Horizontal gene transfer contributed to the evolution of extracellular surface structures

The single-cell layered ectoderm of the fresh water polyp Hydra fulfills the function of an epidermis by protecting the animals from the surrounding medium. Its outer surface is covered by a fibrous structure termed the cuticle layer, with similarity to the extracellular surface coats of mammalian epithelia. In this paper we have identified molecular components of the cuticle. We show that its outermost layer contains glycoproteins and glycosaminoglycans and we have identified chondroitin and chondroitin-6-sulfate chains. In a search for proteins that could be involved in organising this structure we found PPOD proteins and several members of a protein family containing only SWT (sweet tooth) domains. Structural analyses indicate that PPODs consist of two tandem β-trefoil domains with similarity to carbohydrate-binding sites found in lectins. Experimental evidence confirmed that PPODs can bind sulfated glycans and are secreted into the cuticle layer from granules localized under the apical surface of the ectodermal epithelial cells. PPODs are taxon-specific proteins which appear to have entered the Hydra genome by horizontal gene transfer from bacteria. Their acquisition at the time Hydra evolved from a marine ancestor may have been critical for the transition to the freshwater environment

DNPTrapper: an assembly editing tool for finishing and analysis of complex repeat regions

BACKGROUND: Many genome projects are left unfinished due to complex, repeated regions. Finishing is the most time consuming step in sequencing and current finishing tools are not designed with particular attention to the repeat problem. RESULTS: We have developed DNPTrapper, a shotgun sequence finishing tool, specifically designed to address the problems posed by the presence of repeated regions in the target sequence. The program detects and visualizes single base differences between nearly identical repeat copies, and offers the overview and flexibility needed to rapidly resolve complex regions within a working session. The use of a database allows large amounts of data to be stored and handled, and allows viewing of mammalian size genomes. The program is available under an Open Source license. CONCLUSION: With DNPTrapper, it is possible to separate repeated regions that previously were considered impossible to resolve, and finishing tasks that previously took days or weeks can be resolved within hours or even minutes

Investigation of the GATA repetitive DNA sequence of the domestic horse (Equus caballus) of: a thesis presented in partial fulfilment of the requirements for the degree of Master of Science in Genetics at Massey University

The variation in copy number and organisation of the simple quadruplet repeat (GATA)n in the genome of most animals has made it a .potential tool for DNA fingerprinting. This study was undertaken to explore this application and to investigate its abundance and organisation in the horse genome. Using the synthetic oligomer (G ATA)5 end-labelled with 32P as a probe, the copy number of (GATA)n in genomic DNA from leukocytes of male and female horses was determined, and the extent of its polymorphism investigated on Southern blots of DNA digested with various restriction enzymes. To investigate its organisation, a genomic clone containing (GATA)n was isolated, characterized by restriction mapping and sequenced. (GATA)n constituted 1% of the horse genome. Like the mouse, there was no quantitative sex variation. Mbo I digestion generated a large number of horse DNA fragments of various sizes up to 5kb which hybridized to the (G AT A)5 probe. Simpler profiles were produced by digestion with Taq I, Alu I, Hae Ill and Hinf I. The profiles were highly conserved between individuals and between family members indicating the (G AT A)5 is unlikely to be informative as a DNA fingerprinting probe. Some intensely hybridizing DNA fragments appeared to be maternally transmitted. This seems to be a novel observation. A 3.6kb fragment which hybridized to the (G ATA)5 probe was cloned from horse genomic DNA. It was restriction mapped, the GATA-containing region identified and sequenced. Only about 150bp contained tandemly repeated GATA motifs in strings of about 3-6 repeats interspersed with (GAT)1-2 regions. The lack of quantitative sex variation suggests that (GATA)n may not have a role in sex determination in horses. Also, its lack of polymorphism makes it unlikely to be informative as a DNA fingerprinting probe

Browsing repeats in genomes: Pygram and an application to non-coding region analysis

