Determination of Synteny within the F

ClusterBrandon Aquino & Lourdes Lopez

AbstractBacteriophages are a type of virus that solely infect bacterium and utilize the infected bacterial host for replication of its genome and protein synthesis. Mycobacteriophages are classified into distinct clusters and subclusters based on phylogenetic analysis. Within each recorded cluster, the order in which the gene products are transcribed are unique. We purified and isolated a phage member of the F Cluster family: ‘Byougenkin’. Based on the theory of Darwinian evolution, genetic information will be allowed to disseminate as the prime genetic sequence to all members of a cluster if expression of certain gene products and their order provides optimum fitness. This sequence or gene products/arrangement should remain conserved across all Cluster F phages, creating synteny: the preserved order of genes of related species [F Cluster] which results from descent from a common ancestor. The F Cluster family is composed of around 105 annotated members. Due to the high mutation rate of bacteriophages, minute variations will be present within each of the phages. Variations which lower the fitness of the phage will result in its extinction, thus removing that variation from the F Cluster gene pool. We hypothesized that Byougenkin will maintain the general synteny shared amongst all other F Cluster phages. We also expected to observe the conservation of gene blocks as well as minute variations as a result of coevolution. Genome analysis programs such as DNA Master and Phamerator were utilized to determine the amount of genetic variation of Byougenkin to around 15 similar family members. Gepard dot analysis can be performed to determine specific variations between Byougenkin and n-phage. Using the collected data we can determine a general map of the syntenic genes of F Cluster phages.

Objectives

Prediction of Synteny of the F Cluster

Determine Similarity of Byougenkin to Prediction

F Cluster Members UtilizedByougenkin (ours

LlamaBipolar

CabriniansDaenerysDorothyGumbie

Inventum

FruitloopMutaforma13

Pacc40Phatniss

DanteDeadP

GirafalesRockyHorror

Software UtilizedDNA Master

Annotation of Byougenkin & Genome Analysis

PhameratorObtain gene annotation for each genome

Genome Pair Rapid Dotter (GEPARD)Creation of Gepard Dot Plots

Microsoft ExcelData Analysis & Calculation

Fig. 1 F Cluster Comparisons

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 500%

10%

20%

30%

40%

50%

60%

70%

80%

90%

100%

63%

88%

100%

81%

88%

94%

44% 44% 44% 44%

75%

88%

94%

69%

63%

69% 69%

75%

56%

50%

0%

6%

0% 0% 0% 0% 0% 0% 0%

63% 63% 63%

0% 0%

56%

0% 0%

6%

0%

38%

0%

13%

6% 6%

0% 0% 0% 0% 0% 0%

Fig. 2 % Conserved G1-50

51 53 55 57 59 61 63 65 67 69 71 73 75 77 79 81 83 85 87 89 91 93 95 97 990%

10%

20%

30%

40%

50%

60%

70%

80%

90%

100%

0%

6%

0% 0% 0% 0% 0%

19%

0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0%

19%

0% 0%

Fig. 3 % Conserved G51-100

Gepard Dot Plot Comparisons

Bipolar Llama

Gepard Dot Plot Comparisons

Cabrinians Daenerys

Dorothy GUmbie

Gepard Dot Plot Comparisons

Inventum Fruitloop

Gepard Dot Plot Comparisons

Mutaforma13 Pacc40

Gepard Dot Plot Comparisons

Phatniss Dante

Gepard Dot Plot Comparisons

DeadP Girafales

Gepard Dot Plot Comparisons

RockyHorror

Gepard Dot Plot Comparisons

Fig. 4 Conserved Blocks G1-201 Terminase Small Subunit 2 Terminase Large Subunit3 Portal Protein 4 Capsid Maturation Protein 5 Scaffolding Protein 6 Major Capsid 7 Head-to-tail connector8 Head-to-tail connector9 Head-to-tail connector

10 Head-to-tail connector11 Major Tail Subunit 12 Tail Assembly Chaperone13 Tail Assembly14 Tapemeasure15 Minor Tail Protein16 Minor Tail Protein17 Minor Tail Protein18 Minor Tail Protein19 Minor Tail Protein (D-ala-D-ala- carboxypeptidase)20 Minor Tail Protein

Fig. 5 Conserved Blocks G30-32

30 lysin A31 lysin B32 Holin

Fig. 6 Conserved Blocks G35-4435 DNAq36 hypothetical protein 37 hypothetical protein 38 immunity repressor39 hypothetical protein 40 integrase protein41 gp4642 HTH binding protein43 CRO protein44 antirepressor

ConclusionSynteny was conserved primarily at the beginning of the genome

with few blocks further downstream.

Throughout the genome, other gene products are conserved though these conserved gene products maintain the same general

order

This is probably a result of coevolution with other bacteria

ReferencesKrumsiek J, Arnold R, Rattei T Gepard: A rapid and sensitive tool

for creating dotplots on genome scale. Bioinformatics 2007; 23(8): 1026-8. PMID: 17309896