Pamphobeteus cf. antinous "Peru" - Female

[awiec]

No clue yet. First I need to see that I can extract DNA from a molt (doing that next week, already talked my lab into trying it), than I need to check that this DNA is of good enough quality to sequence it and then I need to get that specific sequencing method running - it's a bit more developement and validation than people usually think. If all that works (lets say 6 weeks from now -IF it works) then we can talk.

It would probably cost a couple thousand to do several species, assembling the genome is a whole 'nother ballgame. You can actually just take a leg from the spider, if you just hold the leg long enougj they will pop it off themselves, the arachnid lab I visited did that trick to get tissue samples.

 

[boina]

It would probably cost a couple thousand to do several species, assembling the genome is a whole 'nother ballgame. You can actually just take a leg from the spider, if you just hold the leg long enougj they will pop it off themselves, the arachnid lab I visited did that trick to get tissue samples.

I'm not intending to sequence the genome, just the COX1 gene that's used for barcoding. In reagents it will be no more than a few dollars per spider. The COX1 (or CO1) sequence is known for quite a few species, so all I will have to do is compare the sequence I get to the database.

And yes, I know about the possibility of taking a leg, but I don't want to do that. Yes, the leg will grow back, but I'd still prefer it if I can do it from a molt. And the big advantage of doing that is you can just dry the molt and then ship it around the world with no harm to the DNA. The whole leg needs to be preserved somehow, otherwise it will just rot. If the molt doesn't work I can still think about getting a leg, but I won't give up without trying.

 

[awiec]

I'm not intending to sequence the genome, just the COX1 gene that's used for barcoding. In reagents it will be no more than a few dollars per spider. The COX1 (or CO1) sequence is known for quite a few species, so all I will have to do is compare the sequence I get to the database.

And yes, I know about the possibility of taking a leg, but I don't want to do that. Yes, the leg will grow back, but I'd still prefer it if I can do it from a molt. And the big advantage of doing that is you can just dry the molt and then ship it around the world with no harm to the DNA. The whole leg needs to be preserved somehow, otherwise it will just rot. If the molt doesn't work I can still think about getting a leg, but I won't give up without trying.

The reagents are super cheap but I was thinking in terms of how deep of coverage that you would want and what type of sequencing that you'd want. I deal with plants so for us if we don't have a large number of individuals to sequence it isn't worth the time. Though with my university's genomics core, you could get a sequence for a single individual with decent depth and coverage for less than $700 with a MiSeq machine, its much more for a lane on the HiSeq or Illumina machines. Hell you could even do Sanger sequencing for the cost of peanuts if you only want to do a species or two.

 

[boina]

The reagents are super cheap but I was thinking in terms of how deep of coverage that you would want and what type of sequencing that you'd want. I deal with plants so for us if we don't have a large number of individuals to sequence it isn't worth the time. Though with my university's genomics core, you could get a sequence for a single individual with decent depth and coverage for less than $700 with a MiSeq machine, its much more for a lane on the HiSeq or Illumina machines. Hell you could even do Sanger sequencing for the cost of peanuts if you only want to do a species or two.

I don't think you understand what I want to do. Using Next Generation Sequencing (MiSeq, HiSeq) for genetic barcoding is absurd - You have one gene of 600 bp and a machine that does X,000,000 sequences. You'd need at least 100.000 spiders to fill just one run...

Of course I'll do Sanger sequencing. That's what Sanger is for. Again: I do not want to sequence the genome. I want to sequence one gene of 600 bp. That's about half an hour of hands on time on a Sanger sequencer, and then 16 samples run another half an hour on the machine, so I definitely can do more than 'a species or two'. Depth and Coverage don't come into play with Sanger - I've gotten that misunderstanding before from people who have only ever done NGS before - but those are things that apply only to NGS. Sanger is completely different. The whole sequencing principle is different.

