Phage?
New
Sequence
Horizontal
Transfer
Molecular
Evolution
2 Interrelated Modules on Bioinformatics
Module 1:
To show the ways in which the NCBI
online database classifies and organizes
information on DNA sequences, evolutionary
relationships, and scientific publications.
Module 2:
To identify an unknown nucleotide
sequence from the Wolbachia endosymbiont by
using the NCBI search tool BLAST
Teaching Time
–
45 minutes
OH NO!
1.
No programming skills needed
2.
Familiarity with personal computer
and internet browser
3.
Customizable and free
Advantages
What are the broad goals of this lab?
To provide an introduction to bioinformatics
(NCBI)
To introduce you to searching for articles,
sequences, scientists (perhaps yourself)
To use phylogenies
To put your
Wolbachia
research in the
context of what
’
s been published
What are the specific goals of this lab?
To look for brand new W strains
To make a phylogenetic tree of W
To ultimately compare the W tree to an
insect phylogeny to infer lateral vs. vertical
transmission of your W strains
To contribute to a national
“
student
”
sequence database on the genetic diversity of
W 16S rRNA gene
Wolbachia
–
Host Interactions:
Mutualism and Reproductive Parasitism
Parthenogenesis
in
wasps
Male
-
killing
in insects
Feminization
in isopods
Cytoplasmic incompatibility
in
arthropods
Required for nematode
fertility and larval
development
Required for insect
oogenesis
(Dedeine et al. 2001)
Dunning
-
Hottop et al 2006
Wolbachia
Anaplasma
Ehrlichia
Neorickettsia
Rickettsia
Alpha Proteobacteria
Obligatory
Intracellulars
in Arthropods
Wolbachia
–
Anaplasma
Split
W
ins
-
W
nem
Split (~120MY)
Application of Bioinformatics to
Wolbachia
Mutualist
Wolbachia
:
Parasite
Outcomes: A New
Wolbachia
Species?
Wolbachia
: Complete genomic sequences from a
related parasite and mutualist
wBm
(Foster et al. 2005)
wMel
(Wu et al. 2004)
1.08 Mb
806 genes
1.27 Mb
1270 genes
696
shared
genes
Wu et al 2004
Foster et al 2005
Your Wolbachia Sequence
:
What do you do with it?
ORIGIN
1 ttcttgtatc ccaaacatct cgagcttctt gtacaccaaa ttaggtattc actatggaat
61 tcagagttca cttgcaagct gataatgagc agaaaatttt tcaaaaccag atgaaacccg
121 aacctgaagc ctcttacttg attaatcaaa gacggtctgc aaattacaag ccaaatattt
181 ggaagaacga tttcctagat caatctctta tcagcaaata cgatggagat gagtatcgga
BLAST:
•
Compare new genes to old ones
•
Compare genes from different species or
hosts
•
Identify possible functions based on
similarities to known sequences.
Query a database for sequences homologous to
an input (ie, query) sequence.
GATG
C
C
A
T
A
G
A
G
C
T
G
T
A
G
T
C
GT
A
CCC
T <
—
—
>
C
T
A
G
A
G
A
G
C
-
G
T
A
G
T
C
AG
A
GTG
T
CTTTGAGTTCC
BLAST is like using ‘Google’ for DNA sequences
National Center for Biotechnology Information (NCBI)
http://www.ncbi.nlm.nih.gov
Release 2008: 99 billion base pairs
99 million sequences
Target database: Adjustable using the pull
-
down menu
A Traditional
GenBank Record
LOCUS AY182241 1931 bp mRNA linear PLN 04
-
MAY
-
2004
DEFINITION Malus x domestica (E,E)
-
alpha
-
farnesene synthase (AFS1) mRNA,
complete cds.
ACCESSION AY182241
VERSION AY182241.2 GI:32265057
KEYWORDS .
SOURCE Malus x domestica (cultivated apple)
ORGANISM Malus x domestica
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots;
rosids; eurosids I; Rosales; Rosaceae; Maloideae; Malus.
REFERENCE 1 (bases 1 to 1931)
AUTHORS Pechous,S.W. and Whitaker,B.D.
TITLE Cloning and functional expression of an (E,E)
-
alpha
-
farnesene
synthase cDNA from peel tissue of apple fruit
JOURNAL Planta 219, 84
-
94 (2004)
REFERENCE 2 (bases 1 to 1931)
AUTHORS Pechous,S.W. and Whitaker,B.D.
