Whole genome comparison of two closely related plant species

Question

[LDT]

Dear all,

I want to compare two closely related plant species, (Arabidopsis thaliana, Brasica napa) and I am looking for the latest or the state of art tools to do that.

What I want to find is

1. regions that are conserved across genome
2. regions that are unique in each genome

So far I have found Mauve and Mummer? Any other ideas or way to do this?

[GenoMax]

Some past threads of interest:

How to get the sequence differences between multiple bacterial genomes

Compare two very close genomes (.fasta)

https://academic.oup.com/bioinformatics/article/37/15/2081/6124302

[corrector]

you can also have a look in here https://cmdcolin.github.io/awesome-genome-visualization/?latest=true

Answer 1

[SanjidaR_NCBI]

NCBI has a Comparative Genome Viewer. There are some pre-computed alignments available, see here:

https://ncbi.nlm.nih.gov/genome/cgv/browse/GCA_911865555.2/GCF_000001735.4/33815/3702 https://ncbi.nlm.nih.gov/genome/cgv/33815/3702

You could request that they create an alignment between the assemblies that you're interested in.

However, Brassica napus is quite poplyploid relative to Arabidopsis thaliana, so it might be tricky to get a good alignment. Have you looked at the literature already -e.g. https://www.nature.com/articles/hortres201424/? Some of the comparisons you're looking for may already be available.