Expansion and Evolution of the X-Linked Testis Specific Multigene Families in the melanogaster Species Subgroup

The testis specific X-linked genes whose evolution is traced here in the melanogaster species subgroup are thought to undergo fast rate of diversification. The CK2ßtes and NACβtes gene families encode the diverged regulatory β-subunits of protein kinase CK2 and the homologs of β-subunit of nascent peptide associated complex, respectively. We annotated the CK2βtes-like genes related to CK2ßtes family in the D. simulans and D. sechellia genomes. The ancestor CK2βtes-like genes preserved in D. simulans and D. sechellia are considered to be intermediates in the emergence of the D. melanogaster specific Stellate genes related to the CK2ßtes family. The CK2ßtes-like genes are more similar to the unique autosomal CK2ßtes gene than to Stellates, taking into account their peculiarities of polymorphism. The formation of a variant the CK2ßtes gene Stellate in D. melanogaster as a result of illegitimate recombination between a NACßtes promoter and a distinct polymorphic variant of CK2ßtes-like ancestor copy was traced. We found a close nonrandom proximity between the dispersed defective copies of DINE-1 transposons, the members of Helitron family, and the CK2βtes and NACβtes genes, suggesting an involvement of DINE-1 elements in duplication and amplification of these genes

Both piRNA and siRNA Pathways Are Silencing Transcripts of the Suffix Element in the Drosophila melanogaster Germline and Somatic Cells

In the Drosophila melanogaster germline, the piRNA pathway silences retrotransposons as well as other transcribed repetitive elements. Suffix is an unusual short retroelement that was identified both as an actively transcribed repetitive element and also as an element at the 3′ ends of the Drosophila non-LTR F element. The copies of suffix that are F element-independent are far more actively transcribed than their counterparts on the F element. We studied the patterns of small RNAs targeting both strands of suffix in Drosophila ovaries using an RNase protection assay and the analysis of the corresponding RNA sequences from the libraries of total small RNAs. Our results indicate that suffix sense and antisense transcripts are targeted mainly by 23–29 nucleotides in length piRNAs and also by 21 nucleotides in length siRNAs. Suffix sense transcripts actively form longer RNA species, corresponding either to partial digestion products of the RNAi and Piwi pathways or to another RNA silencing mechanism. Both sense and antisense suffix transcripts accumulated in the ovaries of homozygous spn-E, piwi and aub mutants. These results provide evidence that suffix sense and antisense transcripts in the germ line and soma are targeted by both RNAi and Piwi pathways and that a Dicer-independent pathway of biogenesis of siRNAs could exist in Drosophila cells

Recombination between the ancestor <i>CK2βtes</i>-<i>like</i> gene (GD15860 or GM17570) and <i>NACβtes</i> promoter region.

<p>Signature sequence of putative <i>CK2βtes</i>-like partner is designated in bold italics. The distances in nucleotides from the start of signature sequence and ORF start are indicated in brackets. Broken line shows the site of fusion of the <i>CK2βtes</i>-like and <i>NACβtes</i> sequences as a result of recombination. The tree represents the similarity of the nucleotide sequences in the selected box measured as the number of base differences <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0037738#pone.0037738-S1" target="_blank">[42]</a> and was constructed using the UPGMA method <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0037738#pone.0037738-Sneath1" target="_blank">[43]</a>. The percentage of replicate trees in which the associated sequence clustered together in the bootstrap test (500 iterations) are shown next to the branches. Branches corresponding to partitions reproduced in less than 50% bootstrap replicates are collapsed.</p

Multiple alignment of <i>DINE-1</i>copies in syntenic regions of <i>D. melanogaster</i> and <i>D. simulans/D. sechellia</i>.

<p>(<b>A</b>) Alignment of known and novel <i>DINE-1</i> copies with <i>D. melanogaster DINE-1</i> consensus sequence (DINEYang) <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0037738#pone.0037738-Yang2" target="_blank">[26]</a>; consensus regions are designated according to <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0037738#pone.0037738-Yang2" target="_blank">[26]</a>; (<b>B</b>) Alignment of the <i>simINE_ben</i> and <i>DNAREP1_DM</i> consensus sequence <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0037738#pone.0037738-Kapitonov3" target="_blank">[36]</a>.</p

Fate of multigene families in the course of the divergence of <i>melanogaster</i> group species.

<p>Fate of multigene families in the course of the divergence of <i>melanogaster</i> group species.</p

Molecular Characterization and Chromosomal Distribution of a Species-Specific Transcribed Centromeric Satellite Repeat from the Olive Fruit Fly, Bactrocera oleae

Satellite repetitive sequences that accumulate in the heterochromatin consist a large fraction of a genome and due to their properties are suggested to be implicated in centromere function. Current knowledge of heterochromatic regions of Bactrocera oleae genome, the major pest of the olive tree, is practically nonexistent. In our effort to explore the repetitive DNA portion of B. oleae genome, a novel satellite sequence designated BoR300 was isolated and cloned. The present study describes the genomic organization, abundance and chromosomal distribution of BoR300 which is organized in tandem, forming arrays of 298 bp-long monomers. Sequence analysis showed an AT content of 60.4%, a CENP-B like-motif and a high curvature value based on predictive models. Comparative analysis among randomly selected monomers demonstrated a high degree of sequence homogeneity (88% - 97%) of BoR300 repeats, which are present at approximately 3,000 copies per haploid genome accounting for about 0.28% of the total genomic DNA, based on two independent qPCR approaches. In addition, expression of the repeat was also confirmed through RT-PCR, by which BoR300 transcripts were detected in both sexes. Fluorescence in situ hybridization (FISH) of BoR300 on mitotic metaphases and polytene chromosomes revealed signals to the centromeres of two out of the six chromosomes which indicated a chromosome-specific centromeric localization. Moreover, BoR300 is not conserved in the closely related Bactrocera species tested and it is also absent in other dipterans, but it's rather restricted to the B. oleae genome. This feature of species-specificity attributed to BoR300 satellite makes it a good candidate as an identification probe of the insect among its relatives at early development stages