Synteny analysis of unfinished sequencing species

[fanwei]

Dear everyone,

Are complete genomic sequences or chromosome sequences necessary for synteny analysis ?
If i just have some scaffold sequences of a species, Can i use it to analyze synteny of a targeted gene?

Thank you very much!

[SES]

It depends on what your questions is. For looking a patterns of micro-synteny, you only need to compare small regions, and it isn't necessary to have whole chromosomes. However, it doesn't make sense to analyze synteny for a single gene because you need at least a few genes in a scaffold to possibly infer some type of rearrangement.

[SNPsaurus]

If you have other ways to order the genes, such as a linkage or physical map, then you would be able to look for chromosome-scale rearrangements. But as SES says, you'll need some large scaffolds otherwise and then only be able to see changes if there are so many that every small region of the genome is altered.

[fanwei]

Learn a lot! Thank you !