Edit: yes, coverage may play a role in Sanger seq., too, when it comes to de novo assembly of genomes, but only then. I forgot that, because that has absolutely nothing to do with what I want to do and is a completely different ball game. I want to sequence one known gene. In a 600 bp sequence there will be no mistakes using Sanger (when well done), ergo I don't need 'coverage', but just one simple sequence.

I work in a (large-ish) lab that does it's own sequencing, NGS and Sanger, because both have their place in sequencing for different applications, so I have access to everything I need.

Edit 2: See here for an overview of what I want to do.

 

[awiec]

I don't think you understand what I want to do. Using Next Generation Sequencing (MiSeq, HiSeq) for genetic barcoding is absurd - You have one gene of 600 bp and a machine that does X,000,000 sequences. You'd need at least 100.000 spiders to fill just one run...

Of course I'll do Sanger sequencing. That's what Sanger is for. Again: I do not want to sequence the genome. I want to sequence one gene of 600 bp. That's about half an hour of hands on time on a Sanger sequencer, and then 16 samples run another half an hour on the machine, so I definitely can do more than 'a species or two'. Depth and Coverage don't come into play with Sanger - I've gotten that misunderstanding before from people who have only ever done NGS before - but those are things that apply only to NGS. Sanger is completely different. The whole sequencing principle is different.

Edit: yes, coverage may play a role in Sanger seq., too, when it comes to de novo assembly of genomes, but only then. I forgot that, because that has absolutely nothing to do with what I want to do and is a completely different ball game. I want to sequence one known gene. In a 600 bp sequence there will be no mistakes using Sanger (when well done), ergo I don't need 'coverage', but just one simple sequence.

I work in a (large-ish) lab that does it's own sequencing, NGS and Sanger, because both have their place in sequencing for different applications, so I have access to everything I need.

Edit 2: See here for an overview of what I want to do.

I was half asleep when I replied, after re-reading I realized that you wouldn't want NGS for your situation. Though I would still would like to see all sorts of tarantula genomes sequenced one day.

 

[SingaporeB]

I don't think you understand what I want to do. Using Next Generation Sequencing (MiSeq, HiSeq) for genetic barcoding is absurd - You have one gene of 600 bp and a machine that does X,000,000 sequences. You'd need at least 100.000 spiders to fill just one run...

Of course I'll do Sanger sequencing. That's what Sanger is for. Again: I do not want to sequence the genome. I want to sequence one gene of 600 bp. That's about half an hour of hands on time on a Sanger sequencer, and then 16 samples run another half an hour on the machine, so I definitely can do more than 'a species or two'. Depth and Coverage don't come into play with Sanger - I've gotten that misunderstanding before from people who have only ever done NGS before - but those are things that apply only to NGS. Sanger is completely different. The whole sequencing principle is different.

Edit: yes, coverage may play a role in Sanger seq., too, when it comes to de novo assembly of genomes, but only then. I forgot that, because that has absolutely nothing to do with what I want to do and is a completely different ball game. I want to sequence one known gene. In a 600 bp sequence there will be no mistakes using Sanger (when well done), ergo I don't need 'coverage', but just one simple sequence.

I work in a (large-ish) lab that does it's own sequencing, NGS and Sanger, because both have their place in sequencing for different applications, so I have access to everything I need.

Edit 2: See here for an overview of what I want to do.

I hope you maintain your interest in pamphobeteus species. Seems to me every tarantula seller with a web site has their own unique pampho species for sale. Not many pictures of adults though.

 

[efmp1987]

If a specimen were to have some genetic anomaly (ex: hypo/hypermelanism) are the differences on the genetic level sufficient to allow a mistake in the classification? I've always wondered about this but haven't done any reading on it myself. I couldn't find the exact terms to search and I would gain nothing from it!

 

[Kieron2626123]

What are the subtle differences between the Bolivian antinous and those Peruvian cf. antinous?

Peru have hairy patella

 

[antinous]

Peru have hairy patella

They also are a bit bigger than the Bolivian species right?

 

[The Grym Reaper]

They also are a bit bigger than the Bolivian species right?

Yeah, the Bolivian antinous is meant to be the smaller of them IIRC