Transcript D. melanogaster

Genomics and Shallow Genomics in
Drosophilidae: A Comparative Approach.
Patrick M. O’Grady
University of Vermont
Department of Biology
Talk Outline
• Drosophilidae Genomics
• Genomic Studies of Other Insects
• Genome Enabled Studies
Genomics in Drosophilidae I & II
• Whole genome sequence of D. melanogaster
(Rubin et al., 2000) and D. pseudoobscura
(http://www.hgsc.bcm.tmc.edu/projects/drosophila/) have been
determined.
• Two additional taxa, D. yakuba and D. simulans,
have been approved (and earmarked as “high
priority”) by NIH for whole genome sequencing.
(Begun & Langley; January 2003).
D. pseudoobscura
Sophophora
The melanogaster and
obscura species groups
are sister taxa placed in
the subgenus Sophophora.
melanogaster ~150 species
obscura ~60 species
Drosophila
(in part)
D. mauritiana
D. sechellia
D. simulans
D. melanogaster
D. yakuba
D. santomea
D. teissieri
D. erecta
D. orena
after Remsen & O’Grady (2002)
melanogaster subgroup.
• Full drosophilid genome is ~1/30th the size of
the “typical” mammal.
• 8X coverage, with basic annotation, can be
done in 2-3 months. Full annotation will be
over a longer time period.
• Cost is about $1,000,000 per genome.
How Genomes Get Funded…
(the oversimplified version)
• Write up a white paper
– Feedback from larger community
– Strong justification for the work
• Paper goes to NIH/NHGRI panel(s)
• If approved for sequencing, large genome
centers bid to do the work
Genomics in Drosophilidae III
• Committee of drosophilid biologists met in March
2003 to discuss the possibility of proposing
additional taxa for sequencing.
– From a variety of backgrounds (ecology, evolutionary
biology, systematics, population genetics,
developmental biology, etc.).
Concerns
• Assembly and annotation of existing genomes.
– Phylogenetic shadowing
– Gene finding, role of regulatory sequences, genome
component of transposable elements, adaptive
evolution, functional validation of gene sequences.
• Expand the taxonomic coverage to include a
greater diversity of drosophilids.
• Submitted a white paper proposing full genome
sequencing for 8 species (Clark et al., June 2003)
melanogaster group
- D. sechellia (3X)
- D. erecta
- D. ananassae
melanogaster subgroup
D. mauritiana
D. sechellia
D. simulans
D. melanogaster
D. yakuba
D. santomea
D. teissieri
D. erecta
D. orena
About 12-15 MYA
D. ananassae
after Remsen & O’Grady (2002)
ananassae subgroup
2
6
1
melanogaster group
Well-sampled range of 1-15 MY.
obscura group
-D. persimilis (3X)
The obscura-melanogaster
common ancestor was about
25 MYA.
willistoni group
- D. willistoni
D. willistoni diverged from the
common ancestor of the
melanogaster-obscura groups
about 35-40 MYA.
2
6
1
1
1
1
subgenus Drosophila
- D. virilis
- D. repleta
- D. grimshawi
The Sophophora-Drosophila
divergence was 40-50 MYA.
About the same as the
divergence between each
subgenus Drosophila group.
All 8 are now ranked as “high
priority.” Will have 12 full
genomes over the next 2-3
years.
“I’m completely confident that 10
years from now we’ll have the
sequences of 50 Drosophila.”
- Gerry Rubin, HHMI
Genomics in Other Insects
• Diptera: Aedes aegypti, Anopheles gambiae
– http://klab.agsci.colostate.edu/
• Lepidoptera: Bombyx mori
– http://www.ab.a.u-tokyo.ac.jp/lep-genome/new_lepgenome.htm
• Hymenoptera: Apis mellifera
– http://www.genome.gov/10002154
• Coleoptera: Tribolium castaneum
– http://www.genome.gov/10002154
Diptera
Strepsiptera
Siphonaptera
Mecoptera
Trichoptera
Lepidoptera
Hymenoptera
Neuroptera
Megaloptera
Raphidioptera
Coleoptera
Hemiptera
Psocodea
Plecoptera
Dictyoptera
Odonata
after Whiting et al., (1997)
• What is the best way to sample Diptera and other
insect groups?
