Does anyone know of a source for a carefully constructed fungal mock community to use as a control in high-throughput sequencing?
I know there is a bacterial mock community available from BEI Resources, but haven't found a corresponding product for fungi. Thanks!
Hi Matthew.Perhaps the "UNITE" system could be a first approach, useful to achieve your goals.
https://unite.ut.ee/index.php
Thanks, Latisnere. I am aware of the UNITE database, and it is a helpful resource. To clarify what I'm looking for, a mock community in this sense would be a pool of genomic DNA from a number of fungal species, for which ITS copy number known for each species, relative abundance of genomic DNA is variable among species, etc.
I would like to have such a mock community to process along with the samples I am preparing for high-through put sequencing. This is a helpful way to gauge how appropriate sequencing processing pipelines are; in the final dataset, community membership in the mock community sample should resemble very closely the known, true community membership of that mock community.
Hello Matthew. Did you already try in ATCC or CBS?. You can buy "voucher strains" there, and construct your own mock community. Unless you are looking for a "Already builded mock community", this organizations could be useful to your objectives.
Here the links:
http://www.cbs.knaw.nl/
http://www.atcc.org/en/Products/Collections/
Good luck with the construction of your fungal community or, the searching of a community already builded. Will be an interesting contribution to fungal community knowledge and as a good example of a control system in characterization of hypothetical fungal communities.
I also work with analysis of fungal communities associated to soil and will be interesting read your research contributions in this topic.
I know the question was posted a few months ago, but I am wondering if you figure something out (besides creating your own fungal mock community)? Thanks.
Hi Matt, Which region of the fungal genome do you typically work in?
Hi all,
You might be interested in the Caporaso Lab effort to share mock communities: mockrobiota.
Especially mock-9 and mock-10 from B.Wolfe. These data were yield through HiSeq sequencing and target the ITS1 region.
A search for "MiSeq Mock Community" yields your question.
https://github.com/caporaso-lab/mockrobiota
There is a recent paper in Molecular Ecology Resources that might be useful
ITS all right mama: investigating the formation of chimeric sequences in the ITS2 region by DNA metabarcoding analyses of fungal mock communities of different complexities
ANDERS BJØRNSGAARD AAS, MARIE LOUISE DAVEY and HA#VARD KAUSERUD
Molecular Ecology Resources (2016) doi: 10.1111/1755-0998.12622
Here is a recent preprint that might be helpful.
https://www.biorxiv.org/content/early/2017/11/03/213470
Article A fungal mock community control for amplicon sequencing experiments
Anyone following this question may be interested in this paper I have had accepted at Molecular Ecology Resources.
Cool paper! Any chance you have a stock of those mock communities that you would be willing to share?
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