Hello,
I need some suggestions for performing a Synteny analysis for a single gene. So, I have found some SNPs that tagged a gene after conducting GWAS analyses. I have 19 reference genomes. So, I conducted GWAS based on each of the reference genomes separately. I have 150 individuals. For some reference genomes, I obtain the same significant association and the same gene, but for other reference genomes, there were no significant associations although the Gene is present in those genomes. Later, I found that there was no SNP in the vicinity of that gene in those genomes where no significant associations were obtained. So, I want to do a Synteny analysis among the 19 reference genome for this particular gene. I have the gene annotation and transposable elements annotation files. I want to produce a final figure like the attached one below with genoplotR package. But I have no idea how to start and from where to start.
Can you please give some suggestions on how to do this or if you know any good tutorial then please share that.
Thank you.
