Comparative Genome and Proteome Analysis of Anopheles gambiae and Drosophila melanogaster

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Comparative Genome andProteome Analysis of
Anophelesgambiae and Drosophilamelanogaster

• Evgeny M. Zdobnov, Christian von Mering, Ivica
  Letunic, David Torrents, Mikita Suyama, Richard
  R. Copley, George K. Christophides, Dana
  Thomasova, Robert A. Holt, G. Mani Subramanian,
  Hans-Michael Mueller,
• George Dimopoulos, John H. Law, Michael A. Wells,
  Ewan Birney, Rosane Charlab, Aaron L. Halpern,
  Elena Kokoza, Cheryl L. Kraft, Zhongwu Lai,
  Suzanna Lewis, Christos Louis, Carolina
  Barillas-Mury, Deborah Nusskern, Gerald M. Rubin,
  Steven L. Salzberg, Granger G. Sutton, Pantelis
  Topalis, Ron Wides, Patrick Wincker, Mark
  Yandell, Frank H. Collins, Jose Ribeiro, William
  M. Gelbart, Fotis C. Kafatos, Peer Bork

Presented by Leon G Xing
SCIENCE VOL 298 4 OCTOBER 2002
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Why Anopheles gambiae?

• It is the principal vector of malaria
• It carries many other infectious diseases
• Malaria afflicts more than 500 million people
• More than 1 million people die each year from
  malaria

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The Culprit
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Why Drosophila melanogaster

• One of the most intensively studied organisms in
  biology
• Serves as a model system for the investigation of
  many developmental and cellular processes common
  to higher eukaryotes
• Modest genome size 180 MB
• Its genome has been sequenced in 2000

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Mosquito vs. Fruit Fly

• They diverged about 250 million years ago
• (Human and pufferfish diverged about 450
  million years ago)
• Share considerable similarities
• Half of the genes in both genomes
• are interpreted as orthologs
• Average sequence identity about 56,

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Mosquito vs. Fruit Fly

• Anopheles genome is twice the size of Drosophila
• Female Anopheles feeds on blood (Hematophagy),
  which is essential for egg development and
  propagation
• Viruses and parasites use Anopheles as a vehicle
  for transmission

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Orthologs

• Genes in different species that evolved from a
  common ancestral gene by speciation
• Typically retain the same function in the course
  of evolution

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Paralogs

• Genes related by duplication within an organism
  and have evolved a related but different function

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Predict the function of a new protein

• A powerful approach is to use bioinformatics and
  domain database searches to find its
  characterized orthologs
• We know a lot about Drosophila but dont know
  much about Anopheles
• Compare their genomes may deduce a lot of
  information

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Drosophila melanogaster Genome

• The assembled and annotated genome sequence of 5
  Drosophila melanogaster chromosomes is in GenBank
  
• Its the collaboration between Celera and the
  Berkeley Drosophila Genome Project
• Published in the March 24, 2000 issue of Science.

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Drosophila Genome

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Anopheles vs DrosophilaGene Comparison at
Protein Level

• The proteins are classified into 4 categories
  based on
• 12,981 deduced Anopheles proteins out of 15,189
  annotated transcripts
• Omit transposon-derived bacterial like sequences,
  and alternative transcripts

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Classification of Anopheles proteins

• 11 orthologs
• Anopheles proteins with one clearly identifiable
  counterpart in Drosophila and vice versa
• 47 of the Anopheles
• 44 of the Drosophila proteins

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Classification of Anopheles proteins

• Many-to-many orthologs.
• Gene duplication has occurred in one or both
  species after divergence
• Includes 1779 Anopheles proteins

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Classification of Anopheles proteins

• The third category
• Have homologs in Drosophila and/or other species
  but without easily discernable orthologous
  relationships
• 3590 Anopheles predicted proteins

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Classification of Anopheles proteins

• The fourth category
• Has little or no homology in Drosophila but
  instead have best matches to other species.
• 1283 proteins

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Classification of Anopheles proteins

• Remaining proteins
• No detectable homologs in any other species with
  a fully sequenced genome
• 1437 in Anopheles
• 2570 in Drosophila
• Might be new or quickly evolving genes.

