international online community for dna barcoding professionals
To provide up-to-date information on fungal barcoding and to facilitate communication and the development of collaboration.
Latest Activity: Feb 17
Paper in progress - deadline for submission, before end of Mar. 2014. Please let me know if you contributed to this and your name is not in the author list below:
Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi
Barbara Robbertse1,Conrad L. Schoch1,Vincent Robert2,V. Duong2,Gianluigi Cardinali3,Laszlo Irinyi4,Wieland Meyer4,R. Henrik Nilsson5,Karen Hughes6,Andrew N. Miller7,Paul M. Kirk8,Kessy Abarenkov9,M. Catherine Aime10,Hiran. A Ariyawansa11,Martin Bidartondo12,Teun Boekhout2,Bart Buyck13,Qing Cai14,Linda Jie Chen11,Pedro W. Crous2,Ulrike Damm2,Wilhelm Z. De Beer15,Bryn T.M. Dentinger16,Pradeep K. Divakar17,Margarita Dueñas18,Nicolas Feau19,Katerina Fliegerova20,Miguel A. García21,Gareth W. Griffith22,Johannes Z. Groenewald2,Marizeth Groenewald2,Marieka Gryzenhout23,Liangdong Guo24,Sarah Hambleton25,Richard Hamelin26,Karen Hansen27,Valérie Hofstetter28,Jos Houbraken2,Kevin Hyde11,Peter R. Johnston29,Samantha C. Karunarathna11,Urmas Kõljalg9,Gábor M. Kovács30,Ekaphan Kraichak31,Krisztina Krizsan32,Karl-Henrik Larssen33,Steven Leavitt31,Peter M. Letcher34,Kare Liimatainen35,Jian-Kui Liu11,Jean D. Lodge36,Janet Jennifer Luangsa-ard37,H. Thorsten Lumbsch31,Sajeewa S.N. Maharachchikumbura11,Dimuthu Manamgoda11,María P. Martín18,Andrew Minnis38,Giuseppina Mulè39,Karen K Nakasone40,Tuula Niskanen35,Ibai Olariaga41,Tamás Papp32,Tamás Petkovits32,Raquel Pino-Bodas42,Martha J. Powell34,Huzefa A. Raja43,Dirk Redecker44,Keith A. Seifert25,Bhushan Shrestha11,Soili Stenroos42,Benjamin Stielow2,Sung-Oui Suh45,Kazuaki Tanaka46,Leho Tedersoo9,M. Teresa Telleria18,Dhanushka Udayanga11,Wendy A. Untereiner47,Javier Dieguez Uribeondo18,Csaba Vágvölgyi32,Cobus Visagie2,Donald M. Walker48,Bevan S. Weir29,Michael Weiß49,Zhuang Wen-Ying50,Nalin N. Wijayawardene11,Michael J. Wingfield15,JP Xu51,Zhu L. Yang14,Ning Zhang52,Scott Federhen1
The need for accurate DNA sequence data, tied to both correct taxonomic names and clearly annotated specimen data has never been greater. Over the past few decades, DNA based phylogenetic comparisons have shown that morphology based species recognition often underestimates fungal diversity. In addition to this, the increase in molecular ecology projects employing high-throughput sequencing requires fast and effective methods for en masse identification.In this paper we focus on selecting and re-annotating a set of marker sequences while attempting to represent each currently accepted order of Fungi. Our particular focus is on sequences from the ITS region derived from type specimens and ex-type cultures. We propose a set of standards and protocols in order to improve the submission of new sequences and suggest how type and other reference sequences can be used to improve fungal taxonomy.
An important part of this wil be to formalize ex-type and authoritative specimen data so it can also be tracked across multiple genes in GenBank. The first reference sets can be found here: ITS RefSeq Set . Unique biorepository acronyms in the link below
2013: Links to recent useful ITS papers
ITS Barcode standards for acceptance by GenBank:
Fungal ITS Barcode Paper is available here:
Letters in reply to the paper:
Please feel free to continue the discussion in the forum
A new open access journal with John Spouge as editor
Talks for plenaries at the Adelaide Barcoding meeting posted here:
Literature group on Mendeley to add barcode papers: http://www.mendeley.com/groups/689651/fungal-barcoding/papers/
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
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.
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.
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.
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.