Genome Sequencing of Lycomia zaccaria gen. nov. sp. nov. , - - PowerPoint PPT Presentation

Jordan Krebs Tom Sontag, Jeffrey Newman Lycoming College

Genome Sequencing of Lycomia zaccaria gen.

• nov. sp. nov., Chryseobacterium haifense, and

Kaistella koreensis and Comparison to Two Closely Related Genomes

Species Introduction

Chryseobacterium shigense Chryseobacterium vrystaatense Chryseobacterium luteum Chryseobacterium sp. KM Chryseobacterium joostei Chryseobacterium jejuense Chryseobacterium oranimense Chryseobacterium gleum Chryseobacterium soli Chryseobacterium soldanellicola Chryseobacterium sp. CTM Chryseobacterium sp. VR86 Chryseobacterium greenlandense Kaistella koreensis Chryseobacterium haifense Lycomia zaccaria JJC 3519

0.005

Phylogenetic and molecular evolutionary analyses were conducted using MEGA version 5 (Tamura, Peterson, Stecher, Nei, and Kumar 2011).

3519

Methods

Function‐Based Analysis Sequence‐Based Analysis Download Reference Genomes Sequence Genomes Assemble

• C. gleum

3519 L. zaccaria JJC C. haifense Find and Annotate Genes Upload into RAST K. koreensis

RAST

RAST‐ Rapid Annotation based on Subsystem Technology

• L. zaccaria JJC

Amino Acids and Derivatives Fatty Acids, Lipids, and Isoprenoids Carbohydrates Membrane Transport Protein Metabolism Metabolism of Aromatic Compounds DNA Metabolism Cell Division and Cell Cycle RNA metabolism Nitrogen Metabolism Cell Wall and Capsule Phosphorus Metabolism Cofactors, Vitamins, Prosthetic Groups, Pigments Regulation and Cell Signaling Virulence, Disease, and Defense Potassium Metabolism Nucleosides and Nucelotides Sulfur Metabolism Stress Response Dormancy and Sporulation Miscellaneous Iron Acquistion and Metabolism Secondary Metabolism Phages, Prophages, Transposable elements, Plasmids Subsystems Respiration

RAST

Sequence Based Analysis

81 43 89 20 64 73 25 9 86 140 74 115 81 40 118

12 20

• L. zaccaria JJC

3.2 Mbp

• C. gleum

5.6 Mbp

• K. koreensis

3.8 Mbp

• C. haifense

3.5 Mbp 3519 2.8 Mbp

Figure inspired by Figure of http://xsplat.wordpress.com

• K. koreensis
• C. gleum
• L. zaccaria JJC

3519

Beta‐lactamase Gliding motility Ornithine , Xaa‐Pro Aminopeptidases DEAD‐box protein A Mn superoxide dismutase GroEL, GroES, GrpE Catalase

Molybdenum cofactors biosynthesis Trehalose permease (FucP) Trehalase Sulfite reductase Siderophore synthesis Flexirubin synthesis (darA) Alanine racemase Phage tail fiber protein Retron‐type RNA‐ directed DNA polymerase Integron integrase Minor curlin subunit CsgB (nucleation) Serine phospatase RsbU – regulator of sigma subunit Sucrose‐6‐phosphate hydrolase Alpha‐acetolactate decarboxylase Bacterophytochrome heme

• xygenase BphO

Catechol 1,2‐dioxygenase D‐beta‐hydroxybutyrate dehydrogenase Methylglyoxal synthase

Formate‐THF ligase P yruvate, phosphate‐ dikinase Beta‐lactamase/Penicillin binding proteins Cytosine deaminase Arginino‐ succinate Syn. Fumarate hydratase Butyryl‐CoA dehydro‐ genase Serine acetyl‐ trans‐ ferase Thiol peroxi‐ dase, Tpx‐type Amino‐ deoxych‐

• rismate

lyase methyleneTHF reductase Cystathionine

• syn. & lyase
• C. haifense

Amino Acids and Derivatives Carbohydrates Protein Metabolism DNA Metabolism RNA metabolism Cell Wall and Capsule Cofactors, Vitamins, Prosthetic Groups, Pigments Virulence, Disease, and Defense Nucleosides and Nucelotides Stress Response Miscellaneous Respiration Fatty Acids, Lipids, and Isoprenoids Membrane Transport Metabolism of Aromatic Compounds Cell Division and Cell Cycle Nitrogen Metabolism Phosphorus Metabolism Regulation and Cell Signaling Potassium Metabolism Sulfur Metabolism Dormancy and Sporulation Iron Acquistion and Metabolism Secondary Metabolism Phages, Prophages, Transposable elements, Plasmids Subsystems

Adapted from Zhaxybayeva O et al. PNAS 2009;106:5865‐5870

References

• 1. Aziz, R.K., Bartels, D., Best, A.A., DeJongh, M., Disz, T., Edwards, R.A., Formsma, K., Gerdes, S., Glass, E.M., Kubal, M., Meyer, F.,

Olsen, G.J., Olson, R., Osterman, A.L., Overbeek, R.A., McNeil, L.K., Paarmann, D., Paczian, T., Parrello, B., Pusch, G.D., Reich, C., Stevens, R., Vassieva, O., Vonstein, V., Wilke, A., & Zagnitko O. (2008). The RAST Server: Rapid Annotations using Subsystems

• Technology. BMC Genomics 9:75
• 2. Hantsis‐Zacharov, E. & Halpern, M. (2007). Chryseobacterium haifense sp. nov., a psychrotolerant bacterium isolated from raw
• milk. Int J Syst Evol Microbiol 57, 2344–2348.
• 3. Holmes, B., Owen, R. J., Steigerwalt, A. G. & Brenner, D. J. (1984). Flavobacterium gleum, a new species found in human clinical
• specimens. Int J Syst Bacteriol 34, 21–25.
• 4. Kampfer, P., Vaneechoutte, M., Lodders, N., De Baere, T., Avesani, V., Janssens, M., Busse, H.‐J. & Wauters, G. (2009).

Description of Chryseobacterium anthropi sp. nov. to accommodate clinical isolates biochemically similar to Kaistella koreensis and Chryseobacterium haifense, proposal to reclassify Kaistella koreensis as Chryseobacterium koreense comb. nov. and emended description of the genus Chryseobacterium. Int J Syst Evol Microbiol 59, 2421–2428.

• 5. Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M., and Kumar, S. (2011). MEGA5: Molecular Evolutionary Genetics

Analysis using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods. Molecular Biology and Evolution (submitted).

• 6. Vandamme, P., Bernardet, J.‐F., Segers, P., Kersters, K. & Holmes, B. (1994). New perspectives in the classification of the

flavobacteria: description of Chryseobacterium gen. nov., Bergeyella gen. nov., and Empedobacter nom. rev. Int J Syst Bacteriol 44, 827–831.

• 7. Zhaxybayeva, O., Swithers, K.S., Lapierre, P., Fournier, G.P., Bickhart, D.M., DeBoy, R.T., Nelson, K.E., Nesbø, C.L., Doolittle, W.F.,

Gogarten, J.P., and Noll, K.M. (2009). On the chimeric nature, thermophilic origin, and phylogenetic placement of the

• Thermotogales. Proc. Natl. Acad. Sci. U.S.A. 106: 5865‐5870.

Acknowledgements

From left to right: Back: Dr. Newman, Andrew Gale (‘15), Dillon Snyder (‘14), Tom Sontag (‘14), Logan Mariano (‘13), Me, Clark Thompson (‘13) Front: Jessica Hoffman (‘15), and Jessica Lehman (‘13)