TITLE Direct Submission
JOURNAL Submitted (18
-
NOV
-
2002) PSI
-
Produce Quality and Safety Lab,
USDA
-
ARS, 10300 Baltimore Ave. Bldg. 002, Rm. 205, Beltsville, MD
20705, USA
REFERENCE 3 (bases 1 to 1931)
AUTHORS Pechous,S.W. and Whitaker,B.D.
TITLE Direct Submission
JOURNAL Submitted (25
-
JUN
-
2003) PSI
-
Produce Quality and Safety Lab,
USDA
-
ARS, 10300 Baltimore Ave. Bldg. 002, Rm. 205, Beltsville, MD
20705, USA
REMARK Sequence update by submitter
COMMENT On Jun 26, 2003 this sequence version replaced gi:27804758.
FEATURES Location/Qualifiers
source 1..1931
/organism="Malus x domestica"
/mol_type="mRNA"
/cultivar="'Law Rome'"
/db_xref="taxon:3750"
/tissue_type="peel"
gene 1..1931
/gene="AFS1"
CDS 54..1784
/gene="AFS1"
/note="terpene synthase"
/codon_start=1
/product="(E,E)
-
alpha
-
farnesene synthase"
/protein_id="AAO22848.2"
/db_xref="GI:32265058"
/translation="MEFRVHLQADNEQKIFQNQMKPEPEASYLINQRRSANYKPNIWK
NDFLDQSLISKYDGDEYRKLSEKLIEEVKIYISAETMDLVAKLELIDSVRKLGLANLF
EKEIKEALDSIAAIESDNLGTRDDLYGTALHFKILRQHGYKVSQDIFGRFMDEKGTLE
DFLHKNEDLLYNISLIVRLNNDLGTSAAEQERGDSPSSIVCYMREVNASEETARKNIK
GMIDNAWKKVNGKCFTTNQVPFLSSFMNNATNMARVAHSLYKDGDGFGDQEKGPRTHI
LSLLFQPLVN"
ORIGIN
1 ttcttgtatc ccaaacatct cgagcttctt gtacaccaaa ttaggtattc actatggaat
61 tcagagttca cttgcaagct gataatgagc agaaaatttt tcaaaaccag atgaaacccg
121 aacctgaagc ctcttacttg attaatcaaa gacggtctgc aaattacaag ccaaatattt
181 ggaagaacga tttcctagat caatctctta tcagcaaata cgatggagat gagtatcgga
241 agctgtctga gaagttaata gaagaagtta agatttatat atctgctgaa acaatggatt
//
Header
Feature Table
Sequence
The Flatfile Format
LOCUS AY182241 1931 bp mRNA linear PLN 04
-
MAY
-
2004
DEFINITION Malus x domestica (E,E)
-
alpha
-
farnesene synthase (AFS1) mRNA,
complete cds.
ACCESSION AY182241
VERSION AY182241.2 GI:32265057
KEYWORDS .
SOURCE Malus x domestica (cultivated apple)
ORGANISM Malus x domestica
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots;
rosids; eurosids I; Rosales; Rosaceae; Maloideae; Malus.
REFERENCE 1 (bases 1 to 1931)
AUTHORS Pechous,S.W. and Whitaker,B.D.
TITLE Cloning and functional expression of an (E,E)
-
alpha
-
farnesene
synthase cDNA from peel tissue of apple fruit
JOURNAL Planta 219, 84
-
94 (2004)
REFERENCE 2 (bases 1 to 1931)
AUTHORS Pechous,S.W. and Whitaker,B.D.
TITLE Direct Submission
JOURNAL Submitted (18
-
NOV
-
2002) PSI
-
Produce Quality and Safety Lab,
USDA
-
ARS, 10300 Baltimore Ave. Bldg. 002, Rm. 205, Beltsville, MD
20705, USA
REFERENCE 3 (bases 1 to 1931)
AUTHORS Pechous,S.W. and Whitaker,B.D.
TITLE Direct Submission
JOURNAL Submitted (25
-
JUN
-
2003) PSI
-
Produce Quality and Safety Lab,
USDA
-
ARS, 10300 Baltimore Ave. Bldg. 002, Rm. 205, Beltsville, MD
20705, USA
REMARK Sequence update by submitter
COMMENT On Jun 26, 2003 this sequence version replaced gi:27804758.
The Header
LOCUS AY182241 1931 bp mRNA linear PLN 04
-
MAY
-
2004
DEFINITION Malus x domestica (E,E)
-
alpha
-
farnesene synthase (AFS1) mRNA,
complete cds.
