[ensembl-dev] coordinate-system 'group' versus 'chromosome'

[Karyn Megy]

Dear Trevor,

For Dr.pseudoobscura we kept the nomenclature from the import source (FlyBase). 

According to their website, the "assembly contains complete chromosome sequences (chr2 and chr3), linkage groups (chr4_group*, chrXL_group* and chrXR_group*), and a concatenation of unplaced contigs (chrU)".  I suspect "linkage groups" are sections of the assembly that are known to be on chr.4, for example, but that their order is unknown.

See: 
	http://genome.ucsc.edu/cgi-bin/hgGateway?clade=insect&org=D.+pseudoobscura&db=0&hgsid=58880251
and 
	http://genome.ucsc.edu/cgi-bin/hgTracks?db=dp3&chromInfoPage=

Note that this only reefers to the assembly, not the annotation.

For this species the karyotype is not available. 

I hope that helps,
Karyn.



On 6 Aug 2012, at 11:45, Anne Parker wrote:

> As I understand it, this nomenclature is specific to the stickleback community - they are in effect chromosomes, but we use the preferred terminology in Ensembl. Perhaps someone more knowledgeable can explain further?
> 
> Cheers
> 
> Anne
> 
> 
> On 6 Aug 2012, at 11:39, PATERSON Trevor wrote:
> 
>> Could someone clarify the significance of naming a top-level coordinate-system as ‘group’ rather than ‘chromosome’?
>> 
>> There is one species (stickleback) in Ensembl that has a top-ranked coordinate system called ‘group’, rather than ‘chromosome’.
>> 
>> There is a karyotype page for stickleback and these ‘groups’ are described as chromosomes: there is no indication of what significance the name ‘group’ has.
>> 
>> I cannot find any other coordinate system called ‘group’, but in EnsemblGenomes the top ranked coord-system of  Drosophila pseudoobscura is named ‘chr-group’ but these do not seem to treated as chromosomes/karyotypes by the web interface.
>> 
>> I don’t think there is an enumeration of allowed coordinate-system names, with definitions  - maybe there could be?
>> 
>> cheers
>> 
>> trevor
>> 
>> Trevor Paterson PhD
>> trevor.paterson at roslin.ed.ac.uk
>> Bioinformatics 
>> The Roslin Institute
>> Royal (Dick) School of Veterinary Studies
>> University of Edinburgh
>> Easter Bush
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>> 
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>> 
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