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 editorshave 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 editorindicates BAC-linkages between cMega-CGCs

Link from –added by the editorindicates 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 cMegaBAC-CGC 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-dog-human 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, 613-617).

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 / Oriented by
1 / Dark green / Linkage markers / Linkage markers
2 / Pale green / Linkage markers / Linked directly or indirectly to oriented CGCs by BACs, or part of an oriented block of linked CGCs
3 / Light yellow / Linked directly or indirectly to anchored CGCs by BACs / Linked directly or indirectly to oriented blocks by BACs, or part of an oriented block of linked CGCs
4 / Dark yellow / Linkage markers or linked directly or indirectly to anchored CGCs by BACs / chicken-mammal or mammalian synteny or cow/human synteny
5 / Orange / Cytogentic markers or linked directly or indirectly to anchored CGCs by Chicken-mammal or Mammalian synteny / chicken-mammal or mammalian synteny or cow/human synteny or dog/human synteny
6 / Pink / Linked directly or indirectly to anchored CGCs by cow/human synteny or unbroken gene / chicken-mammal or mammalian synteny or cow/human synteny or dog/human synteny
7 / Red / Not linked directly or indirectly to an anchored CGC / chicken-mammal or 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, 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.