Is it acceptable to use rice or Arabidopsis thaliana to calculate the LTR insertion time of basal angiosperms?

[XXH123a]

Hello, Professor Ou, Excuse me, I would like to ask if there is a simpler way to solve the problem shown in the title.

1. as the title shows, it is the simplest method. I wonder if it is reasonable for me to do so?
2. nucleotide mutation frequency = number of SNPs and indels in the range of TE sequence / (total length of TE sequence x2), is this method reasonable? I tried to extract the complete LTR-RTs and compare them using mafft, but then I didn't know what to do

[oushujun]

Hello,

You may use a generic molecular clock but you should aware that it’s not accurate and could be off for 1000 times or more. A better approach would be just use divergence instead of absolute age to avoid the inaccurate mutation rate.

Shujun

On Tue, Dec 12, 2023 at 11:00 AM XXH123a @.***> wrote:

Hello, Professor Qu, Excuse me, I would like to ask if there is a simpler way to solve the problem shown in the title.

1. as the title shows, it is the simplest method. I wonder if it is reasonable for me to do so?
2. nucleotide mutation frequency = number of SNPs and indels in the range of TE sequence / (total length of TE sequence x2), is this method reasonable? I tried to extract the complete LTR-RTs and compare them using mafft, but then I didn't know what to do

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[XXH123a]

Thank you for your guidance.