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Fungi

To provide up-to-date information on fungal barcoding and to facilitate communication and the development of collaboration.

Website: http://www.fungalbarcoding.org
Members: 112
Latest Activity: Nov 16

2014 PAPER PUBLISHED AT OXFORD JOURNAL, DATABASE

Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi

Abstract:

http://database.oxfordjournals.org/cgi/content/abstract/bau061?
ijkey=RJd0dJEPsbtzMhq&keytype=ref

Full Text:

http://database.oxfordjournals.org/cgi/content/full/bau061?
ijkey=RJd0dJEPsbtzMhq&keytype=ref

PDF:

http://database.oxfordjournals.org/cgi/reprint/bau061?
ijkey=RJd0dJEPsbtzMhq&keytype=ref

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2013: Links to recent useful ITS papers

Kõljalg et al. Towards a unified paradigm for sequence-based identification of Fungi.pdf

Nilsson et al. Incorporating molecular data in fungal systematics

Nagy et al. on the utility of ITS in fungal phylogenetics

Nilsson et al. on simple guidelines for establishing basic authenticity of new ITS sequences

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Meeting Report: Fungal ITS Workshop (October 2012)

 

 

 

ITS Barcode standards for acceptance by GenBank:

ITS Barcode.doc

 

Fungal ITS Barcode Paper is available here:

PNAS paper

PNAS cover

Letters in reply to the paper:

Letter by Levente Kiss

Reply to Kiss

Please feel free to continue the discussion in the forum

 

A new open access journal with John Spouge as editor

DNA Barcodes

 

Talks for plenaries at the Adelaide Barcoding meeting posted here:

Adelaide DNA Barcode Meeting talks

 

Literature group on Mendeley to add barcode papers: http://www.mendeley.com/groups/689651/fungal-barcoding/papers/

 

 

Meetings

One Fungus = Which Name?

DNA barcoding symposium at MSA 2012

 

 

Background
Guidelines for non-CO1 selection .pdf
IMC9 Handout on barcoding .pdf
Seifert et al. Barcoding talk at IMC9.ppt
LT-CBOL Memorandum of understanding - 7 July 2010 .pdf
Final material transfer agreement (MTA) with Lifetech .doc

Primers & Protocols
List of samples at LifeTech

Barcode Taxonlist 5 Feb 2011 .xls
PrimersTable 30 November .xls

Discussion Forum

ITS barcode requirements V2 7 Replies

Please comment so I can recommend a final set of ITS standards to GenBank for implementation of the BARCODE flag before the end of July.These are also available as an attached word file on the site.…Continue

Started by Conrad Schoch. Last reply by María P. Martín Jul 7, 2012.

Definition of an acceptable Fungal ITS barcode 5 Replies

Hi all,We need to get some thoughts on details of how we want to deal with ITS barcodes. I post a first draft of conditions we want to consider for submission, started by Keith Seifert below. Please…Continue

Started by Conrad Schoch. Last reply by Keith Seifert Feb 15, 2012.

Annotation of proteins with Sequin 2 Replies

Hi all,I will try to submit specific info on determining the amino acids for GenBank with Sequin here soon. Feel free to discuss this and ask questions. Firstly get the latest version of Sequin here:…Continue

Started by Conrad Schoch. Last reply by Conrad Schoch Oct 26, 2011.

Collecting macrofungi for barcoding 1 Reply

Hi all I am about to go on an official barcoding trip in South Africa. Besides the small ascomycetes that is more my specialty, I will also collect some larger fungi.  THis trip has a public profile,…Continue

Started by Marieka Gryzenhout. Last reply by Bevan Weir Oct 3, 2011.

My Comment Wall

Comment

You need to be a member of Fungi to add comments!

Comment by Jigar N Trivedi on February 17, 2014 at 1:53am

Hello everyone, Me and my group are working on assessing Fungal biodiversity of Gujarat through Barcoding. We are having issues with the PCR  even when we get pure DNA on of the samples. This issue is recurrent in the mushroom samples which we have collected from various locations of Gujarat. I have tried various PCR optimization procedures like Gel extraction of  genomic DNA, adding Tween 20, increasing Mgcl2 concentration. Can Anyone from th is group help me to get a solution for this, as this is part of my Doctoral thesis I am expecting reply from the people of the group ASAP 

Comment by Prasanna Kumar on November 27, 2013 at 5:55am

Hi every one. Is anyone working with barcoding marine yeast? I have started sequencing marine yeast collected from Indian waters. Since I believe very little work has been done with marine yeast, I am interested in testing the efficacy of ITS with it. I also look for collaboration if anyone is willing.

