Genome mapping and characterization of the Anopheles gambiae heterochromatin

<p>Abstract</p> <p>Background</p> <p>Heterochromatin plays an important role in chromosome function and gene regulation. Despite the availability of polytene chromosomes and genome sequence, the heterochromatin of the major malaria vector <it>Anopheles gambiae </it>has not been mapped and characterized.</p> <p>Results</p> <p>To determine the extent of heterochromatin within the <it>An. gambiae </it>genome, genes were physically mapped to the euchromatin-heterochromatin transition zone of polytene chromosomes. The study found that a minimum of 232 genes reside in 16.6 Mb of mapped heterochromatin. Gene ontology analysis revealed that heterochromatin is enriched in genes with DNA-binding and regulatory activities. Immunostaining of the <it>An. gambiae </it>chromosomes with antibodies against <it>Drosophila melanogaster </it>heterochromatin protein 1 (HP1) and the nuclear envelope protein lamin Dm₀identified the major invariable sites of the proteins' localization in all regions of pericentric heterochromatin, diffuse intercalary heterochromatin, and euchromatic region 9C of the 2R arm, but not in the compact intercalary heterochromatin. To better understand the molecular differences among chromatin types, novel Bayesian statistical models were developed to analyze genome features. The study found that heterochromatin and euchromatin differ in gene density and the coverage of retroelements and segmental duplications. The pericentric heterochromatin had the highest coverage of retroelements and tandem repeats, while intercalary heterochromatin was enriched with segmental duplications. We also provide evidence that the diffuse intercalary heterochromatin has a higher coverage of DNA transposable elements, minisatellites, and satellites than does the compact intercalary heterochromatin. The investigation of 42-Mb assembly of unmapped genomic scaffolds showed that it has molecular characteristics similar to cytologically mapped heterochromatin.</p> <p>Conclusions</p> <p>Our results demonstrate that <it>Anopheles </it>polytene chromosomes and whole-genome shotgun assembly render the mapping and characterization of a significant part of heterochromatic scaffolds a possibility. These results reveal the strong association between characteristics of the genome features and morphological types of chromatin. Initial analysis of the <it>An. gambiae </it>heterochromatin provides a framework for its functional characterization and comparative genomic analyses with other organisms.</p

Paucity and preferential suppression of transgenes in late replication domains of the D. melanogaster genome

<p>Abstract</p> <p>Background</p> <p>Eukaryotic genomes are organized in extended domains with distinct features intimately linking genome structure, replication pattern and chromatin state. Recently we identified a set of long late replicating euchromatic regions that are underreplicated in salivary gland polytene chromosomes of <it>D. melanogaster</it>.</p> <p>Results</p> <p>Here we demonstrate that these underreplicated regions (URs) have a low density of <it>P</it>-<it>element </it>and <it>piggyBac </it>insertions compared to the genome average or neighboring regions. In contrast, <it>Minos</it>-based transposons show no paucity in URs but have a strong bias to testis-specific genes. We estimated the suppression level in 2,852 stocks carrying a single <it>P</it>-<it>element </it>by analysis of eye color determined by the mini-<it>white </it>marker gene and demonstrate that the proportion of suppressed transgenes in URs is more than three times higher than in the flanking regions or the genomic average. The suppressed transgenes reside in intergenic, genic or promoter regions of the annotated genes. We speculate that the low insertion frequency of <it>P-elemen</it>ts and <it>piggyBac</it>s in URs partially results from suppression of transgenes that potentially could prevent identification of transgenes due to complete suppression of the marker gene. In a similar manner, the proportion of suppressed transgenes is higher in loci replicating late or very late in Kc cells and these loci have a lower density of <it>P-elements </it>and <it>piggyBac </it>insertions. In transgenes with two marker genes suppression of mini-<it>white </it>gene in eye coincides with suppression of <it>yellow </it>gene in bristles.</p> <p>Conclusions</p> <p>Our results suggest that the late replication domains have a high inactivation potential apparently linked to the silenced or closed chromatin state in these regions, and that such inactivation potential is largely maintained in different tissues.</p

Low Genetic Diversity in Wide-Spread Eurasian Liver Fluke <i>Opisthorchis felineus</i> Suggests Special Demographic History of This Trematode Species

<div><p></p><p><i>Opisthorchis felineus</i> or Siberian liver fluke is a trematode parasite (Opisthorchiidae) that infects the hepato-biliary system of humans and other mammals. Despite its public health significance, this wide-spread Eurasian species is one of the most poorly studied human liver flukes and nothing is known about its population genetic structure and demographic history. In this paper, we attempt to fill this gap for the first time and to explore the genetic diversity in <i>O. felineus</i> populations from Eastern Europe (Ukraine, European part of Russia), Northern Asia (Siberia) and Central Asia (Northern Kazakhstan). Analysis of marker DNA fragments from <i>O. felineus</i> mitochondrial <i>cytochrome c oxidase subunit 1</i> and <i>3</i> (<i>cox1, cox3</i>) and nuclear rDNA <i>internal transcribed spacer 1</i> (<i>ITS1</i>) sequences revealed that genetic diversity is very low across the large geographic range of this species. Microevolutionary processes in populations of trematodes may well be influenced by their peculiar biology. Nevertheless, we suggest that lack of population genetics structure observed in <i>O. felineus</i> can be primarily explained by the Pleistocene glacial events and subsequent sudden population growth from a very limited group of founders. Rapid range expansion of <i>O. felineus</i> through Asian and European territories after severe bottleneck points to a high dispersal potential of this trematode species.</p></div

Mismatch distribution curve for <i>O. felineus</i> haplotypes.

<p>Expected values under expanding population model and observed values are shown as solid green and dashed red lines, respectively (r – ruggedness index).</p

Pairwise fixation indices (Fst values) between <i>O. felineus</i> populations calculated from the nucleotide datasets for c<i>ox1</i>/<i>cox3</i>/<i>ITS1</i>.

*<p>- p<0.05,</p>**<p>- 0.1>p>0.05.</p

Geographical localities where the specimens were collected.

<p>Lettered names of collection sites correspond to those in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0062453#pone-0062453-t001" target="_blank">Table 1</a>.</p

Diversity indices calculated from the nucleotide data sets for <i>cox1</i>, <i>cox3</i> and <i>ITS1</i>.

<p>Abbreviations are number of isolates examined (N), segregating sites (S), number of haplotypes (H), haplotype diversity (Hd) and nucleotide diversity (π).</p>*<p>- p<0.05.</p

Neutrality indices calculated from the nucleotide datasets for <i>cox1</i>, <i>cox3</i> and <i>ITS1</i>.

*<p>- p<0.05.</p