2 Interrelated Modules on Bioinformatics
description
Transcript of 2 Interrelated Modules on Bioinformatics
2 Interrelated Modules on Bioinformatics2 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!OH NO!
1. No programming skills needed
2.Familiarity with personal computer and internet browser
3.Customizable and free
What are the broad goals of this lab?What are the broad goals of this lab?
To provide an introduction to bioinformatics To provide an introduction to bioinformatics (NCBI)(NCBI)
To introduce you to searching for articles, To introduce you to searching for articles, sequences, scientists (perhaps yourself)sequences, scientists (perhaps yourself)
To use phylogeniesTo use phylogenies
To put your To put your WolbachiaWolbachia research in the research in the context of whatcontext of what’’s been publisheds been published
What are the specific goals of this lab?What are the specific goals of this lab?
To look for brand new W strainsTo look for brand new W strains
To make a phylogenetic tree of WTo make a phylogenetic tree of W
To ultimately compare the W tree to an To ultimately compare the W tree to an insect phylogeny to infer lateral vs. vertical insect phylogeny to infer lateral vs. vertical transmission of your W strainstransmission of your W strains
To contribute to a national To contribute to a national ““studentstudent”” sequence database on the genetic diversity of sequence database on the genetic diversity of W 16S rRNA geneW 16S rRNA gene
WolbachiaWolbachia – Host Interactions: – Host Interactions: Mutualism and Reproductive ParasitismMutualism and Reproductive Parasitism
Parthenogenesis in wasps
Male-killing in insects
Feminization in isopods
Cytoplasmic incompatibility in arthropods
Rep
rodu
ctiv
e pa
rasi
tism
Mut
ualis
m
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
ObligatoryIntracellularsin Arthropods
Wolbachia –Anaplasma Split
Wins-Wnem
Split (~120MY)
Application of Bioinformatics to Application of Bioinformatics to WolbachiaWolbachia
Mutualist
Wolbachia:
Parasite
Outcomes: A New Outcomes: A New WolbachiaWolbachia Species? Species?
Wolbachia: Complete genomic sequences from a related parasite and mutualist
wBm (Foster et al. 2005)wMel (Wu et al. 2004)
1.08 Mb1.08 Mb 806 genes806 genes
1.27 Mb1.27 Mb 1270 genes1270 genes
696 shared genes
Wu et al 2004 Foster et al 2005
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: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.
GATGGATGCCCCAATTAAGGAAGGCCTTGGTTAAGGTTCCGTGTAACCCCCCT <T <——
——> > CCTTAAGGAAGGAAGGCC--GGTTAAGGTTCCAGAGAAGTGGTGTTCTTTGAGTTCCCTTTGAGTTCC
National Center for Biotechnology Information (NCBI)National Center for Biotechnology Information (NCBI)http://www.ncbi.nlm.nih.govhttp://www.ncbi.nlm.nih.gov
Release 2008: 99 billion base pairs 99 million sequences
Target database: Adjustable using the pull-down menuTarget database: Adjustable using the pull-down menu
A TraditionalA TraditionalGenBank RecordGenBank Record
LOCUS AY182241 1931 bp mRNA linear PLN 04-MAY-2004DEFINITION Malus x domestica (E,E)-alpha-farnesene synthase (AFS1) mRNA, complete cds.ACCESSION AY182241VERSION AY182241.2 GI:32265057KEYWORDS .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, USAREFERENCE 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 submitterCOMMENT 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//
The Flatfile FormatThe Flatfile Format
LOCUS AY182241 1931 bp mRNA linear PLN 04-MAY-2004DEFINITION Malus x domestica (E,E)-alpha-farnesene synthase (AFS1) mRNA, complete cds.ACCESSION AY182241VERSION AY182241.2 GI:32265057KEYWORDS .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, USAREFERENCE 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 submitterCOMMENT On Jun 26, 2003 this sequence version replaced gi:27804758.