Comment by Kris Jett on April 23, 2012 at 7:50am

Dear Fungi group members, 

Someone has asked questions about "minimum standards for polyphasic differentiation of fungal genera" and "how many known fungal species we have and how many of them are molds?" in the Taxon-based Barcoding discussion board. I just wanted to let this group know in case any of you could provide answers.

 

Thanks so much, and keep up the good work!

Comment by Thorsten Lumbsch on July 21, 2011 at 6:34pm

Sorry - my previous comment was trunctaed. Here I try again:

 

Dear colleagues,

 

I am suggesting to use parts of the obtained data for the barcoding paper for another analysis and separate publication. This second paper will focus on using the GMYC method to delimit species. More details on the method that has been proposed for delimitation of species and detection of cryptic species in barcoding projects, please check the following two publications:

1) Pons et al.: Sequence-Based Species Delimitation for the DNA Taxonomy of Undescribed Insects. Syst. Biol. 55: 595-609 (2006)

2) Monaghan et al.: Accelerated Species Inventory on Madagascar Using Coalescent-Based Models of Species Delineation. Ssyt. Biol. 58: 298-311 (2009)

In short the method attempts at identifying a shift in branch lengths between tokogenetic (intraspecific) and phylogenetic (interspecific) relationships. We have used the method recently in different groups of lichenized ascomycetes and it seems very promising. My suggestion would be to have a paper comparing the performance of the method in a number of different fungi.

If you are interested, please submit your data until August 1, 2011 to me (tlumbsch@fieldmuseum.org). Everyone submitting data will be co-author.

What data are needed and in which format?

To make things easier for me and my colleagues, please make sure to provide the data in a form that does not require any reformatting and other extra work. Thanks a lot for your understanding.

We would need data sets with at least 2-3 samples per species and a minimum of four, closely related taxa (if you have a lot of samples per species, we can also analyze data sets with a lower number of species). Also there should be at least two loci available for all samples in the data set. The more loci, the better, but the data set should not contain missing data. Further the data set should not contain identical sequences – these should be removed before sending the files. Also make sure the names of the taxa are unique in the first eight letters of the name. The files should be sent as combined aligned (make sure no ambiguous sites are present in the alignments) data sets in fasta format.

We will then run ML analysis for each data set separately, transform them into chronograms using Beast and run the GMYC analysis using the splits package in R.

Do not hesitate to contact me if you have any questions. We will not be able to do any analysis before the end of May for different reasons (teaching etc), but would be happy to receive data sets as soon as you have them ready.

 

Thanks a lot.

 

Cheers,

 

Thorsten

Dear colleagues,

 

I am suggesting to use parts of the obtained data for the barcoding paper for another analysis and separate publication. This second paper will focus on using the GMYC method to delimit species. More details on the method that has been proposed for delimitation of species and detection of cryptic species in barcoding projects, please check the following two publications:

1) Pons et al.: Sequence-Based Species Delimitation for the DNA Taxonomy of Undescribed Insects. Syst. Biol. 55: 595-609 (2006)

2) Monaghan et al.: Accelerated Species Inventory on Madagascar Using Coalescent-Based Models of Species Delineation. Ssyt. Biol. 58: 298-311 (2009)

In short the method attempts at identifying a shift in branch lengths between tokogenetic (intraspecific) and phylogenetic (interspecific) relationships. We have used the method recently in different groups of lichenized ascomycetes and it seems very promising. My suggestion would be to have a paper comparing the performance of the method in a number of different fungi.

If you are interested, please submit your data until August 1, 2011 to me (tlumbsch@fieldmuseum.org). Everyone submitting data will be co-author.

What data are needed and in which format?

To make things easier for me and my colleagues, please make sure to provide the data in a form that does not require any reformatting and other extra work. Thanks a lot for your understanding.

We would need data sets with at least 2-3 samples per species and a minimum of four, closely related taxa (if you have a lot of samples per species, we can also analyze data sets with a lower number of species). Also there should be at least two loci available for all samples in the data set. The more loci, the better, but the data set should not contain missing data. Further the data set should not contain identical sequences – these should be removed before sending the files. Also make sure the names of the taxa are unique in the first eight letters of the name. The files should be sent as combined aligned (make sure no ambiguous sites are present in the alignments) data sets in fasta format.

We will then run ML analysis for each data set separately, transform them into chronograms using Beast and run the GMYC analysis using the splits package in R.

