Why the allhic results were not consistent with my genetic linkage map?

[baishengjun]

Hi，

I use allhic to generate the seq.HiCcorrected.fasta, then I use my genetic linkage map to group contigs. Finally, I use allhic to generate the genome. The following image shows the relationship between genome and genetic linkage map generated by allmap. It seems that the genome was not consistent with my genetic linkage map, and additional 2 chromosomes were also in the same phenomenon. Should I adjust it to consist with my genetic linkage map? and why allhic result in this problem?

[tangerzhang]

Hi @baishengjun It may be caused by Hi-C scaffolding but also may resulted from the genetic map. According to my experience, the genetic map sometimes suffers from genotyping errors, leading to large scale assembly errors. For instance, the pineapple genome (cultivar F153) published in Nature Genetics (2015) by our team has two chimeric chromosomes, which were further corrected in our another pineapple NG paper (2019). The first pineapple was assembled by a genetic map, which the second was from Hi-C scaffolding. It means that Hi-C scaffolding is capable of generating a high-quality assembly and likely outperforms genetic map. I suggest you can further assess the assembly using Hi-C heatmap and check whether the inconsistence is resulted from mis-scaffolding of Hi-C.