The HeaderThe Header
LOCUS AY182241 1931 bp mRNA linear PLN 04-MAY-2004DEFINITION Malus x domestica (E,E)-alpha-farnesene synthase (AFS1) mRNA, complete cds.ACCESSION AY182241VERSION AY182241.2 GI:32265057KEYWORDS .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, USAREFERENCE 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 submitterCOMMENT On Jun 26, 2003 this sequence version replaced gi:27804758.
Header: Locus LineHeader: Locus LineLOCUS AY182241 1931 bp mRNA linear PLN 04-MAY-2004LOCUS AY182241 1931 bp mRNA linear PLN 04-MAY-2004
Molecule typeMolecule typeDivisionDivision
Modification DateModification Date
Locus nameLocus name
LengthLength
LOCUS AY182241 1931 bp mRNA linear PLN 04-MAY-2004DEFINITION Malus x domestica (E,E)-alpha-farnesene synthase (AFS1) mRNA, complete cds.ACCESSION AY182241VERSION AY182241.2 GI:32265057KEYWORDS .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, USAREFERENCE 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 submitterCOMMENT On Jun 26, 2003 this sequence version replaced gi:27804758.
Header: Database IdentifiersHeader: Database Identifiers
ACCESSION AY182241
VERSION AY182241.2 GI:32265057
ACCESSION AY182241
VERSION AY182241.2 GI:32265057
Accession•Stable•Reportable•Universal
Accession•Stable•Reportable•Universal
LOCUS AY182241 1931 bp mRNA linear PLN 04-MAY-2004DEFINITION Malus x domestica (E,E)-alpha-farnesene synthase (AFS1) mRNA, complete cds.ACCESSION AY182241VERSION AY182241.2 GI:32265057KEYWORDS .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, USAREFERENCE 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 submitterCOMMENT On Jun 26, 2003 this sequence version replaced gi:27804758.
Header: OrganismHeader: 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.
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 TableThe Feature Table
Coding sequenceCoding sequence
start (atg)start (atg) stop (tag)stop (tag)
DNADNA RNARNA
cDNAcDNA
phenotypephenotype
DNA sequencesDNA sequencesgenomesgenomes
protein protein sequence sequence databasesdatabases
proteinprotein
Bioinformatics is NOT just information technology. It can teach the central dogmas of molecular biology
GATGGATGCCCCAATTAAGGAAGGCCTTGGTTAAGGTTCCGTGTAACCCCCCT <T <- 100% - 100% GATGGATGCCCCAATTAAGGAAGGCCTTGGTTAAGGTTCCGTGTAACCCCCCT <T <- 100% - 100%
GATGGATGCCCCAATTAAGGAAGGCCTTGGTTAAGGTTCCGTGTAACCCCCCT <T <- 100% - 100% GATGGATGCCCCAATTAAGGAAGGCCTTGGTTAAGGTTCCGTGTAACCCCCCT <T <- 100% - 100%
GATGGATGCCCCAATTAAGGAAGGCCTTGGTTAAGGTTCCGTGTAACCCCCCT <T <- 100% - 100% GATGGATGCCCCAATTAAGGAAGGCCTTGGTTAAGGTTCCGTGTAACCCCCCT <T <- 100% - 100%
GATGGATGCCCCAATTAAGGAAGGCCTTGGTTAAGGTTCCGTGTAACCCCCCT <T <- 100% - 100% GATGGATGCCCCAATTAAGGAAGGCCTTGGTTAAGGTTCCGTGTAACCCCCCT <T <- 100% - 100%
Insect Phylogeny
Top 5 Wolbachia BLAST matches
GATGGATGCCCCAATTAAGGAAGGCCTTGGTTAAGGTTCCGTGTAACCCCCCT <T <- 100% - 100% GATGGATGCCCCAATTAAGGAAGGCCTTGGTTAAGGTTCCGTGTAACCCCCCT <T <- 100% - 100%
Outcomes:Outcomes:
Lateral Transfer ?Lateral Transfer ?
LetLet’’s Begin Our Bioinformatic Exercise s Begin Our Bioinformatic Exercise Lab 5Lab 5
HTTP://WWW.DIGITALWORLDBIOLOGY.COM/BLAST