Transcript Eukaryotic genomes

Genomes
School B&I TCD Bioinformatics
May 2010
Genome sizes
Completed eukaryotic nuclear genomes
Type of organism
Species
Primitive microsporidian
E. cuniculi
Fungi
S. cerevisiae
Sc. pombe
N. crassa
Nematode worm
C. elegans
Insect: Fruit fly
D. melanogaster
mosquito
A. gambiae
Malarial parasite
P. falciparum
Plants: Thale cress
A. thaliana
rice
O. sativa
Human
H. sapiens
Mouse
M. musculus
Rat
R. norvegicus
Chicken
G. gallus
Genome size (106 base pairs)
2.5
12.1
13.8
40
100
180
278
22.8
116.8
400
3400
3454
2556
1200
What’s it all about?
• With complete chromosome or big chunks
– Can put genes in context, synteny, neighbours
• With complete genome
– Have all paralogs of gene family
– So can identify orthologs – genes similar by
descent and so by function
• Gene clusters
– Operons or “operons”
– Tissue expression
– Positive selection / excessively variable regions
Caron Human Genome
Highly expressed genes are clustered (densely)
Tissue expression mammals
Where are tissue expressed
genes clustered?
Mouse/Human Synteny
Three resources
• Golden Path at UCSC
– Jim Kent and his group at Santa Cruz
• Ensembl
– Ewan Birney, Wellcome Trust, EBI, Sanger
• NCBI Genome Database
– US government
UCSC Golden Path
• Access to human, mouse, rat, chicken etc.
• Two modes:
– BLAT search
• BLAT search - find sequences of >95% similarity
and length >40 bases on the genome.
– Genome browser
• Choose and display data you want: repeats, SNPs,
ESTs
Golden Path UCSC
• Vertebrate genomes
available
• Human
• Chimp
• Rhesus
• Dog
• Cow
• Mouse
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Rat
Cat
Opossum
Chicken
Xenopus
Zebrafish
Tetraodon
Fugu
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Ensembl is a joint project between EMBL - EBI and the
Sanger Institute to develop a software system which
produces and maintains automatic annotation on eukaryotic
genomes.
• Continually updated and improved.
Ensembl genomes
• Mammals
• Not mammals
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Homo sapiens
Pan troglodytes (chimp)
Macacca mulatto (monkey)
Mus musculus (mouse)
Rattus norvegicus (rat)
Oryctylagus cuniculus (rabbit)
Canis familiaris (dog)
Bos taurus (cow)
Dasypus novemcinctus (armadillo)
Loxodonta africana (elephant)
Echinops telfari (tenrec)
Monodelphis domestica (opossum)
… and others
Gallus gallus (chicken)
Xenopus tropicalis (frog)
Danio rerio (zebra fish)
Tetraodon nigroviridis (puffer fish)
Ciona intestinalis (chordate)
Drosophila melanogaster (fly)
Anopheles gambiae (mosquito)
Aedes aegypti (mosquito 2)
Apis mellifera (bee)
Caenorhabditis elegans (worm)
Saccharomyces cerevisiae
NCBI Genome Center
• Start here for any genome
– Bacterial
– Archaeal
– Eukaryotic
• Uniform arrangement of information
NCBI genes and disease
• Resource for find authoritative info about
diseases.
• http://www.ncbi.nlm.nih.gov/books/bookres.fcgi/gnd/tocstatic.html
• is one of the many NCBI on-line BOOKS
• Classifies diseases and syndromes by
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Cancer
Immune system
Muscle and bone
Signals and Transporters
Nervous system
Etc.
OMIM
• On line Mendelian Inheritance in Man
• Everything you need to know
– Diseases and syndromes
– But also quirky stuff
• But only 2% of syndromes are simple
mendelian (single gene)
How to classify genes
• What species?
• What function?
– What gene family
– What domains/motifs
• What pathway?
• What genomic neighborhood/synteny?
• What ligands / interactions?
Summary
• Different ways/contexts of viewing data
• Bioinformatics is integrative biology
• Your task is …
• To access available resources to maximise
our understanding