Hi, dear author, is it possible to extract the mitochondrial genome using Rad-seq dataset in MitoZ with or without reference methods?

[Maotingru]

Hi, dear author, is it possible to extract the mitochondrial genome using Rad-seq dataset in MitoZ with or without reference methods? What command or parameter setting should I use if I can use a reference mitochondrial genome to improve accuracy? I have not been able to find this setting... I am looking forward to your answer!

[linzhi2013]

Dear Maotingru,

MitoZ was not designed for RAD-sequencing data, however, you can try to use the all or all2 command to assemble mitogenomes with MitoZ. I'm not sure how fragmented is when DNA has been processed with RAD-experiment. If the mtDNA is not affected much by RAD-experiment (e.g. some (or most of) mtDNA regions have gone away after RAD treatment), there is still a chance to assemble the mitogenome.

Cheers Guanliang

[comery]

Hi Maotingru, As Guanling mentioned, MitoZ was not designed to deal with RAD-seq data. What I can come up with to do so are two suggestions:

a) Actually, RAD-seq has no substantial differences with whole-genome sequencing, only except lower genome coverage and fragmented distribution. So if you want to use assemble mitochondrial genome using RAD-seq data, you may need to increase input reads to cover this problem; b) using a reference to guide assembly is also a good idea, you can map your RAD-seq reads to the reference using bwa, and then call consensus sequence using samtools. Here is a tutorial for this analysis. read more

After that, you can use MitoZ to annotate your assembly.

best wishes, Chentao