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Yan Wei Lim (San Diego State University) Ann Lesnefsky (Stanford University) Sarah Douglas (Harvard University) Julian Damashek (Stanford University) Bradley.

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Presentation on theme: "Yan Wei Lim (San Diego State University) Ann Lesnefsky (Stanford University) Sarah Douglas (Harvard University) Julian Damashek (Stanford University) Bradley."— Presentation transcript:

1 Yan Wei Lim (San Diego State University) Ann Lesnefsky (Stanford University) Sarah Douglas (Harvard University) Julian Damashek (Stanford University) Bradley Tolar (University of Georgia) Hopkins Microbiology Course 2011 Comparative Vibrio Genomics

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4 PA2DPA2G No of.fnn Contigs Genes 4,7654,334 Genes of known or predicted molecular function 1,5441,414 Pathways Metabolic reactions 1,2421,200 Transport reactions 13 Compounds1,

5 Sample IDSampling SiteTotal Number of Contigs HA7EHopkins_ PA16EPoint Lobos HA8HHopkins PA1EPoint Lobos PA2DPoint Lobos PA2GPoint Lobos

6 SpeciesUIDChrom1Chrom2Chrom3 Vibrio anguillarum 775id68057NC_015633NC_ Vibrio cholerae M66 2id59355NC_012578NC_ Vibrio cholerae MJ 1236id59387NC_012668NC_ Vibrio cholerae O1 biovar El Tor N16961id57623NC_002505NC_ Vibrio cholerae O395id58425NC_009457NC_ Vibrio Ex25id41601NC_013456NC_ Vibrio fischeri ES114id58163NC_006840NC_006841NC_ Vibrio fischeri MJ11id58907NC_011184NC_011186NC_ Vibrio harveyi ATCC BAA 1116id58957NC_009783NC_009784NC_ Vibrio parahaemolyticus RIMD id57969NC_004603NC_ Vibrio splendidus LGP32id59353NC_011753NC_ Vibrio vulnificus CMCP6id62909NC_004459NC_ Vibrio vulnificus MO6 24 Oid62243NC_014965NC_ Vibrio vulnificus YJ016id58007NC_005139NC_005140NC_005128

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8 USELESS

9 Chrom1 Chrom2 Chrom1 Chrom2 Genes present in all publicly-available Vibrio genomes = “core genes” Compiled into database of core Vibrio genes Chrom1 Chrom2 Compare genes in our Vibrio genomes to Vibrio core gene database Core gene set: genomic estimation of what makes a Vibrio a Vibrio, clues about distinctive Vibrio phenotype With closed genomes: highlight “abnormal” genes PYTHON!

10 AWESOME! Genome Comparison PA1E as the Reference SEED – RAST

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12 PA16EHA7EPA1EHA8HPA2DPA2G PA16E HA7E PA1E HA8H PA2D PA2G

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14 V. cholerae V. vulnificus V. fischeri V. harveyi V. splendidus Vibrio sp. Ex25 V. anguillensis V. parahaemolyticus V. cholerae

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23 All PA2G 16S sequences fall in Aliivibrio clade Aliivibrio fischeri also bioluminescent PA2D_c176PA2G_c157PA2G_c160PA2G_c148PA2G_c168PA2G_c8PA2G_c128 PA2D_c PA2G_c PA2G_c PA2G_c PA2G_c PA2G_c PA2G_c PA2D_c176PA2D_c186PA2D_c167PA2D_c172PA2D_c144PA2D_c161 PA2D_c PA2D_c PA2D_c PA2D_c PA2D_c PA2D_c

24 Hybrid HSL-two-component quorum sensing uses two autoinducers to regulate density-dependent light production LuxI  synthesis of N-(3-hydroxybutanoyl)-homoserine lactone LuxN  AI-1 = N-(3-hydroxybutanoyl)-homoserine lactone LuxQ  AI-2 = unknown structure LuxP  require for AI-2 detection

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26 Pathway-tools MEGAN

27 HA8H PA2G PA2D PA16E PA1E HA7E

28 PA2G More Efficient Biosynthetic Pathway

29 Important for osmoregulation Alternative carbon and nitrogen source under normal osmolarity Present in all genomes except PA2G (Bioluminescent)

30 HA8H PA2G PA2D PA16E PA1E HA7E

31 Aerobactin The Siderophores

32 Clustered Randomly Interspersed Short Palindromic Repeat Direct RepeatSpacer Region HA8H 1 PA16E HA8H 2 Image: Wikipedia

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35 Class_genome.acgtfreq Class_genome.codfreq SeqCount ENCprime Class_genome_results.txt >class_genome_annotation Nc NcP Magical python scrubbing V. Splendidus core genome blastn Class genome core genes Rrrrrrrrrrrrr

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39 Photo by Erin Nuccio

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43 SpeciesANI % similarity Total fragments compared 16S rRNA % similarity S. kujiense DSM S. autotrophica DSM S. denitrificans DSM

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47 Photo by Shelbi Russell

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