in 2000 which genomes where compared?
what where the results? who shared most genes with human?
how does this differ in disease genes
Human not completed
D. melanogaster (fly)
S. cerevisae (yeast)
C. elegans (worm)
many mammal (human/ mouse) genes known already -> used as well
results: shared genes w/ BLAST E<10^-10
mammals and fly shared 50%
yeast 37%
worm 35%
used OMIM for human disease gene set of size 289
E < 10^-6
230 in fly (80%)
212 in worm (73%)
120 in yeast (42%)
-> disease associated genes conserved across species
-> model organisms useful for studying diseases
compare seq divergence w/i Drosophila to w/i mammals
2007: 12 Drosophila species sequenced
seq divergance compareable with w/i mammals
7000 genes: single copy orthologs (one-to-one) in all 12 species
-> may represent “core“ genome for Drosophila
+ 5000 genes: Homology across all species, but not one-to-one
-> multi-gene familys w/ multiple paralogs (difficult to determine number of functional ones)
what was the first plant genome to be sequenced? when? genomesize? genenumber?
2000: Arabidopsis thaliana (mustard weed)
125 Mbp
25000 genes
gene number of mustard weed, fly, worm and human
mustard weed (Arabidopsis): 25k
human: 21k
worm: 19k
fly: 14k
what explains the high gene number in mustard weed/ Arabidopsis?
more genes present as paralogs compared to fly and worm for instance
-> higher percentage of genes that are part of multi-gene families
probably, lots of gene duplication events throughout its evolution
what was the first comparative genomic analysis in plants? what was the result? how does it compare to animals?
2002: two rice (Oryza sativa) strains: compared with/ Arabidopsis (mustard weed)
rice genome size: 430Mbp
genes: 40k-50k
80-85% of predicted mustard weed genes had homologous in rice
only 50% of predicted rice genes homologs in mustard weed (bc rice has more genes, makes sense)
comparison to animals:
of the genes shared in rice and mustard weed (~20k) 30.5% homologous in yeast, worm or fly
of rice genes w/o homologous in musard weed, only 2.4%
what did original IHGP human genome paper claim about horizontal gene transfer?
“hundreds of human genes appear likely to have resulted from horizontal gene transfer from bacteria at some point in the vertebrate lineage”
i.e.:
There are bacterial genes in the human genome
Genes were transferred directly from bacteria to humans (or other vertebrates)
-> identified 223 human proteins w/ significant homology to bacteria proteins, w/o match in non-vertabrate genome (eg yeast, fly, worm)
criticisms and alternate explanations opposed to horizontal gene transfer
Independent gene loss in some eukaryotes
Finding: when more non-vertebrate eukaryote genomes are searched, homologs to these genes can be found.
= support for independent gene loss in some eukaryotes
phylogenetic analysis of the sequences can be used to test the hypothesis:
if there was horizontal transfer, the human genes should be more similar in sequence to the bacterial genes than to other non-vertebrate eukaryotes
-> This does not appear to be the case
At present, the number of potential bacterial genes in the human genome has dropped below 40, and will likely decrease as more diverse eukaryotic genomes are sequenced
comparison human/ mouse genome
>98% of genes have homologs
on small scale well conserved
-> genes found in conserved blocks = SYNTENY
on large scale: chromosomal rearangements
-> but location of these blocks not conserved:
eg: chrom 16 in mouse spread over 6 different human genomes
this type of rearangement common among vertabrates
what is Synteny
same genes in same order in 2 species (conversed blcok of DNA)
Zuletzt geändertvor 7 Tagen