Strategy for sequencing genomes of nascent polyploid species

Question

[panosprov]

Dear community,

I am new to sequencing and for my first post-doc project I am planning on sequencing the genomes of two very closely related species. IN fact, species 1 is diploid and species 2 is recently emerged polyploid form of species 1. I am interested in studying genome reorganization and epigenetic alteration during the transition to polyploidy.

Since transposable elements are likely major players during the rapid genome reorganization phase after the emergence of triploidy, I need to create a genome assembly that provides this amount of detail.

Do you think I should use PacBio Hifi reads over PacBio CLR reads? Or a combination of both? They are advertised as being able to resolve haplotypes, and span repetitive elements. Anyone having experience with a similar project?

thank you in advance for your time!

[samuel.a.odonnell]

If you are after long reads, epigenetic modifications and haplotype phasing, i would say ONT would be your best bet.

First, you can get much much longer reads (and raw error rate is improving rapidly let alone consensus)

You can detect modifications directly from the reads without any specific library prep modifications

Longer reads helps connect heterozygous variants in order to phase haplotypes, perhaps more important with a polyploid derived from a whole genome duplication

Answer 1

[lieven.sterck]

some experience in this field yes.

I would go for the HiFi ones (not even sure you can still get the CLR ones, perhaps with the older machines/chemistry). Another alternative can be ONT reads (even more cost-effective).

Long reads are indeed your best option to be able to span repeat regions. Especially the ones up to 10-30kb, longer repeat regions will still cause problems (though much less than using short read technology). They also will help to resolve haplotypes.

If you are new to all this (== genome assembly ) , you should take into account that this is not an analysis you quickly run, let along finish. This is of course linked to the estimated genome size of the species you plan to tackle.