, physiology, neuroscience, and disease. The whole family Drosophilidae, which contains over 4,400 species, offers a plethora of cases for comparative and evolutionary studies. Despite a long history of phylogenetic inference, many relationships remain unresolved among the genera, subgenera, and species groups in the Drosophilidae. To clarify these relationships, we first developed a set of new genomic markers and assembled a multilocus data set of 17 genes from 704 species of Drosophilidae. We then inferred a species tree with highly supported groups for this family. Additionally, we were able to determine the phylogenetic position of some previously unplaced species. These results establish a new framework for investigating the evolution of traits in fruit flies, as well as valuable resources for systematics.

Hydrogen bonds determine the structures of the ternary heterocyclic complexes C2H4O···2HF, C2H5N···2HF and C2H4S···2HF: density functional theory and topological calculations.

A theoretical study of structural, electronic, topological and vibrational parameters of the ternary hydrogen-bonded complexes C(2)H(4)O···2HF, C(2)H(5)N···2HF and C(2)H(4)S···2HF is presented here. Different from binary systems with a single proton donor, the tricomplexes have the property of forming multiple hydrogen bonds, which are analyzed from a structural and vibrational point of view, but verified only by means of the quantum theory of atoms in molecules (QTAIM). As traditionally done in the hydrogen bond theory, the charge transfer between proton donors and acceptors was computed using the CHELPG calculations, which also revealed agreement with dipole moment variation and a cooperative effect on the tricomplexes. Furthermore, redshift events on proton donor bonds were satisfactorily identified, although, in this case, an absence of experimental data led to the use of a theoretical argument to interpret these spectroscopic shifts. It was therefore the use of the QTAIM parameters that enabled all intermolecular vibrational modes to be validated. The most stable tricomplex in terms of energy was identified via the strength of the hydrogen bonds, which were modeled as directional and bifurcated.

A chemometrical study of intermolecular properties of hydrogen-bonded complexes formed by C2H4O...HX and C2H5N...HX with X = F, CN, NC, and CCH.

We presents a chemometrical study of the intermolecular properties of the C(2)H(4)O...HX and C(2)H(5)N... HX hydrogen-bonded complexes with X = F, CN, NC, and CCH. Through the MP2 perturbation theory and B3LYP hybrid functional, as well as modifications on 6-31ijGk basis sets with i = triple-zeta, j = diffuse and k = polarization functions, systematic tendencies in the R((n...HX)) hydrogen bond distances and upsilon((n...HX)) stretch frequencies were determined by the hierarchical cluster analysis, two level factorial designs and principal component analysis. Based on well-fitted math models, not only because polarization functions provide a great variance on statistical analysis, but this basis set reproduces more efficiently the available experimental results. Moreover, independent of whether the quality on basis set is increased, the effects yielded by both DFT and MP2 were not considered important in the statistical analysis.

The molecular properties of heterocyclic and homocyclic hydrogen-bonded complexes evaluated by DFT calculations and AIM densities.

This theoretical study presents a comparative analysis of the molecular properties of heterocyclic (C2H4O...HF and C2H5...HF) and homocyclic (C3H6...HF) hydrogen-bonded complexes. Initially, the equilibrium geometries of these complexes were analyzed in detail at the B3LYP/6-311++G(d,p) level of theory. Subsequently, the interaction energies and polarizabilities were also evaluated, as well as the infrared stretch frequencies and absorption intensities. In addition, by combining intermolecular criteria and charge density concepts, calculations of Bader's theory of atoms in molecules were used to determine the maxima and minima for electron density in order to measure the strength of the n...H and ppi...H hydrogen bonds. Finally, the possibility of an F...H(alpha) secondary interaction between the fluoride (F) of hydrogen fluoride and the axial hydrogen atoms (H(alpha)) of the C2H4O and C2H5N heterocyclic rings was explored.

The electronic structure of the C2H4O...2HF tri-molecular heterocyclic hydrogen-bonded complex: a theoretical study.

The geometries of three isomers of the C2H4O...2HF tri-molecular heterocyclic hydrogen-bonded complex were examined through B3LYP/aug-cc-pVDZ calculations. Analysis of structural parameters, determination of CHELPG (charge electrostatic potential grid) intermolecular charge transfer, interpretation of infrared stretching modes, and Bader's atoms in molecules (AIM) theory calculations was carried out in order to characterize the hydrogen bonds in each isomer of the C2H4O...2HF complex. The most stable structure was determined through the identification of hydrogen bonds between C2H4O and HF, (O...H), as well as in the hydrofluoric acid dimer, (HF(D-R)...HF(D)). However, the existence of a tertiary interaction (F(lambda)...H(alpha)) between the fluoride of the second hydrofluoric acid and the axial hydrogen atoms of C2H4O was decisive in the identification of the preferred configuration of the C2H4O...2HF system.