Download BIOQuesthedgehog phylogeny1

HEDGEHOG-EMONY
Pamela “Sonic” Pape-Lindstrom
Everett Community College (Washington)
David “Desert” Matlack
Earlham College (Indiana)
Shane “Indian” Webb
North Georgia College & State University
INTRODUCTION
The hedgehog gene family codes for
secreted signaling proteins important in
embryonic development including:
 Neural tube development and motor
neuron specification
 Left-right symmetry
 Body plan
 Limb development
 Retinal development
Originally named for the mutant
phenotype in Drosophila, hedgehog
exists in a single copy in all nonvertebrates.
Vertebrates possess three paralogs
produced via two gene duplication
events in a vertebrate ancestor. The
vertebrate genes are now known as
Indian hedgehog, Sonic hedgehog and
Desert hedgehog.
Hypothesis: Hedgehog subtypes in
vertebrates should form monophyletic
groups (supporting the idea that these
genes arose via duplication events, e.g.
are members of a gene family).
METHODS
 Ndjinn search of SwissProt & Genbank
repositories via Workbench (workbench.sdsc.edu)
 Blastp search of a conservative region of
hedgehog (VMNQWPGVKLRVTEGWDED)
via NCBI (www.ncbi.nlm.nih.gov) to find additional data
 ClustalW multiple sequence alignment w/in
Workbench
o Default settings
o Rooted tree (Warning: produces only a single output
tree via dubious methods)
 Number of Operational Taxonomic Units:
o 10 non-vertebrate sequences
o 21 vertebrate sequences
 ClustalW output gene tree examined for
hierarchical structure
RESULTS
Conserved region of hedgehog
ehh_Danio
DGLHSEESLHYEGRAVDITTSDRDRNKYRMLARLAVEAGFDWVYYESKGHVHCSVKSEHS
IHH_Echidna DGLHSEESLHYEGRAVDITTSDRDRNKYRMLARLAVEAGFDWVYYESKGHVHCSVKSEHS
ihh_Danio
DGLHSEESLHYEGRAVDITTSDRDRNKYRMLARLAVEAGFDWVYYESKGHVHCSVKSEHS
IHH_MOUSE
DGHHSEESLHYEGRAVDITTSDRDRNKYGLLARLAVEAGFDWVYYESKAHVHCSVKSEHS
IHH_HUMAN
DGHHSEESLHYEGRAVDITTSDRDRNKYGLLARLAVEAGFDWVYYESKAHVHCSVKSEHS
IHH_XENLA
DGHHFEESLHYEGRAVDITTSDRDRNKYGMLARLAVEAGFDWVYYESKAHIHCSVKSEHS
shh_Mus
DGHHSEESLHYEGRAVDITTSDRDRSKYGMLARLAVEAGFDWVYYESKAHIHCSVKAENS
shh_Rattus
DGHHSEESLHYEGRAVDITTSDRDRSKYGMLARLAVEAGFDWVYYESKARIHCSVKAENS
shh_Homo
DGHHSEESLHYEGRAVDITTSDRDRSKYGMLARLAVEAGFDWVYYESKAHIHCSVKAENS
SHH_HUMAN
DGHHSEESLHYEGRAVDITTSDRDRSKYGMLARLAVEAGFDWVYYESKAHIHCSVKAENS
shh_Gallus
DGHHSEESLHYEGRAVDITTSDRDRSKYGMLARLAVEAGFDWVYYESKAHIHCSVKAENS
SHH_XENLA
DGHHLEESLHYEGRAVDITTSDRDRSKYGMLGRLAVEAGFDWVYYESKAHIHCSVKAENS
shh_Danio
DGHHFEESLHYEGRAVDITTSDRDKSKYGTLSRLAVEAGFDWVYYESKAHIHCSVKAENS
SHH_BRARE
DGHHFEESLHYEGRAVDITTSDRDKSKYGTLSRLAVEAGFDWVYYESKAHIHCSVKAENS
shh_Danio
DGRHLEESLHYEGRAVDITTSDRDKSKYGMLSRLAVEAGFDWVYYESKAHIHCSVKAENS
DHH_HUMAN
DGHHAQDSLHYEGRALDITTSDRDRNKYGLLARLAVEAGFDWVYYESRNHVHVSVKADNS
DHH_HUMAN
DGHHAQDSLHYEGRALDITTSDRDRNKYGLLARLAVEAGFDWVYYESRNHVHVSVKADNS
dhh_Mus
DGHHAQDSLHYEGRALDITTSDRDRNKYGLLARLAVEAGFDWVYYESRNHIHVSVKADNS
DHH2_XENLA
DGHHAHDSLHYEGRALDITTSDRDRNKYGMLARLAVEAGFDWVYYESKAHIHVSVNTDNS
DHH1_XENLA
DGHHAHDSLHYEGRALDITTSDRDRNKYGMLARLAVEAGFDWVYYESKAHIHVSVKADNS
dhh_Danio
DGHHPPGSLHYEGRAVDITTSDRDTKKYGLLAQLAVEAGFDWVHYESKYHVHCSVKADHS
hh_Scorpion DGPHAINSLHYEGRAVDITTSDRDRSKYGMLARLAVDAGFDWVYYESRAHIHCSVKSESA
hh_Artemia
EGLHASNSLHYEGRAVDITTSDRDRSKYGMLARLAVEAGFDWVYYESRAHIHTSVKSESS
Drosophila_hh DYHHGQESLHYEGRAVTIATSDRDQSKYGMLARLAVEAGFDWVSYVSRRHIYCSVKSDSS
hh_Drosophila DYHHGQESLHYEGRAVTIATSDRDQSKYGMLARLAVEAGFDWVSYVSRRHIYCSVKSDSS
HH_DROHY
DRQHGQESLHYEGRAVTIATSDHDQSKYGMLARLAVEAGFDWVSYVSRRHIYCSVKSDSS
hh_Anopheles DHMHAPESLHYEGRAVDIMTSDKDRSKIGMLARLAVEAGFDWVFYESRSHIHCSVKSDSS
hh_Octopus
QGHHAPTSLHYEGRAVDITTSDRVRSRYGMLARLAVEAGFDWVYYESRSHIHCSVRSDSL
hh_seaurchin DQPN-VEPLHAEGRAVDITTSDRDKNKYGALARLAVEAGFDWVNYESKAWVHCSVKSESA
hh2_Ciona
DGVHRKGSLHYEGRAVDIKTSDNDLSKNGLLARLAVESGFDWVYYESKFYVHASVRADNS
hh1_Ciona
GNDKANDPLHYEGRAVDITTDDADRNKYPILARLAVVAGFDWVKYDGK-VVHCSVKSEES
:
.** ****: * *.*
.:
*.:*** :***** * .: :: **.::
Danio
Indian
Sonic
Danio
Vertebrata
Desert
Urochordata
Arthropoda
Mollusca
Echinodermata
CONCLUSIONS
 We recovered a monophyletic Vertebrata
 Indian and Sonic hedgehog form
monophyletic groups. Desert did not due
to the position of zebrafish (Danio)
 Duplication events occurred in the
ancestor of vertebrates (vertebrates
possess all three paralogs) (supporting
Kumar, et al. 1996, Genetics 142: 965-972).
 Sonic and Indian hedgehog were
recovered as sister paralogs in our
analysis (contrary to Shimeld, 1999, Dev. Genes
Evol. 209(1): 40-47)
Additional:
 Hedgehog appears quite useful for
reconstructing animal interrelationships.
 It would make a good case study for
multiple biological courses.