Do not hesitate to contact me if you have any questions. We will not be able to do any analysis before the end of May for different reasons (teaching etc), but would be happy to receive data sets as soon as you have them ready.

 

Thanks a lot.

 

Cheers,

 

Thorsten

Comment by Thorsten Lumbsch on July 11, 2011 at 7:02pm

Hi to all, just a short reminder that the deadline for submission of data will be coming soon (August 1, 2011) - see below.

 

Cheers,

Thorsten

 

Dear colleagues,

I am suggesting to use parts of the obtained data for the barcoding paper for another analysis and separate publication. This second paper will focus on using the GMYC method to delimit species. More details on the method that has been proposed for delimitation of species and detection of cryptic species in barcoding projects, please check the following two publications:
1) Pons et al.: Sequence-Based Species Delimitation for the DNA Taxonomy of Undescribed Insects. Syst. Biol. 55: 595-609 (2006)
2) Monaghan et al.: Accelerated Species Inventory on Madagascar Using Coalescent-Based Models of Species Delineation. Ssyt. Biol. 58: 298-311 (2009)
In short the method attempts at identifying a shift in branch lengths between tokogenetic (intraspecific) and phylogenetic (interspecific) relationships. We have used the method recently in different groups of lichenized ascomycetes and it seems very promising. My suggestion would be to have a paper comparing the performance of the method in a number of different fungi.
If you are interested, please submit your data until August 1, 2011 to me (tlumbsch@fieldmuseum.org). Everyone submitting data will be co-author.
What data are needed and in which format?
To make things easier for me and my colleagues, please make sure to provide the data in a form that does not require any reformatting and other extra work. Thanks a lot for your understanding.
We would need data sets with at least 2-3 samples per species and a minimum of four, closely related taxa (if you have a lot of samples per species, we can also analyze data sets with a lower number of species). Also there should be at least two loci available for all samples in the data set. The more loci, the better, but the data set should not contain missing data. Further the data set should not contain identical sequences – these should be removed before sending the files. Also make sure the names of the taxa are unique in the first eight letters of the name. The f

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Comment by Pradeep Kumar Divakar on May 5, 2011 at 4:30am

Dear all,

This is a very nice idea and suggestion by Thorsten Lumbsch on species delimitation using GMYC method and good way to explore the datasets to have separate publication. Species delimitation is a crucial issue for DNA barcoding. Groups like fungi, where morphological features are scarce to delimit properly the species, correct delimitation using appropriate methodologies are prerequisite. Thus, I strongly support these coalescent based methods for species delimitation. Perhaps, it would also be good to include a method by O Meara et al. 2010. New Heuristic Methods for Joint Species Delimitation and Species Tree Inference. Syst. Biol. 59(1):59–73. A heuristic method based on coalescent model in which KC and nonparametric delimitation criteria are used.

With best regards

Divakar

 

A message from Thorsten Lumbsch to all members of Fungi on Connect.BarcodeofLife.net!

Dear colleagues,

I am suggesting to use parts of the obtained data for the barcoding paper for another analysis and separate publication. This second paper will focus on using the GMYC method to delimit species. More details on the method that has been proposed for delimitation of species and detection of cryptic species in barcoding projects, please check the following two publications:
1) Pons et al.: Sequence-Based Species Delimitation for the DNA Taxonomy of Undescribed Insects. Syst. Biol. 55: 595-609 (2006)
2) Monaghan et al.: Accelerated Species Inventory on Madagascar Using Coalescent-Based Models of Species Delineation. Ssyt. Biol. 58: 298-311 (2009)
In short the method attempts at identifying a shift in branch lengths between tokogenetic (intraspecific) and phylogenetic (interspecific) relationships. We have used the method recently in different groups of lichenized ascomycetes and it seems very promising. My suggestion would be to have a paper comparing the performance of the method in a number of different fungi.
If you are interested, please submit your data until August 1, 2011 to me (tlumbsch@fieldmuseum.org). Everyone submitting data will be co-author.
What data are needed and in which format?
To make things easier for me and my colleagues, please make sure to provide the data in a form that does not require any reformatting and other extra work. Thanks a lot for your understanding.
We would need data sets with at least 2-3 samples per species and a minimum of four, closely related taxa (if you have a lot of samples per species, we can also analyze data sets with a lower number of species). Also there should be at least two loci available for all samples in the data set. The more loci, the better, but the data set should not contain missing data. Further the data set should not contain identical sequences – these should be removed before sending the files. Also make sure the names of the taxa are unique in the first eight letters of the name. The f

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