Bacteriophage genome annotation pdf

Using galaxy for phage genome annotation phage directory. Definitive demonstration by synthesis of genome annotation. We have identified 78 putative open reading frames, 95 pairs of inverted repeats, and 6 palindromes. Students use internetbased resources in class to add annotations for products and functions to genes from 933w.

Isolation, molecular characterization and insight into the genome sequence of e. Guiding principles of bacteriophage genome annotation 6. Isolation, molecular characterization and insight into the. Here, we describe an overview of the annotation of a bacteriophage genome sequence using the freely available program dna master. The term was derived from bacteria and the greek phagein, to devour. Several tools are available that have been adapted to run on phage genomes. Bacteriophages play key roles in microbial evolution1,2, marine nutrient cycling3 and human disease4. It lysogenizes its hosts as a circular, lowcopynumber plasmid.

Pdf phage genome annotation using the rast pipeline. Genome annotation and intraviral interactome for the streptococcus. Bacterial genome annotation torsten seemann annette mcgrath simon gladman anna syme victorian life sciences computation initiative vlsci the university of melbourne small genome annotation t. Comparison of bacteriophage annotation methods by alicia. Bacteriophage evolution differs by host, lifestyle and genome. To address the need for improved phage annotation tools that scale, we created an automated throughput annotation pipeline. Genome of bacteriophage p1 journal of bacteriology. Bacteriophage genome assembly and annotation workshop. Supplies and technical support for the isolation and genome annotation were provided by the howard hughes medical institute science education alliance national genome research initiative.

Complete genome sequence of bacteriophage vvaw1, which. Bacteriophages and their genomes pubmed central pmc. Calls were compared to the reference genome from the literature in order to determine the accuracy of the eight selected programs in regard to bacteriophage genome annotation. Dna annotation or genome annotation is the process of identifying the locations of genes and all of the coding regions in a genome and determining what those genes do. While numerous bacillus phages have been isolated up till now only very few bacillus cereus phages have been characterized in detail. Almost all of the listeria bacteriophages described to date. Here we present data on the large, virulent, broadhostrange b. Pdf a method for improving the accuracy and efficiency. Complete phage genome sequences allow a proposed characterization of the potential packaging mechanisms and more precise genome annotation. Bacteriophage p8625 is a lytic bacteriophage that infects the verrucomicrobial strain imcc8625, a marine bacterium affiliated with verrucomicrobia subdivision 4. Abril, sergi castellano, in encyclopedia of bioinformatics and computational biology, 2019. The mainstays of phage genome annotation are autoannotation. Bacteriophage hk239 is unique in that it has a wide range of exclusion including lambda, p1vir, p2, hk022, and t4rii.

Bacteriophage, vibriophage, vibrio vulnificus, podophage, aquatic, virus. Predicting genome terminus sequences of bacillus cereus. Simple genome sequences, like those of bacteriophage bacterial viruses, are excellent resources for teaching students about genome analysis. Sequence and annotation of the wizard007 mycobacterium.

To learn more about hk239, the genome was sequenced and annotated. In this study, we present a genome annotation method developed in our lab that builds on the seaphages guidelines in an e ort to overcome these shortcomings. Summary phage t4 has provided countless contributions to the paradigms of genetics and biochemistry. Seemann gcc 2016 bloomington in, usa mon 27 jun 2016. The genome was sequenced in its entirety, rendering a 38 kb sequence located on a single, linear, circularly permuted chromosome. Genome sequence and analysis of a broadhost range lytic. The most common type of bacteriophage isolated belonged to the genus t4likevirus, with. Asmscience annotation of the bacteriophage 933w genome. Bacteriophage genomes annotation da wang and david bollivar biology department, illinois wesleyan university this project mainly focuses on analyzing the genomes functions of the bacteriophage shrimp, which was purified and extracted in last semester. We compare phanotate to other gene callers by annotating a set of 23 complete phage genomes. The tpa2 genome has a modular gene structure that shares some similarity to those of mycobacterium phages. Currently there are no tools specifically designed for annotating genes in phages. Obtaining the complete genome sequence of a bacteriophage is an essential prerequisite for any type of functional genomics study as well as for regulatory approval for phagebased biocontrol and therapy applications in food industry and medicine.

We have determined the complete nucleotide sequences of two strains of a p1 thermoinducible mutant, p1 c1100. Functional genome annotation is the process of attaching metadata such as gene ontology terms to structural annotations. Genome annotation a term used to describe two distinct processes. Here, we present the annotation and genomic features of the bacteriophage, vvaw1. In contrast to genetics, which refers to the study of individual genes and their roles in inheritance, genomics aims at the collective characterization and quantification of all of an organism. We have determined the complete nucleotide sequences of two strains of a p1 thermoinducible mutant, p1 c 1100. Bacteriophages were jointly discovered by frederick twort 1915 in england and by felix dherelle 1917 at the pasteur institute in france. The number of sequenced phage genomes is approximately 8000 and increasing rapidly. Eight programs were used to annotate the lambda genome. The phage genome can be made of either double or singlestranded dna or rna, depending on the bacteriophage in question. We will be running a bacteriophage genome assembly and annotation workshop at wms on monday 9th of january.