– Phylogenetic approach? Target model systems?
• What questions can be addressed using genomic
data?
– Generalist vs. specialist, widespread vs. rangerestricted, virulence, life history characters, etc...
“In many ways we are like children in an enchanted
forest, wandering almost aimlessly from discovery to
discovery. For the moment, at least, that should be
sufficient. At some point we will inevitably emerge
into a clearing where principles and patterns in the
organization and evolution of the genome are
evident. Until then, let us be thankful that the
pleasures of the forest are so numerous and
diverse.”
R. J. MacIntyre (1985)
• Genome-enabled research
– Systematics
Mitogenomics: nearly
Nearly complete
complete
– Genome Evolution
– Comparative Genomics mt genomes
Shallow nuclear genomics:
multiple nuclear loci.
• Nuclear loci
– Goal is one gene per
chromosome division
– 68 are “in production”
– Another 810 have been
designed
– 2R and 3L have not been
heavily targeted to date
• Examined about 200
species to date (~250 are
planned.
X Chromosome
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
Chromosome 2L
21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40
Chromosome 2R
41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60
Chromosome 3L
61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80
Chromosome 3R
81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100
Chromosome 4
101 102 103 104
D.funebris103952
D.putrida103964
D.pallidipennis104815
D.cardini103963
D.dunni103969
D.guarani103966
D.ornatipennis103965
D.griseolineata103986
D.guttifera103968
D.immigrans103956
D.hypocausta103972
D.nasuta103957
D.lineosa103961
Z.tuberculatus105498
Z.badyi105640
Z.sepsoides105642
Z.ghesquierei105641
S.caliginosa105680
S.palmae106323
D.canalinea103953
D.pavani103955
D.hydei105429
D.navojoa105433
D.mojavensis106302
D.mercatorum106304
D.camargoi103971
D.gibberosa103960
D.nannoptera105440
D.acanthoptera105622
D.aracatas103962
D.montana103959
D.virilis105500
D.sordidula103954
D.robusta103967
D.melanica105499
D.polychaeta103958
D.crinumlily104814
D.melanogasterNM 079818
D.simulans105634
D.malerkotliana105504
D.pseudoobscura105505
H.duncani105637
S.latifasciaformis105638
D.percnosoma105685
D.waddingtoni105687
D.waddingtoni105707
D.conformis105686
D.melanoloma105708
D.austrosaltans106314
D.willistoni106322
C.procnemis106326
S.pattersoni105497
S.lebanonensis105639
Topology is similar when sampling 5,000
characters compared to 40,000.
Support levels (bootstrap, jackknife)
increase slowly.
This amount of data is particularly useful
for resolving rapid radiations (Hawaiian
Drosophila).
• Genome-enabled research
– Systematics
– Genome Evolution
– Comparative Genomics
Chromosome Evolution in Drosophila.
Muller’s Elements
species
D. melanogaste r
D. affinis
D.willistoni
D. virilis
D. robusta
D. grimshawi
# A B
C
D
E
4 X 2L 2R 2L 3R
5 XL 4
3 XR 2
3 XL 2R 2L XR 3
6 X
4
5
3
2
4 XL 3 2R XR 2L
6 X
3
2
5
4
F
4
5
6
4
6
– Transposition events from element to element are
thought to be rare: gene content of major chromosome
elements is conserved.
– Extensive internal reshuffling via paracentric inversions.
• First comparative genomic studies compared
polytene chromosome banding patterns between
different Drosophila species (Muller, 1940; Sturtevant and
Novitski, 1941).
Used to physically map genes
In D. melanogaster we know the position of all genes
Information concerning other species is lacking, but
can easily be inferred by combining polytene and
molecular data.
• Comparisons of synteny and colinearity
– Syntenic genes are on the same linkage group in different
species.
– Colinear genes are in the same order in different species.
– What is the
rate of genic
transposition in
the genome?
– How often are
so called “coadapted” gene
complexes
formed and lost.
J. Ranz, et al., (1999)
–
–
–
–
Margaret Kidwell (UA)
Bill Heed (UA)
Rob DeSalle (AMNH)
Kenneth Kaneshiro (UH Manoa)
• Technical Support:
– Amy Turmelle, Jake Wintermute, Jim Bonacum