knabe
Well-known member
http://www.genomeweb.com/node/915449?emc=el&m=370499&l=2&v=aea3af4a27
The resulting assembly has around 91% of the assembled genome anchored onto chromosomes.
when human was first announced finished with clinton, blair, francis collins,and the dude from celera, i think it was 95% finished. human is over 99.5% finished.
not sure yet what they mean when they say anchored. in a worse case scenario, it could mean the reads are anchored onto 30 chromosomes with further editing and resequencing to be done, best case, is that 91% is really done. this leaves vast gaps for repeats such as huntingtons in human which wasn't unraveled till a repeat area was discovered in assembly.
"The team's analyses also suggest that the cattle genome has undergone numerous rearrangements, spurred by repetitive elements and duplications such as segmental duplication, retrotransposons, and retroviral long terminal repeats. For example, they found 1,020 segmental duplications involving more than three percent of the genome. and with these duplications sometimes occuring in areas that are harder to tease out through the sequencing data assembly process, there will be more.
In particular, the cattle genome contained duplications in genes involved in immune function, olfactory receptors, reproduction, lactation, and digestion. Ten immune system-related genes were also among the 71 genes under positive selection in the domestic cow genome."
positive selection increases the prevalence of adaptive traits. meaning man can influence this through selection without knowing it.
"The bovine HapMap data show that cattle have undergone a rapid recent decrease in effective population size from a very large ancestral population, possibly due to bottlenecks associated with domestication, selection, and breed formation," University of Missouri researcher Jerry Taylor, who was part of the Bovine HapMap team, said in a statement. "The recent decline in diversity is sufficiently rapid that loss of diversity should be of concern to animal breeders." NO KIDDING.
with such recent relative inbreeding in several breeds including angus, hereford, maine anjou, it's pretty clear, at least to me, there are obvious opportunities/problems and not just from a defect perspective.
The resulting assembly has around 91% of the assembled genome anchored onto chromosomes.
when human was first announced finished with clinton, blair, francis collins,and the dude from celera, i think it was 95% finished. human is over 99.5% finished.
not sure yet what they mean when they say anchored. in a worse case scenario, it could mean the reads are anchored onto 30 chromosomes with further editing and resequencing to be done, best case, is that 91% is really done. this leaves vast gaps for repeats such as huntingtons in human which wasn't unraveled till a repeat area was discovered in assembly.
"The team's analyses also suggest that the cattle genome has undergone numerous rearrangements, spurred by repetitive elements and duplications such as segmental duplication, retrotransposons, and retroviral long terminal repeats. For example, they found 1,020 segmental duplications involving more than three percent of the genome. and with these duplications sometimes occuring in areas that are harder to tease out through the sequencing data assembly process, there will be more.
In particular, the cattle genome contained duplications in genes involved in immune function, olfactory receptors, reproduction, lactation, and digestion. Ten immune system-related genes were also among the 71 genes under positive selection in the domestic cow genome."
positive selection increases the prevalence of adaptive traits. meaning man can influence this through selection without knowing it.
"The bovine HapMap data show that cattle have undergone a rapid recent decrease in effective population size from a very large ancestral population, possibly due to bottlenecks associated with domestication, selection, and breed formation," University of Missouri researcher Jerry Taylor, who was part of the Bovine HapMap team, said in a statement. "The recent decline in diversity is sufficiently rapid that loss of diversity should be of concern to animal breeders." NO KIDDING.
with such recent relative inbreeding in several breeds including angus, hereford, maine anjou, it's pretty clear, at least to me, there are obvious opportunities/problems and not just from a defect perspective.
