Comparative Genomics: Vibrio spp. - sta.uwi.edu · Vibrio spp. ICGEB Workshop Group 4 Albert...
Transcript of Comparative Genomics: Vibrio spp. - sta.uwi.edu · Vibrio spp. ICGEB Workshop Group 4 Albert...
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Comparative Genomics:
Vibrio spp.
ICGEB Workshop Group 4
Albert Auguste, Reia Guppy, Amalia Hosein, Andrés
López, Maria Jose Muňoz, Silvia Vasquez, Jerome
Foster
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Study organism
Vibrio spp. of anaerobic
bacteria (curved rods)
> 70 species, across 4
families
symbiotic, communalistic,
pathogenic
at least 12 are important
human pathogens
(Vibrionaceae)
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Study organism
Pathogenic species are major causative agents of
several clinical illnesses in humans (gastroenteritis ,
wound infections w/ septicaemia)
Transmission usually by consumption of raw/uncooked
shellfish, or exposure to contaminated or warm sea
water
E.g. V. cholerae, V. parahaemolyticus, V. vulnificus
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Study organism
Invasive infections such as that of V. cholerae may
rapidly progress to death
Patients w/ liver malfunction are at high morbidity &
mortality risk (e.g. V. vulnificus)
CDC, 2008: 131 per 100,00 lab-confirmed infections of
Vibrio spp. in the U.S.
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Study organism
Other Vibrio spp. are marine pathogens e.g.
V. Harveyi - pathogen of fish and invertebrates, including
sharks, sea bass, seahorses, lobster, and shrimp
V. splendidus inflicts disease and death in many marine
species including fish, oysters, mussels, and scallops
Non-pathogenic include V. fischeri, V. logei
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Vibrio genome organization
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Project Objectives Compare nonpathogenic vs. pathogenic Vibrio
spp.
similarities?
unique traits?
genome organization?
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Methodology
Pairwise comparison between Vibrio spp. using
ACT (Artemis Comparison Tool; Carver et al., 2005)
V. fischeri as a “reference” species for all
comparisons
basal in taxonomy & phylogeny* of Vibrio spp to other
available complete genomes (based on 16s rRNA;
Thompson et al., 2009)
non-pathogenic in both humans & marine life
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Dataset of eight (8) complete & published Vibrio
genomes each with 2 chromosomes ( I and II)
WebACT used to generate sequence & blast
comparisons (blastn only*)
ACT used on local server for actual comparative
analyses
Methodology
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Total of 14 ACT runs (7 x 2 chromosomes), V. fischeri
(MJ11) vs.
V. cholerae (M66_2)
V. cholerae (MJ_1236)
V. harveyi (ATCC_BAA_1116)
V. parahaemolyticus (RIMD 2210633)
V. vulnificus (YJ016)
V. Sp. Ex25
V. splendidus (LGP32)
Methodology
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RESULTS
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ACTs for Chromosome IV. sp Ex25 V. harveyi V. splendidusV. cholerae MJ66
V. vulnificus V. cholerae MJ1236 V. parahaemolyticus
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ACTs for Chromosome IIV. sp Ex25 V. harveyi
V.splendidus
V. cholerae MJ66
V. vulnificus V. cholerae MJ 1236 V. parahaemolyticus
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Selected genes for comparison
TCP – encodes pili protein (pathogenicity island)
toxR – virulence regulation
rtxA – modulation of toxicity
ompU – membrane protein assoc. with virulence
Pili– genes associated with pili formation
(responsible for attachment to epithelium)
PutA – part of PutAB operon (osmotic tolerance)
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Strain
Genes
TCP Pili ompU rtxA toxR PutA
Vibrio fischeri 1 5 1 - - -
V. Cholerae (MJ1236) 1 8 1 - 1 -
V. harveyi** - - - - - -
V. parahaemolyticus - 6 1 1 1 -
V. vulnificus - 8 1 - 1 -
V. sp Ex25 - 8 1 1* 1 -
V. splendidus - 9 1 - - -
V. cholerae (MJ66) 2 8 1 5 1 -
TABLE 1. Select genes for pathogenesis and virulence (chromosome 1)
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Strain
Genes
TCP Pili ompU rtxA toxR PutA
Vibrio fischeri 1 5 1 - - -
V. Cholerae (MJ1236) 1 8 1 - 1 -
V. harveyi** - - - - - -
V. parahaemolyticus - 6 1 1 1 -
V. vulnificus - 8 1 - 1 -
V. sp Ex25 - 8 1 1* 1 -
V. splendidus - 9 1 - - -
V. cholerae (MJ66) 2 8 1 5 1 -
TABLE 1. Select genes for pathogenesis and virulence (chromosome 1)
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Strain
Genes
TCP Pili ompU rtxA toxR PutA
Vibrio fischeri 1 5 1 - - -
V. Cholerae (MJ1236) 1 8 1 - 1 -
V. harveyi** - - - - - -
V. parahaemolyticus - 6 1 1 1 -
V. vulnificus - 8 1 - 1 -
V. sp Ex25 - 8 1 1* 1 -
V. splendidus - 9 1 - - -
V. cholerae (MJ66) 2 8 1 5 1 -
TABLE 1. Select genes for pathogenesis and virulence (chromosome 1)
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Strain
Genes
TCP Pili ompU rtxA toxR PutA
Vibrio fischeri 2 - - - - 1
V. Cholerae (MJ1236) - - - - - -
V. harveyi** - - - - - -
V. parahaemolyticus - 3 1 - 2 -
V. vulnificus - 1` - - - -
V. Sp Ex25 - 2 1 - - 1
V. splendidus - - - - - -
V. cholerae (MJ66) - - - - - 1
TABLE 2. Select genes for pathogenesis and virulence (chromosome 2)
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Strain
Genes
TCP Pili ompU rtxA toxR PutA
Vibrio fischeri 2 - - - - 1
V. Cholerae (MJ1236) - - - - - -
V. harveyi** - - - - - -
V. parahaemolyticus - 3 1 - 2 -
V. vulnificus - 1` - - - -
V. Sp Ex25 - 2 1 - - 1
V. splendidus - - - - - -
V. cholerae (MJ66) - - - - - 1
TABLE 2. Select genes for pathogenesis and virulence (chromosome 2)
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CDSs (at 100% Identity) showing reassortment (V. Fischeri vs V. Cholerae M66)
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Chrom. 2: Bifunctional protein PutA, absent in V. sp Ex25 (possibly
reassorted & pseudogeneized?)
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Limitations
Only pairwise comparisons possible
time constraints
Inexperience with software e.g.
CDS key queries - “PutA” vs “puta”
Tblastx run error (WebACT) – only Blastn used
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CONCLUSIONS
Seems to be numerous reassortments among Vibrio spp.
in comparison to V. fischeri
Genomes very similar but “messy” (reassortments,
duplicated stretches of sequence)
Common gene products across all species, e.g. pilus-
associated genes
Toxin genes maintained across pathogenic species
Group needs more practice in analyzing this kind of data
(steep learning curve)!!
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ACKNOWLEDGEMENTS
All the module instructors (esp. Dr. Pain!)
Organizers @ UWI, UNU-BIOLAC & ICGEB