Pipeline phage genome annotation genome rast annotation of phage genome annotation starting with dna sequences and. The genomic sequence and annotation of bacteriophage. Because their genomes are relatively small, elucidating the genetic diversity of the phage population, deciphering their origins, and identifying the evolutionary mechanisms that shape the population would seem readily feasible. Differently from patric, annotation via galaxy is a lot more manual. T4 biology and its genomic sequence provide the bestunderstood model for modern functional genomics and proteomics. However, manual inspection and refinement is essential to the production of the most accurate genome annotations. Tsourkas school of life sciences, university of nevada las vegas, las vegas, nv 89154, usa. The genome is 41,538 bp in length and there are 71 open reading frames. Phage genome annotation using the rast pipeline springer. Function assignment best format details download pdf. Guiding principles of bacteriophage genome annotation objective this protocol contains the guiding principles of bacteriophage genome annotation. The complete genome sequence of the escherichia phage adb2 genome can be accessed under the gen bank accession number jx912252.

Functional annotation of gene products of bacteriophage dp1. This exercise allows students to annotate the genome of the bacteriophage 933w, a virus isolated from pathogenic escherichia coli o157. Genome sequence and characterization of the tsukamurella. Annotation is challenging, highly underestimated in difficulty, highly undervalued until a community goes to use its genome sequenceannotation can be done to high accuracy on a single gene level by single investigators with expertise in gene families. Bacteriophages are composed of proteins that encapsulate a dna or rna genome, and may. It is necessary because the sequencing of dna produces sequences of unknown function. An introduction to phage wholegenome sequencing and annotation jason j. There will be disappointment when the research communities realize that they dont have the gold standard of sequence as present in arabidopsis and rice. An introduction to phage whole genome sequencing and annotation jason j.

Gene prediction can be largely accomplished through the use of several freely available programs. Draft genome sequences of 14 escherichia coli phages. We describe here a bioinformatic tool, phamerator, that assorts proteincoding genes into phamilies. The revised sequence presented here includes 12,436 bp of additional sequence not present in the previously available phage k genome genbank accession no. The genome annotation was performed by integrating the rast phage annotation tool mcnair et al. An introduction to phage whole genome sequencing and. A method for improving the accuracy and efficiency of. This week, were covering an introductory phage genome annotation. Complete genome analysis of a siphoviridae phage tsk1. Both the bacteriophage and the host bacterial strain were isolated from surface seawater samples collected off the east coast of korea.

The mainstays of phage genome annotation are autoannotation programs such as glimmer and genemark. Bacteriophage means to eat bacteria, and are called so because virulent bacteriophage can cause the compete lysis of a susceptible bacterial culture. Annotation and bioinformatic analysis of bacteriophage genomes. Annotation of bacteriophage genome sequences using dna master. Genomics is an interdisciplinary field of biology focusing on the structure, function, evolution, mapping, and editing of genomes. Bacteriophages are the most numerous entities on earth. Variations on gene expression, including overlapping genes, internal translation. Currently, researchers typically apply bacterial gene callers for annotation of phage dna, followed by largely manual analyses using web forms.

Wholegenome sequencing reveals that the tpa2 genome is circularly permuted 61,440 bp and that 70% of its sequence is novel. Bacteriophage t4 genome microbiology and molecular. The genomes of most phages range in length from 40,000 bp to 400,000 bp 40kb 400kb, so being able to manipulate them using. The p1 genome 93,601 bp contains at least 117 genes, of which almost twothirds had not been sequenced previously and 49 have no homologs in. Printing these pages, reading them carefully, and having them close at hand during the process of gene calling are highly recommended. Annotating the genome of a bacteriophage part 1 the process of annotating a genome is a filemanipulationrich endeavor. Use this table to correctly transcribe functional assignments. For example, there are no conserved genes in phage genomes that can be used to build universal. The whole genome sequencing and genome annotation of tsk1 bacteriophage revealed that it has a 49,836 bp long genome, having 75 orfs and no trna gene. Phages are obligate intracellular parasites that multiply inside bacteria by making. These unique adaptations provide challenges for the bioinformatics analysis of phage genomes. Genome annotation an overview sciencedirect topics. Guiding principles of bacteriophage genome annotation.

Bacteriophage genomes have mosaic architectures and are replete with small open reading frames of unknown function, presenting challenges in their annotation, comparative analysis, and representation. When considering methods for sequencing the smallpox virus genome in 1991 12, a wholegenome shotgun sequencing method. This is not how to assign functions, but rather, once you know what function you want to assign. Pdf phages are complex biomolecular machineries that have to survive in a bacterial world. Sequencing of a genome is followed by annotation, where.

Structural genome annotation is the process of identifying genes and their intronexon structures. Genome annotation is the process of identifying functional elements along the sequence of a genome, thus giving meaning to it. Bacteriophage k is a member of the virulent twortlike group of myophages infecting staphylococcus aureus. Complete genome sequence of bacteriophage p8625, the first. Understanding where your files are and what you are doing to them will be very helpful. In particular, orf calling, genome annotation, noncoding rna ncrna identification, and the identification of transposons and insertions are all complicated in phage genome analysis. Sequencing of a genome is followed by annotation, where genes, start codons, and functions are putatively identified. Bacteriophages occupy a unique position in biology, representing an absolute majority of all organisms in the biosphere. Bacteriophage introductions are designed to provide information beyond basic descriptive data of the genome number of genes and transfer rnas trnas. Its complete genome sequence of 168,903 bp encodes about 300 gene products. The actinobacteriophage database protocols for annotation. An annotation irrespective of the context is a note added by way of explanation or commentary. Once a genome is sequenced, it needs to be annotated to make sense of it.