DNA tree species confirmation

[Bonsai Nut]

For those of you with "mystery" tree species that you want definitively identified, I would like to recommend the Plant Diagnostic Lab at Utah State University.

I have been working with some chestnut seeds that had been sourced by a friend from a lone chestnut tree in western Virginia that the tree owner thought was an American chestnut. Since most American chestnut trees have died from chestnut blight, finding a lone survivor might indicate a rare tree that had resistance to the blight. However, once the seeds sprouted, I saw many signs that suggested the tree might in fact be a Chinese chestnut (which has become naturalized on the east coast). Since I wanted to be certain, I submitted tissue samples (leaves) to the Utah State Lab, where they sequenced the DNA and confirmed "The sequence of the plant sample you sent matched 100% Chinese chestnut (Castanea mollissima)."

The service costs $30 plus the cost of shipping the samples to the lab. And it is important to note - I am pretty sure they cannot identify cultivars. But if you have that "mystery" tree that you wanted confirmed... I would recommend this lab. Communication was excellent, and the entire process was simple and friendly. FWIW they only charge you the $30 after they have successfully sequenced the DNA.

Utah Plant Pest Diagnostic Lab Utah Pests Extension Department of Biology Office: (435) 797-2435 | Mobile: (385) 367-3773 Utah State University | BNR 203

 

[Wulfskaar]

Nice! I did see this note though:

Out of State Samples: Please contact the lab before sending in any samples from outside of the state of Utah. We will evaluate wether we can accept your sample or not on a case-by-case basis.

 

[Leo in N E Illinois]

A duplicate of this post should be permanently posted in the resources part of the website. Thanks.

 

[Bonsai Nut]

Nice! I did see this note though:

Out of State Samples: Please contact the lab before sending in any samples from outside of the state of Utah. We will evaluate wether we can accept your sample or not on a case-by-case basis.

Note that this lab also deals with plant diseases and insect pests. They are most concerned about transporting these pathogens into the state of Utah. I sent them an email explaining what I wanted, and their response was as long as the plant is healthy, no problem.

 

[bwaynef]

I've never used them to identify a plant species, but I'd bet Clemson's Diagnostic Lab could do the same. (I have had them identify a tip blight on Juniper for me though.)

 

[Deep Sea Diver]

Agreed, they do an excellent job. I used the Utah folks to identify a Maple with very unusual leaves a month or so ago.

Supposed to be an Autumn Blaze but turns out to be a Silver Maple…. See:

Morphs I have known..... hybrids in nature

For years collecting samples of the conifers of the Pacific Northwest in the Cascades for science students, we always ended running into morphs, or hybrids. One case of two species seemingly hybridizing frequently was of two fir trees, Silver Fir and Noble Fir. We never ran DNA into the woods...

www.bonsainut.com

Love @Leo in N E Illinois idea to have this and possibly others as one of our resources. I could do this if no one else wants to, yet would take a couple weeks due to visitors

Cheers
DSD sends

 

[Cajunrider]

For those of you with "mystery" tree species that you want definitively identified, I would like to recommend the Plant Diagnostic Lab at Utah State University.

I have been working with some chestnut seeds that had been sourced by a friend from a lone chestnut tree in western Virginia that the tree owner thought was an American chestnut. Since most American chestnut trees have died from chestnut blight, finding a lone survivor might indicate a rare tree that had resistance to the blight. However, once the seeds sprouted, I saw many signs that suggested the tree might in fact be a Chinese chestnut (which has become naturalized on the east coast). Since I wanted to be certain, I submitted tissue samples (leaves) to the Utah State Lab, where they sequenced the DNA and confirmed "The sequence of the plant sample you sent matched 100% Chinese chestnut (Castanea mollissima)."

The service costs $30 plus the cost of shipping the samples to the lab. And it is important to note - I am pretty sure they cannot identify cultivars. But if you have that "mystery" tree that you wanted confirmed... I would recommend this lab. Communication was excellent, and the entire process was simple and friendly. FWIW they only charge you the $30 after they have successfully sequenced the DNA.

Utah Plant Pest Diagnostic Lab Utah Pests Extension Department of Biology Office: (435) 797-2435 | Mobile: (385) 367-3773 Utah State University | BNR 203

Thank you!

 

[Mikecheck123]

Can't recommend them enough. Here's a link to my story. I'm still stunned by the results.

Mystery hybrid elm quiz

So it means something like sexy time? Name checks out this morning.

www.bonsainut.com

 

[Pitoon]

For those of you with "mystery" tree species that you want definitively identified, I would like to recommend the Plant Diagnostic Lab at Utah State University.

I have been working with some chestnut seeds that had been sourced by a friend from a lone chestnut tree in western Virginia that the tree owner thought was an American chestnut. Since most American chestnut trees have died from chestnut blight, finding a lone survivor might indicate a rare tree that had resistance to the blight. However, once the seeds sprouted, I saw many signs that suggested the tree might in fact be a Chinese chestnut (which has become naturalized on the east coast). Since I wanted to be certain, I submitted tissue samples (leaves) to the Utah State Lab, where they sequenced the DNA and confirmed "The sequence of the plant sample you sent matched 100% Chinese chestnut (Castanea mollissima)."

