HELP with synteny

[masha48]

Hi,

 

i need help in understanding what syntenic relationship means between species.

 

for example if we take the mouse gene A on chromosome 5 and a equivalent gene in human B located on chromosome 16. if they have a syntenic relationship, does that mean that human gene B was previously located on human chromosome 5 and through chromosomal rearrangement became located on chromosome 16, or does it mean that similar genes are likely to be found flanking the B gene in humans and the A gene in mouse???????

[cypress]

It means the later only it refers to a definite relationship not a likely relationship so remove the word likely and you have it right . The former would be an example of a non-syntenic relationship.

[CharonY]

There are different definitions for synteny. Classically it was used to define genes on a given chromosome whose distance was unknown. More recently it has been used to actually describe genes co-localized in a genomic block. There are some finer points to it as well, that I will ignore for now. However, neither of these definitions describe the scenario in the OP. A single gene can, obviously not be co-localized in any way. What is being described is most likely an orthologous relationship, i.e. separation by speciation (in theory they could be also be paralogs, if duplication occurred first, but let us ignore that for now). In order to have any form of synteny (according to modern use) the scenario should be like this:

Genes A and B are localized in a given genomic area in humans and in mouse we have an area containing two orthologous genes. They would then have a syntenic relationship.

 

In other words, synteny is normally referred to conserved blocks, not single genes. Now, if the OP is slightly rephrased as e.g.: Gene A and B are within syntenic blocks,

does it mean that similar genes are likely to be found flanking the B gene in humans and the A gene in mouse

 

Not necessarily, as some definitions of synteny do not require the correct order or colinearity. Conversation can also be the existence of orthologous genes in any order.

 

To summarize, if you deal with an old-school geneticist you probably should not use the term synteny to describe the relationship between species. If you look just as a single genes, use paralogous or orthologous instead. If looking at blocks and you use the modern definition you can use synteny, if you want to respect the historic term use conserved gene neighborhood instead, and apply the term collinearity when appropriate.