genome size comparison

Question

[bampress]

I'm comparing the assembled draft genome sizes of two species with close relationship. Is there any pipeline or advice?

[Philipp Bayer]

I'm not sure what you mean - do you want to compare the expected genome size based on k-mer counting, do you want to compare the assembly size based on the genome assembly, or do you want to compare the genome size as measured using flow cytometry?

[bampress]

I modified my quesition. Comparing draft genome assemblies of two species with close relationship.

[GenoMax]

Please use ADD REPLY/ADD COMMENT when responding to existing questions to keep threads logically organized.

[Philipp Bayer]

Then I still don't get it so much, all you can compare is the size of the assembly, is it? Or do you have annotations, or are the contigs in pseudomolecules?

[bampress]

Now I have chromosome pseudomolecules and annotation information. How can I compare the two genomes in detail? Here is an example, [https://www.nature.com/articles/ng.807][1]. And I can't figure out some results of this article. Is there any pipeline or advice to do the same thing?

[Kevin Blighe]

Perhaps you want to do a multiple alignment of your annotated sequences with those of other species?

• Creating A Phylogenetic Tree From A Multiple Sequence Alignment.
• Simple Phylogeny
• http://www.cbs.dtu.dk/courses/humanbio/2010/exercises/ExMulPhyl/Ex_Phylo.php

[bampress]

I'm comparing the genomes at whole genome level and I want to see what in fact cause genome size variation in detail. Just as done here [https://www.nature.com/articles/ng.807][1]

[GenoMax]

Depending on the genome size you may be able to use mauve to do genome level alignments. That would allow you to visualize how the two genomes differ from each other.

[bampress]

Maybe I have more than two genomes to be compared. I have read the introduction of Mauve. It says progressiveMauve can do multiple genome comparison. I'll read further and have a try. Many thx.

[GenoMax]

May want to check findGSE to check genome size variations. If you can't access the paper here is a link to the software repo.

[bampress]

I'll have a look. Many thx!

Answer 1

[Philipp Bayer]

For larger comparisons, MashMap could be faster than mauve, I haven't yet tried v4.0 of Mummer for identical purposes (Mummer can also give you structural variations between the two genomes)

For synteny analyses, I'd use MCScanX, which gives you a table of synteny blocks based on gene-to-gene alignments.

OrthoFinder can give you orthologuous clusters and one-to-one copy clusters for phylogenies. (you can use Orthofinder results in MCScanX). KinFin can functionally annotate clusters and make some pretty plots.

The rest depends on the story you want to tell - are there specific groups of repeats, or miRNAs etc. you want to check?

if you are looking after SNPs, kSNP can give you those between genomes (if the genomes are not massive).

[bampress]

What I'm doing is comparative genomics. Now I have three species whose genomes and annotation are available. The three species belong to one genus. One of my story I want to tell is genome size variation, because there is a significant genome size contration among the species according to k-mer and flow cytometry analysis. And they all have not undergone recent WGD.

[Philipp Bayer]

This paper could be of interest: Adaptation in plant genomes: bigger is different https://www.biorxiv.org/content/early/2017/10/10/196501

[bampress]

Many thx! I'll read the paper and think about it.