The service costs $30 plus the cost of shipping the samples to the lab. And it is important to note - I am pretty sure they cannot identify cultivars. But if you have that "mystery" tree that you wanted confirmed... I would recommend this lab. Communication was excellent, and the entire process was simple and friendly. FWIW they only charge you the $30 after they have successfully sequenced the DNA.

Utah Plant Pest Diagnostic Lab Utah Pests Extension Department of Biology Office: (435) 797-2435 | Mobile: (385) 367-3773 Utah State University | BNR 203

Are the able to provide parentage of hybrids?

 

[Bonsai Nut]

Are the able to provide parentage of hybrids?

Yes. That was one thing I was specifically looking for, because there has been some question about American chestnut / Chinese chestnut hybrids being out there. At least in my case, what I had was 100% Chinese chestnut.

 

[Wires_Guy_wires]

Do you guys get actual data back? As in the sequences or the methods they used? Because I'd love to know how they do this.

 

[Wulfskaar]

I wonder if they can do oaks and their hybrids? I have this thread where I try to identify my oak trees, but my hypothesis is shaky at best and not in agreeance with others.

https://www.bonsainut.com/threads/oak-id-help.53051/

 

[Deep Sea Diver]

Do you guys get actual data back? As in the sequences or the methods they used? Because I'd love to know how they do this.

Just the results, but I just asked the lab if it is possible to obtain sequences.

I wonder if they can do oaks and their hybrids? I have this thread where I try to identify my oak trees, but my hypothesis is shaky at best and not in agreeance with others.

https://www.bonsainut.com/threads/oak-id-help.53051/

Best thing to do is send them a message. Since you are out of state, they require a message before sending samples in any event.

Couldn’t find a U Cal lab to do these samples except here… pricey!

cheers
DSD sends

 

[Deep Sea Diver]

Do you guys get actual data back? As in the sequences or the methods they used? Because I'd love to know how they do this.

Here’s the pertinent part of what I received. Hopefully the attached .txt files will open.

Attached are the sequences for your two samples. We sequenced the internal transcribed spacer region. It is often used to distinguish species in organisms.

cheers
DSD sends

 

[Glaucus]

It is the 18S ribosomal subunit. The "the internal transcribed spacer region" doesn't mean much by itself.

18S ribosomal RNA - Wikipedia

en.wikipedia.org

It basically measures how much evolutionary time has passed. So it can't be used to ID cultivar because those are only hundreds or thousands of years old. So their sequence will be identical.
One can potentially ID cultivars by taking a full 'fingerprint' of a genome.

For this reason it will also not work in the same way on hybrids. A hybrid will have either the 18S sequence or parent A, parent B, or both. So you need to adjust for that. It won't have it's own unique hybrid sequence.
It will kinda work for F1 hybrids because the sample will likely have the spacer sequences linked to both parent species. So it will kinda say 'yes it is a pinus thunbergii' but then also say 'yes, it is a pinus mugo'.
Also, organisms will have more than one copy of the 18S sequence on different chromosomes. So each of these will have their unique spacer regions.

 

[Deep Sea Diver]

Hmm… maybe there is more data that wasn’t sent…. yet wondering why a respected University Plant Diagnostic Lab would use a flawed procedure to identify numerous samples across our country?

I’ll write to the lab and ask for a specific contact as I’m pretty sure the lab sends the prepped samples out to another lab for sequencing, but uses plant primers for sections of chloroplast DNA to compare the results.

Cheers
DSD sends

 

[Glaucus]

It's not flawed. I can explain more. Not sure why you think I was saying that it is flawed. Of course I don't know their exact method, but since you provided the DNA sequences, it is an 18S ribosome technique. Which is the most common method to ID species.
It occurs on several chromosomes, the mitochondrial DNA and in plants the chloroplast DNA. And while most of the ribosomal RNA is highly conserved, the internal transcribed spacers are not.

Maybe you say this because they were able to tell you your sample was a hybrid?

I see that the 'pricey' link you added to UC Davis is not a 18S ribosomal ID test. It is the fingerprinting test I hinted at. This involves amplifying several sequences, not just the ribosomal one. And this gives a fingerprint which makes it easier to link it to cultivar. We once talked about a similar method were DNA fingerprint test was able to distinguish between Nikko and Kozan in satsuki. But you need to validate your primers. You need to select DNA regions that are able to distinguish between cultivars. You need to amplify sequences where some are shared, and some are not. And then you can match unknown samples to known cultivar DNA fingerprints. Based on the pattern of which sequences were amplified and which were not.

 

[Deep Sea Diver]

Very sorry. Always hard to tell tone and nuance online.

Anyways the tree the lab sequenced for me appears to be 100% A. saccharinum vs A. freemainii ‘Autumn Blaze that was advertised.

Yet the A. saccharinum here also appears to either have a mutation or something else to cause the leaves to be misshapen and different from one another.

Best
DSD sends