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Classification of proteins
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Some Notes

• The numbers and derived estimates are
  approximations.
• Annotation of genomes is an ongoing effort
• Some Anopheles genes have not been sequenced yet
• Highly polymorphic regions or in highly
  repetitive contexts prone to errors
• 70 accuracy

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The core of conserved proteins

• The 11 orthologs (6089 pairs) can be considered
  the conserved core
• The average sequence identity is 56
• Humans and pufferfish share 61
• Indicates that insect proteins diverge at a
  higher rate

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Properties of 11 orthologs.
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Orthologous proteins constitute a core of
conserved functions

• Early embryogenesis are conserved between
  Drosophila and Anopheles
• 315 early developmental genes in Drosophila vs
  251 genes showed a clear single ortholog in
  Anopheles

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Orthologous proteins

• 85 of the developmental genes have single
  orthologs
• 47 for the genome as a whole

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Protein family expansions and reductions

• Due to adaptations to environment and life
  strategies
• Leads to changes in cellular and phenotypic
  features
• Implies duplications after speciation

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Protein family expansions and reductions example

• Epsilon subunit of the adenosine
  triphosphate-synthase complex
• Encoded by two genes in both Anopheles and
  Drosophila
• They might share a single-copy ancestral gene
• After speciation they were duplicated
  independently later

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Expansions of proteins with FBN-like domains in
Anopheles.

• Fibrinogen (FBN) are found originally in human
  blood coagulation proteins
• A large expansion of mosquito proteins contains a
  domain resembling the COOH-terminus of the beta
  and gamma chains of FBN

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Expansions of proteins with FBN-like domains in
Anopheles.

• Phylogenetic tree of 58 Anopheles and
  13 Drosophila FBN genes
• They largely belong to two distinct
  species-specific clades
• Identified only two 11 orthologous relationships

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The significant implication of FBN gene expansion

• The massive expansion of the Anopheles gene FBN
  family might be associated with particular
  aspects of the mosquito's biology
• That is, hematophagy and exposure to Plasmodium
• Blood meal is a challenge associated with
  microbial flora in the gut and blood coagulation

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The implication of FBN gene expansion

• The bacteria-binding properties of FBNs might be
  important in controlling or aggregating bacteria
  in the midgut
• These proteins might be used as competitive
  inhibitors i.e. anticoagulants
• Some mosquito FBN proteins are up-regulated by
  invading malaria parasites

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Expansion of FBN-like proteins in Anopheles
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Gene losses in insects

• Some genes are absent in both Anopheles and
  Drosophila but are present in other eukaryotes
• Criteria genes must be present in at least one
  animal but also in fungi or plants

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Gene losses in insects.
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Gene genesis and gene loss

• 1437 predicted genes in Anopheles have no
  detectable homology with genes of other species
• 522 of these have putative paralogs only within
  Anopheles
• At least 26 of such genes expressed in the adult
  female salivary glands

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Strategy for identifying gene losses

• Search for genes that are present in only one of
  the two insects but that do have orthologs in
  other species

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Gene Losses

• Widespread orthologs missing from both Anopheles
  and Drosophila are putative insect-specific gene
  losses
• Example
• Insects are known to unable to synthesize sterols
  
• Absence of several enzymes involved in sterol
  metabolism

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Gene Losses example

• Absence of the DNA repair enzyme uracil-DNA
  glycosylase in insects
• DNA methylation can lead to spontaneous
  deamination of cytosine to uracil
• Drosophila has long been known to have no or only
  very little DNA methylation

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Cladogram based on Orthologs
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Intron gain and loss

• Drosophila are known to have a reduction of
  noncoding regions
• 11,007 out of 20,161 Anopheles introns in 11
  orthologs have equivalent positions in Drosophila
• Almost 10,000 introns have either been lost or
  gained

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The Drosophila Dscam gene

• Able to encode up to 38,000 proteins through
  extensive alternative splicing
• Three different cassettes of duplicated exons
  that can generate exponential combinations of
  splice variants
• The numbers of exons within the cassettes are at
  least similar in Anopheles

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(No Transcript)
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Microsynteny

• Through evolution genome structure may vary
  greatly, but small regions of conserved gene will
  be retained
• Microsynteny studies the localized region of
  sequences with high similarity

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Microsynteny blocks
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Mapping of orthologs and microsyntenyblocks to
chromosomal arms in Anophelesand Drosophila.
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Chromosome mapping

• Both Anopheles and Drosophila have five major
  chromosomal arms (X, 2L, 2R, 3L, and 3R, and a
  small chromosome 4 in Drosophila melanogaster).
• In Drosophila, reassortment of recognizable
  chromosomal arms occurs by fission and fusion at
  the centromeres

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Chromosome mapping

• The most conserved pair of chromosomal arms is
  Dm2L and Ag3R
• 76 of the orthologs and 95 of microsynteny
  blocks in Dm2L mapping to Ag3R

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Chromosome mapping.
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Chromosome mapping surprise

• Significant portions of the Anopheles X
  chromosome appear to have been derived from what
  are presently autosomal Drosophila chromosome
  segments
• 11 of Dm3R and 33 of Dm4

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Homology of chromosomal arms
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Thank you!