In this first assignment, you will gather data from ten bacteria and two outgroups. You should get the 6-phosphogluconate dehydrogenase, decarboxylating (gnd) protein and DNA sequences for the following species:
Encephalitozoon cuniculi (Fungus)
Dictyostelium discoideum (Slime mold)
Synechococcus elongatus (Cyanobacteria)
Cronobacter dublinensis (Proteobacteria)
Candidatus Solibacter usitatus (Acidobacteria)
Leptotrichia goodfellowii (Fusobacteria)
Borrelia garinii (Spirochaetes)
Phycisphaera mikurensis (Planctomycetes)
Mycobacterium tuberculosis (Actinobacteria)
Anaerolinea thermophila (Chloroflexi)
Chlamydia trachomatis (Chlamydiae)
Lactococcus lactis (Firmicutes)
I succeeded in doing this using GenBank. For some species, you have to click on the right places to get the entire genome with DNA sequences, search for "gnd (the quote helps), and click on CDS to get the DNA sequence that encodes the protein highlighted. If the DNA sequence is not loaded, there is a place you can click to load them. I did it all with a slowish internet connection in a reasonable amount of time.
When gathering this data, it is ideal to keep track of the necessary references in order to be able to find the data again. As an example, the record I made for Candidatus Solibacter usitatus is the following:
ORGANISM Candidatus Solibacter usitatus Ellin6076
Bacteria; Acidobacteria; Solibacteres; Solibacterales;
Solibacteraceae; Candidatus Solibacter.
REFERENCE 1 (bases 1 to 9965640)
AUTHORS Copeland,A., Lucas,S., Lapidus,A., Barry,K., Detter,J.C., Glavina
del Rio,T., Hammon,N., Israni,S., Dalin,E., Tice,H., Pitluck,S.,
Thompson,L.S., Brettin,T., Bruce,D., Han,C., Tapia,R., Gilna,P.,
Schmutz,J., Larimer,F., Land,M., Hauser,L., Kyrpides,N.,
Mikhailova,N., Janssen,P.H., Kuske,C.R. and Richardson,P.
CONSRTM US DOE Joint Genome Institute
TITLE Complete sequence of Solibacter usitatus Ellin6076
JOURNAL Unpublished
REFERENCE 2 (bases 1 to 9965640)
AUTHORS Copeland,A., Lucas,S., Lapidus,A., Barry,K., Detter,J.C., Glavina
del Rio,T., Hammon,N., Israni,S., Dalin,E., Tice,H., Pitluck,S.,
Thompson,L.S., Brettin,T., Bruce,D., Han,C., Tapia,R., Gilna,P.,
Schmutz,J., Larimer,F., Land,M., Hauser,L., Kyrpides,N.,
Mikhailova,N., Janssen,P.H., Kuske,C.R. and Richardson,P.
CONSRTM US DOE Joint Genome Institute
TITLE Direct Submission
JOURNAL Submitted (06-OCT-2006) US DOE Joint Genome Institute, 2800
Mitchell Drive B100, Walnut Creek, CA 94598-1698, USA
gene 8897542..8898999
/locus_tag="Acid_7082"
CDS 8897542..8898999
/locus_tag="Acid_7082"
/EC_number="1.1.1.44"
/note="KEGG: sde:Sde_0635 6-phosphogluconate
dehydrogenase, decarboxylating;
TIGRFAM: 6-phosphogluconate dehydrogenase,
decarboxylating;
PFAM: 6-phosphogluconate dehydrogenase domain protein;
6-phosphogluconate dehydrogenase, NAD-binding"
/codon_start=1
/transl_table=11
/product="6-phosphogluconate dehydrogenase
(decarboxylating)"
/protein_id="ABJ87995.1"