ACCESSION AY182241
VERSION AY182241.2 GI:32265057
KEYWORDS .
SOURCE Malus x domestica (cultivated apple)
ORGANISM Malus x domestica
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots;
rosids; eurosids I; Rosales; Rosaceae; Maloideae; Malus.
REFERENCE 1 (bases 1 to 1931)
AUTHORS Pechous,S.W. and Whitaker,B.D.
TITLE Cloning and functional expression of an (E,E)
-
alpha
-
farnesene
synthase cDNA from peel tissue of apple fruit
JOURNAL Planta 219, 84
-
94 (2004)
REFERENCE 2 (bases 1 to 1931)
AUTHORS Pechous,S.W. and Whitaker,B.D.
TITLE Direct Submission
JOURNAL Submitted (18
-
NOV
-
2002) PSI
-
Produce Quality and Safety Lab,
USDA
-
ARS, 10300 Baltimore Ave. Bldg. 002, Rm. 205, Beltsville, MD
20705, USA
REFERENCE 3 (bases 1 to 1931)
AUTHORS Pechous,S.W. and Whitaker,B.D.
TITLE Direct Submission
JOURNAL Submitted (25
-
JUN
-
2003) PSI
-
Produce Quality and Safety Lab,
USDA
-
ARS, 10300 Baltimore Ave. Bldg. 002, Rm. 205, Beltsville, MD
20705, USA
REMARK Sequence update by submitter
COMMENT On Jun 26, 2003 this sequence version replaced gi:27804758.
Header: Locus Line
LOCUS AY182241 1931 bp mRNA linear PLN 04
-
MAY
-
2004
Molecule type
Division
Modification Date
Locus name
Length
LOCUS AY182241 1931 bp mRNA linear PLN 04
-
MAY
-
2004
DEFINITION Malus x domestica (E,E)
-
alpha
-
farnesene synthase (AFS1) mRNA,
complete cds.
ACCESSION AY182241
VERSION AY182241.2 GI:32265057
KEYWORDS .
SOURCE Malus x domestica (cultivated apple)
ORGANISM Malus x domestica
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots;
rosids; eurosids I; Rosales; Rosaceae; Maloideae; Malus.
REFERENCE 1 (bases 1 to 1931)
AUTHORS Pechous,S.W. and Whitaker,B.D.
TITLE Cloning and functional expression of an (E,E)
-
alpha
-
farnesene
synthase cDNA from peel tissue of apple fruit
JOURNAL Planta 219, 84
-
94 (2004)
REFERENCE 2 (bases 1 to 1931)
AUTHORS Pechous,S.W. and Whitaker,B.D.
TITLE Direct Submission
JOURNAL Submitted (18
-
NOV
-
2002) PSI
-
Produce Quality and Safety Lab,
USDA
-
ARS, 10300 Baltimore Ave. Bldg. 002, Rm. 205, Beltsville, MD
20705, USA
REFERENCE 3 (bases 1 to 1931)
AUTHORS Pechous,S.W. and Whitaker,B.D.
TITLE Direct Submission
JOURNAL Submitted (25
-
JUN
-
2003) PSI
-
Produce Quality and Safety Lab,
USDA
-
ARS, 10300 Baltimore Ave. Bldg. 002, Rm. 205, Beltsville, MD
20705, USA
REMARK Sequence update by submitter
COMMENT On Jun 26, 2003 this sequence version replaced gi:27804758.
Header: Database Identifiers
ACCESSION AY182241
VERSION AY182241.2 GI:32265057
Accession
•
Stable
•
Reportable
•
Universal
LOCUS AY182241 1931 bp mRNA linear PLN 04
-
MAY
-
2004
DEFINITION Malus x domestica (E,E)
-
alpha
-
farnesene synthase (AFS1) mRNA,
complete cds.
ACCESSION AY182241
VERSION AY182241.2 GI:32265057
KEYWORDS .
SOURCE Malus x domestica (cultivated apple)
ORGANISM Malus x domestica
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots;
rosids; eurosids I; Rosales; Rosaceae; Maloideae; Malus.
REFERENCE 1 (bases 1 to 1931)
AUTHORS Pechous,S.W. and Whitaker,B.D.
TITLE Cloning and functional expression of an (E,E)
-
alpha
-
farnesene
synthase cDNA from peel tissue of apple fruit
JOURNAL Planta 219, 84
-
94 (2004)
REFERENCE 2 (bases 1 to 1931)
AUTHORS Pechous,S.W. and Whitaker,B.D.
