Analysing fusion/fission chromosomes

[mnshgl0110]

@lassancejm I copied the issue here as it related to syri and not plotsr.

Hi,

I would like to visualize the synteny and rearrangements between a few (mammalian) genomes. While the 'classic' circos-type layout works, I think plotsr's layout has benefits and I wanted to give it a whirl. I produced the alignments using mummer. However, syri complains and gives me the following error:

Reading Coords - WARNING - Chromosomes IDs do not match.
Reading Coords - ERROR - Unequal number of chromosomes in the genomes. Exiting 

The assemblies are at the chromosome level, but differ indeed in chromosome number due to fusion/fission. Is there a way to circumvent this problem?

Thanks!

[mnshgl0110]

Hi,

Syri requires to find synteny between homologous chromosomes, so it cannot deal with fusion/fission events very well. But, if it is possible to merge chromosomes, to get ancestral pre-fission chromsomes, then syri can be used.

Best Manish

[aaannaw]

Hello @mnshgl0110 I met the same problem. My two chromosome level genome has unequal pseduo-chromosome numbers. Could you share me any later resolutions with me? Thank you so much !

[mnshgl0110]

Hi @aaannaw. As mentioned above, the only solution is to merge chromosomes to get larger homologous chromosomes. You can try chroder as that can also give you set of "ancestral" homologous chromosomes by merging current pseudo-chromosomes.

[aaannaw]

Hi@mnshgl0110 I have A and B assemblies with different chromosome numbers (A:31, B:32). I want to identify SVs between A and B assemblies. So I have used chroder to merge current pseudo-chromosomes from two sepecies:~/miniconda3/bin/chroder -o 05.chroder -F T A-B.coord A.fasta B.fasta (note: A is reference fasta). Then I got the chroder.qry.fasta and chroder.ref.fasta. The chroder.ref.fasta file is empty and I guess thechroder.qry.fastais the B merged assemblies. However the chroder.qry.fasta sequence is quite different with initial query B assembly. I guess chroder software do the reverse complement? All in all , after usingchroder, I have merged 1th and 32th chromosomes of B into one chromosome. But the merged sequence is weird, not only to concatenate the sequence from 1th and 32th chromosomes. Could you give me any suggestions? Thanks so much !

[aaannaw]

Hello We have two chromosomal level assemblies from two species and the two species has fission/fusion events and thus is different in chromosomal numbers. I have used chroder to merge B species chromosomal to be equal to the A species. But when I compare the collinear between two species, I found before using chroder( A picture ) , Chr1 from A species assembly has a large invesion with Chr1 from B species assembly. But after running chroder(B picture) , the inversion disappear. I guess the chroder software automatically deal with reverse complement. If so, how does it distinguish reverse complement with real inversion. looking forward with your reply! Thanks very much!