/db_xref="GI:116229286"
/db_xref="InterPro:IPR006113"
/db_xref="InterPro:IPR006114"
/db_xref="InterPro:IPR006115"
/db_xref="InterPro:IPR006183"
/db_xref="InterPro:IPR006184"
/translation="MEQTADIALIGLAVMGQNLIMNMNDHGYTVVAYNRTTSKVDEFL
NDAAKGSKVIGAHSIEEMVKLLKRPRKIMLMVKAGKPVDEFIETLLPYLEPGDLIIDG
GNSHFPDTIRRTQYLESKGLLFVGTGVSGGEEGARFGPSMMPGGTPAAWPLVKDIFQA
ICAKTPEGEPCCDWVGRDGAGHFVKMTHNGIEYGDMQLICEAYQLMKEGLGMSNEEMH
EVFAEWNKGELDSYLIEITRDILGYKDPATGEQTLDKILDTAGQKGTGKWTSVSSLDL
GMPVTLIGEAVYARCLSAMKDDRVKASKILTGPKAKFPGDKKAFVEDIRQALLASKIV
SYAQGFMLLAEAAKEYKWDLNYGSIAMMWREGCIIRSVFLGKIKAAFANNPTLANLLL
DSYFRGLLDRCQGSWRHTVSEAVLNGVPVPAFTTALAFYDGYRSERLPANLLQAQRDY
FGAHTFERVDQPRGKFFHTNWTGKGGNVSAGVYTV"
atggaacaa acggcagaca tcgcattgat cggtctggca
8897581 gtcatgggcc agaacctgat tatgaatatg aacgaccacg ggtacacggt ggtcgcttat
8897641 aaccgcacga cctccaaggt cgatgaattc ctgaacgacg ccgccaaagg cagcaaggtc
8897701 atcggcgcgc actcgatcga ggagatggtc aaacttctca agcgcccccg caagatcatg
8897761 ctcatggtca aggccggcaa gccggtggac gaattcatcg agaccctgct cccctacctc
8897821 gagcccggcg acctgatcat cgatggcggc aattcgcatt tcccggatac catccgccgc
8897881 acccaatacc tcgaaagcaa gggccttctg ttcgtcggca ccggcgtttc cggcggcgag
8897941 gaaggcgcgc gtttcggccc gtccatgatg cccggaggta cccccgccgc gtggcccctc
8898001 gtgaaggaca tcttccaggc catctgcgcc aagacacccg agggcgagcc ctgctgcgat
8898061 tgggtcggcc gcgatggcgc cggccacttc gtcaagatga cccacaacgg catcgagtac
8898121 ggcgatatgc agctcatctg cgaggcctac caactcatga aggaaggcct cggcatgagc
8898181 aacgaagaaa tgcacgaagt cttcgccgaa tggaacaagg gcgagctcga tagctacctc
8898241 atcgaaatca cccgcgacat tctgggctac aaagaccccg ccaccggcga acagaccctc
8898301 gacaaaatcc tcgataccgc cggccaaaag ggtaccggca agtggaccag cgtcagctcg
8898361 ctcgatctcg gcatgcccgt taccctgatc ggcgaagccg tctacgcgcg ctgcctcagc
8898421 gctatgaagg acgatcgcgt caaggcttcc aagatcctca ccggacccaa ggccaagttc
8898481 cccggtgaca agaaggcctt cgtggaagac atccgccagg cccttctcgc ctccaagatc
8898541 gtcagctacg cgcagggctt catgctcctc gccgaagccg ccaaggaata taagtgggac
8898601 ctgaactacg gttccatcgc catgatgtgg cgcgaaggct gcatcatccg cagcgtcttc
8898661 ctcggcaaaa ttaaggccgc gtttgccaac aacccgacgc tggcgaacct gctgctcgat
8898721 agctacttca ggggcctgct ggaccgttgc cagggttcct ggcgccacac cgtttccgaa
8898781 gccgtcctca atggcgtgcc ggtgcccgcc ttcaccaccg ctctcgcctt ctacgatggc
8898841 taccgcagcg aacgcctgcc tgccaacctg ctccaggcac agcgcgatta cttcggcgcc
8898901 cacaccttcg agcgcgtcga tcagccgcgc ggcaagttct tccacaccaa ttggaccggc
8898961 aagggcggca acgtctcggc cggagtctac accgtatga
Next week you will create an alignment. Later you will use your alignments to create phylogenies. I have kept the number of species small in order that you can "look" at the data and get a feel for them. These assignments will highlight some practical difficulties in conducting phylogenetic analyses but they are kept short and reasonable enough for homework and so do not constitute a realistic attempt at recreating bacterial phylogenetics.