TITLE Direct Submission
JOURNAL Submitted (18
-
NOV
-
2002) PSI
-
Produce Quality and Safety Lab,
USDA
-
ARS, 10300 Baltimore Ave. Bldg. 002, Rm. 205, Beltsville, MD
20705, USA
REFERENCE 3 (bases 1 to 1931)
AUTHORS Pechous,S.W. and Whitaker,B.D.
TITLE Direct Submission
JOURNAL Submitted (25
-
JUN
-
2003) PSI
-
Produce Quality and Safety Lab,
USDA
-
ARS, 10300 Baltimore Ave. Bldg. 002, Rm. 205, Beltsville, MD
20705, USA
REMARK Sequence update by submitter
COMMENT On Jun 26, 2003 this sequence version replaced gi:27804758.
Header: Organism
SOURCE Malus x domestica (cultivated apple)
ORGANISM Malus x domestica
Eukaryota; Viridiplantae; Streptophyta; Embryophyta;
Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons;
core eudicots; rosids; eurosids I; Rosales; Rosaceae;
Maloideae
;
Malus.
NCBI
-
controlled taxonomy
FEATURES Location/Qualifiers
source 1..1931
/organism="Malus x domestica"
/mol_type="mRNA"
/cultivar="'Law Rome'"
/db_xref="taxon:3750"
/tissue_type="peel"
gene 1..1931
/gene="AFS1"
CDS 54..1784
/gene="AFS1"
/note="terpene synthase"
/codon_start=1
/product="(E,E)
-
alpha
-
farnesene synthase"
/protein_id="AAO22848.2"
/db_xref="GI:32265058"
/translation="MEFRVHLQADNEQKIFQNQMKPEPEASYLINQRRSANYKPNIWK
NDFLDQSLISKYDGDEYRKLSEKLIEEVKIYISAETMDLVAKLELIDSVRKLGLANLF
EKEIKEALDSIAAIESDNLGTRDDLYGTALHFKILRQHGYKVSQDIFGRFMDEKGTLE
NHHFAHLKGMLELFEASNLGFEGEDILDEAKASLTLALRDSGHICYPDSNLSRDVVHS
LELPSHRRVQWFDVKWQINAYEKDICRVNATLLELAKLNFNVVQAQLQKNLREASRWW
ANLGIADNLKFARDRLVECFACAVGVAFEPEHSSFRICLTKVINLVLIIDDVYDIYGS
EEELKHFTNAVDRWDSRETEQLPECMKMCFQVLYNTTCEIAREIEEENGWNQVLPQLT
KVWADFCKALLVEAEWYNKSHIPTLEEYLRNGCISSSVSVLLVHSFFSITHEGTKEMA
DFLHKNEDLLYNISLIVRLNNDLGTSAAEQERGDSPSSIVCYMREVNASEETARKNIK
GMIDNAWKKVNGKCFTTNQVPFLSSFMNNATNMARVAHSLYKDGDGFGDQEKGPRTHI
LSLLFQPLVN"
The Feature Table
Coding sequence
start (atg)
stop (tag)
DNA
RNA
cDNA
phenotype
DNA sequences
genomes
protein
sequence
databases
protein
Bioinformatics is NOT just information technology.
It can teach the central dogmas of molecular biology
GATG
C
C
A
T
A
G
A
G
C
T
G
T
A
G
T
C
GT
A
CCC
T <
-
100%
GATG
C
C
A
T
A
G
A
G
C
T
G
T
A
G
T
C
GT
A
CCC
T <
-
100%
GATG
C
C
A
T
A
G
A
G
C
T
G
T
A
G
T
C
GT
A
CCC
T <
-
100%
GATG
C
C
A
T
A
G
A
G
C
T
G
T
A
G
T
C
GT
A
CCC
T <
-
100%
Insect Phylogeny
Top 5 Wolbachia BLAST matches
GATG
C
C
A
T
A
G
A
G
C
T
G
T
A
G
T
C
GT
A
CCC
T <
-
100%
Outcomes:
Lateral Transfer ?
Let
’
猠䉥杩渠併爠䉩潩s景牭慴楣⁅硥i捩獥c
䱡戠L
HTTP://WWW.DIGITALWORLDBIOLO
GY.COM/BLAST
Enter the password to open this PDF file:
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-
File size:
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Title:
-
Author:
-
Subject:
-
Keywords:
-
Creation Date:
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Modification Date:
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