Elena -
I see you have gotten some helpful queries about this.
As we have discussed before, there are some groups that are difficult. In my humble opinion this usually a primer issue. I would have to go back through notebooks in my lab to see which groups were the most problematic, but I think serpulids win the prize.
Also some annelids have an intron in their COI - We have found this a few times in several unrelated groups. The intron is usually 3' of the 3' Folmer Primer. There is also a second reasonable primer site about 1000KB a way from the 5' Folmer primer. If you look at some of Kojima's vestimentiferan papers you will be able to find it.
Lastly, we just did a transcriptome of a Crucigera. COI should there. I will look.
If you need more details please let me know.
Ken
On Jun 7, 2011, at 12:40 AM, Elena Kupriyanova wrote:
> Dear friends and colleagues,
>> I accidentally sent the question below from my old (non-functional) email. Could those of you who kindly replied, repeat it to this my account please. Just to clarify – I need examples of groups where sequencing CO1 using “universal” Folmer primers was impossible and designing new primers was difficult. The is the case with serpulid and I want to know how common the situation is in polychaetes.
> Thank you!
> Lena
> **********************************
> Dear all,
>> Please let me know if you had difficulties sequencing the barcoding fragment of CO1 in your favourite polychaete groups. Have those problems been resolved? Has this info been published? Any info is highly appreciated.
>> Wormly,
> Lena
>>>> Dr. Elena Kupriyanova
> Marine Invertebrates
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