BACKGROUND: A large number of studies on genome sequences have revealed the major role played by repeated sequences in the structure, function, dynamics and evolution of genomes. In-depth repeat analysis requires specialized methods, including visualization techniques, to achieve optimum exploratory power. RESULTS: This article presents Pygram, a new visualization application for investigating the organization of repeated sequences in complete genome sequences. The application projects data from a repeat index file on the analysed sequences, and by combining this principle with a query system, is capable of locating repeated sequences with specific properties. In short, Pygram provides an efficient, graphical browser for studying repeats. Implementation of the complete configuration is illustrated in an analysis of CRISPR structures in Archaea genomes and the detection of horizontal transfer between Archaea and Viruses. CONCLUSION: By proposing a new visualization environment to analyse repeated sequences, this application aims to increase the efficiency of laboratories involved in investigating repeat organization in single genomes or across several genomes

XatA, an AT-1 autotransporter important for the virulence of Xylella fastidiosa Temecula1.

Xylella fastidiosa Temecula1 is the causative agent of Pierce's disease of grapevine, which is spread by xylem-feeding insects. An important feature of the infection cycle is the ability of X. fastidiosa to colonize and interact with two distinct environments, the xylem of susceptible plants and the insect foregut. Here, we describe our characterization of XatA, the X. fastidiosa autotransporter protein encoded by PD0528. XatA, which is classified as an AT-1 (classical) autotransporter, has a C-terminal β-barrel domain and a passenger domain composed of six tandem repeats of approximately 50 amino acids. Localization studies indicate that XatA is present in both the outer membrane and membrane vesicles and its passenger domain can be found in the supernatant. Moreover, XatA is important for X. fastidiosa autoaggregation and biofilm formation based on mutational analysis and the discovery that Escherichia coli expressing XatA acquire these traits. The xatA mutant also shows a significant decrease in Pierce's disease symptoms when inoculated into grapevines. Finally, X. fastidiosa homologs to XatA, which can be divided into three distinct groups based on synteny, form a single, well-supported clade, suggesting that they arose from a common ancestor

New Assembly, Reannotation and Analysis of the Entamoeba histolytica Genome Reveal New Genomic Features and Protein Content Information

Entamoeba histolytica is an anaerobic parasitic protozoan that causes amoebic dysentery. The parasites colonize the large intestine, but under some circumstances may invade the intestinal mucosa, enter the bloodstream and lead to the formation of abscesses such amoebic liver abscesses. The draft genome of E. histolytica, published in 2005, provided the scientific community with the first comprehensive view of the gene set for this parasite and important tools for elucidating the genetic basis of Entamoeba pathogenicity. Because complete genetic knowledge is critical for drug discovery and potential vaccine development for amoebiases, we have re-examined the original draft genome for E. histolytica. We have corrected the sequence assembly, improved the gene predictions and refreshed the functional gene assignments. As a result, this effort has led to a more accurate gene annotation, and the discovery of novel features, such as the presence of genome segmental duplications and the close association of some gene families with transposable elements. We believe that continuing efforts to improve genomic data will undoubtedly help to identify and characterize potential targets for amoebiasis control, as well as to contribute to a better understanding of genome evolution and pathogenesis for this parasite

Review Article: Genetic Polymorphism Studies and Insurgence of Human Genetic Diseases

Single nucleotides polymorphism is the biological variant that affects people the most frequently (SNPs). Due of the link to hereditary illnesses, Polymorphisms are significant for hereditary investigations. Throughout this article, researchers examined a specific subset of SNPs that alter the sequencing of the related enzyme. Researchers created a brand-new technique that, beginning with sequencing data, can determine if a novel phenotypic resulting from an SNP is connected to a genetic abnormality. The greatest prevalent sort of genomic variability throughout the human genome is represented by solitary nucleotides polymorphism (SNPs). Understanding whether human genetic variants are associated with Chromosomal and complicated disorders is probably among a more essential objectives of SNP research. Non coding SNPs (NSSNPs), which cause solitary point mutations in molecules, are the subject of intense attention