Assignment of cMegaBAC-CGCs to the virtual sheep genome
The virtual sheep genome spreadsheets contain the following columns, all information
relates back to the cMegaBAC-CGC column. The only columns where additional
information has been added by the editors have been indicated by italics.
Code – see below
HSA – human chromosome
CGC – cMegaBAC-CGCs numbered in ascending order from strt to end of the
human chromosome
OAR – predicted sheep chromosome added by the editor
Sense – initial orientation will be based on the sheep via dog-human synteny
Mod Sense – sense for vsheep genome
Link to - added by the editor indicates BAC-linkages between cMega-CGCs
Link from –added by the editor indicates BAC-linkages between cMega-CGCs
Marker OAR – sheep chromosome numbers of marker(s) in the CGC, if more than
one listed in the order they map to the human genome (do not change order when you
invert orientation of fragment)
Marker cM – coordinates on corresponding sheep chromosome, if more than one
listed in the order they map to the human genome (do not change order when you
invert orientation of fragment)
Cow break – intrachromosomal breaks predicted from cow mapping, #.1, #2, #.3, or
vice versa, are the order that we expect them to occur in the sheep genome.
Dog break – intrachromosomal breaks predicted from dog mapping, #.1, #2, #.3, or
vice versa, are the order that we expect them to occur in the sheep genome.
TTO – outsize tail to tail BACs, suggest large insertion of DNA
TH – tail to head BACs, suggest possible inversion of one cMegaBAC-CGC relative
to the other, or more likely local rearrangements.
THO – outsize tail to head BACs, suggest possible inversion of one cMegaBACCGC relative to the other
HH – head to head local rearrangements, unlikely to be informative
Href – CGCs linked by human refseq gene
Cow-human – Cow human syntenic blocks, however there may be small reordering
and inversions with blocks, does not give orientation information unlike sheep-doghuman synteny
Mammalian synteny – syntenic blocks conserved in the mammals however there
may be small reordering and inversions with blocks, does not give orientation
information unlike sheep-dog-human synteny (Murphy et al., 2005, Science 309, 613617).
Mam-chicken synteny - syntenic blocks conserved in the mammals and chickens
however there may be small reordering and inversions with blocks, does not give
orientation information unlike sheep-dog-human synteny (Bourque et al., 2005,
Genome Res 15, 98-110).
Sheep-Dog-human synteny – syntenic blocks defined by overlapping sheep BACs
and conserved in order and orientation between dog and human genomes.
The cMegaBAC-CGCs were ordered into their most likely order and orientation in the
sheep genome. The table below lists the hierarchy in which the information was used.
Table 1. cMegaBAC blocks confidence codes
code colour
Anchored by
1
Dark green
Linkage markers
2
Pale green
Linkage markers
Oriented by
Linkage markers
Linked directly or indirectly
to oriented CGCs by BACs,
or part of an oriented block
of linked CGCs
Linked directly or indirectly
to oriented blocks by BACs,
or part of an oriented block
of linked CGCs
chicken-mammal or
mammalian synteny or
cow/human synteny
chicken-mammal or
mammalian synteny or
cow/human synteny or
dog/human synteny
3
Light yellow
Linked directly or indirectly to
anchored CGCs by BACs
4
Dark yellow
5
Orange
6
Pink
7
Red
Linkage markers or linked
directly or indirectly to
anchored CGCs by BACs
Cytogentic markers or linked
directly or indirectly to
anchored CGCs by Chickenmammal or Mammalian
synteny
Linked directly or indirectly to chicken-mammal or
anchored CGCs by cow/human mammalian synteny or
synteny or unbroken gene
cow/human synteny or
dog/human synteny
Not linked directly or
chicken-mammal or
indirectly to an anchored CGC mammalian synteny or
cow/human synteny or
dog/human synteny
Version 1.0 of the virtual genome released as spreadsheets 1st August 2006 for
comment from interested parties. Initially to be used in conjunction with the rumhum
browser, http://www.livestockgenomics.csiro.au/perl/gbrowse.cgi/rumhum/, use the
“virtual sheep” predefined viewing state. The virtual sheep genome browser to be
released in the next few weeks.
Comment period will close on Friday 8th September.
A new freeze of the virtual genome, v1.1 will be released soon after the closure of the
comment period.
V1.1 will be released to the broader research community.
V2 will be built using the Btau3.0 and hg18 genome assemblies for expected release
December 2006.