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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 195184 Genes 4,7654,334 Genes of known or predicted molecular function 1,5441,414 Pathways 323299 Metabolic reactions 1,2421,200 Transport reactions 13 Compounds1,008 981

5 Sample IDSampling SiteTotal Number of Contigs HA7EHopkins_200997 PA16EPoint Lobos 2009112 HA8HHopkins 2010140 PA1EPoint Lobos 2010118 PA2DPoint Lobos 2011195 PA2GPoint Lobos 2011184

6 SpeciesUIDChrom1Chrom2Chrom3 Vibrio anguillarum 775id68057NC_015633NC_015637 Vibrio cholerae M66 2id59355NC_012578NC_012580 Vibrio cholerae MJ 1236id59387NC_012668NC_012667 Vibrio cholerae O1 biovar El Tor N16961id57623NC_002505NC_002506 Vibrio cholerae O395id58425NC_009457NC_009456 Vibrio Ex25id41601NC_013456NC_013457 Vibrio fischeri ES114id58163NC_006840NC_006841NC_006842 Vibrio fischeri MJ11id58907NC_011184NC_011186NC_011185 Vibrio harveyi ATCC BAA 1116id58957NC_009783NC_009784NC_009777 Vibrio parahaemolyticus RIMD 2210633id57969NC_004603NC_004605 Vibrio splendidus LGP32id59353NC_011753NC_011744 Vibrio vulnificus CMCP6id62909NC_004459NC_004460 Vibrio vulnificus MO6 24 Oid62243NC_014965NC_014966 Vibrio vulnificus YJ016id58007NC_005139NC_005140NC_005128

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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 http://rast.nmpdr.org/

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12 PA16EHA7EPA1EHA8HPA2DPA2G PA16E099.1498.9377.199.0877.11 HA7E99.14098.9577.0799.0677.02 PA1E98.9398.95077.1398.8477.12 HA8H76.8476.9777.24077.1476.28 PA2D99.0899.0698.8777.12077.21 PA2G76.776.9277.2676.1277.320

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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_c1760.000 PA2G_c1570.0180.000 PA2G_c1600.0250.0070.000 PA2G_c1480.0190.0370.0440.000 PA2G_c1680.0400.0570.0650.0470.000 PA2G_c80.0200.0380.0450.0280.0480.000 PA2G_c1280.0240.0420.0490.0310.0520.0240.000 PA2D_c176PA2D_c186PA2D_c167PA2D_c172PA2D_c144PA2D_c161 PA2D_c1760.000 PA2D_c1860.0560.000 PA2D_c1670.0500.0090.000 PA2D_c1720.0500.0090.0020.000 PA2D_c1440.0520.0110.0040.0030.000 PA2D_c1610.0520.0100.0030.0020.0010.000

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 http://crispr.u-psud.fr

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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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42 http://www.southernfriedscience.com/?tag=rimicaris-exoculata http://scienceblogs.com/deepseanews/2007/03/from_the_desk_of_zelnio_alvini_1.php

43 SpeciesANI % similarity Total fragments compared 16S rRNA % similarity S. kujiense DSM 1699485.73685.7 S. autotrophica DSM 16294 73.107284.1 S. denitrificans DSM 1251 73.417484.0

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47 Photo by Shelbi Russell

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