We commonly use tRNAs in mitochondrial phylogenomic studies. Of course, not individually, but as a part of the entire concatenated dataset. Especially in taxa where the architecture is highly conserved, as it is really easy to "pair" them.

Things get a bit complicated when there are duplications and/or missing genes, but a part of the tRNA dataset can be used even in such cases.

In some cases they can improve the phylogenetic resolution. If I remember correctly, Cameron found it to be the case in insects.

Here are examples of papers where all mitochondrial RNA genes were used: Article Mitochondrial genomes of two diplectanids (Platyhelminthes: ...

And this is an example of a situation where there are duplicated missing genes:

Article The complete mitochondrial genome of parasitic nematode Cama...

Sehej, I am guessing, it because the sequence of tRNA is much shorter than ribosomal RNAs and hence less heterogeneity between related species. Plus it so much easier to isolate large RNA than the small one. Just guessing here. Not an expert on phylogenetic analysis. Here I am talking about old style phylogenetic analysis, not the PCR one. The one Carl Woese used in bacterial phylogenetic analysis. :)

Hi Sehej,

You use the ribosomal DNA for phylogenetic analysis since it has some very well conserved parts for the development of conserved universal primers, that works within almost every species. Between these conserved domains you have segments that are polymorphic between nearly all species.

By this you got one certain reference-sequence fort he compairison of many different genomes.

Have a look at the ITS-Primers. With those you can take one soil sample and can identify most bacterias and fungi within this sample.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1156903/

But you also can use these markers for plants etc.. By this you can create a phylogenetic tree, that includes many diverse species.

Another factor is that ribosomal DNA is highly abundand within the DNA. So you can also take samples of very old DNA e.g. from older bones and you can include already exstincted species into phylogenetic analysis.

If you just would take tRNA you probably could not develop such well conserved primers and could not use it as one certain reference sequence for most or all species.

Regards

Stephan

There are several reasons:

1) The transfer RNAs are very small, it is best to have sequences more than 300 bases long for phylogenetic work, and in recent years it is common to see people using complete genomes or very large assemblies of genes for phylogenetic analyses.

2) There are many transfer RNA genes, usually less than the 61 possible codons (64 minus the TAA, TGA and TAG stop codons) so it would be a bit of a mess to choose which one(s) to use.

3) In most organisms there are many copies of the same transfer RNA gene, so it would be a problem to be sure we are analyzing the same copy in each organism.

Thank you. I see there a lot of different approaches to the reason behind what should be used as a indicator for phylogenetic analysis. I didn't really think about the size being a hurdle at first, which it seems to be.

We commonly use tRNAs in mitochondrial phylogenomic studies. Of course, not individually, but as a part of the entire concatenated dataset. Especially in taxa where the architecture is highly conserved, as it is really easy to "pair" them.

Things get a bit complicated when there are duplications and/or missing genes, but a part of the tRNA dataset can be used even in such cases.

In some cases they can improve the phylogenetic resolution. If I remember correctly, Cameron found it to be the case in insects.

Here are examples of papers where all mitochondrial RNA genes were used: Article Mitochondrial genomes of two diplectanids (Platyhelminthes: ...

And this is an example of a situation where there are duplicated missing genes:

Article The complete mitochondrial genome of parasitic nematode Cama...

As reported by Widmann et al. (2010) tRNAs are among the most ancient, highly conserved sequences on earth, but are often thought to be poor phylogenetic markers because they are short, often subject to horizontal gene transfer, and easily change specificity .

you can read this