November 2008
Total Page：16
File Type：pdf, Size：1020Kb
Supplement to Mycologia Vol. 59(6) November 2008 Newsletter of the Mycological Society of America — In This Issue — Mycology Feature Integrating DNA Barcoding into the Mycological Sciences MSA Business President’s Corner Secretary’s Email Express MSA 2008 Annual Reports Minutes of the MSA 2008 Annual Business Meeting Minutes of the 2008 MSA Annual Council Meeting MSA 2008-2009 Official Roster MSA Awards 2009 Call for Nominations: MSA Awards 2009 Mycological News XII International Congress of Mycology Memories of Margaret Barr Bigelow Peripatetic Mycology APS Widely Prevalent Plant Pathogenic Fungi List FNQ Mycoblitz Advanced Mycology: Freshwater and Marine Ascomycetes USDA-ARS Entomopathogenic Fungal Cultures Collection Mycologist’s Bookshelf Forest Fungi of Central India Microfungi Occurring on Proteaceae in the Fynbos A Manual and Source Book on the Boletes and Their Allies Conservation of Rare or Little-Known Species Fungi in the Ancient World Compendium of Soil Fungi Recently Received Books Previously Listed Books Take a Break Mushroom Modoku #2 Cookery Corner – Mushroom Minsk Mycological Jobs CBS Group Leader Position Assistant Professor of Mycology at Western Illinois Graduate Student Assistantship in Marine Mycology Graduate Research Assistantship in Fungal Systematics MS Graduate Student Opportunity Mycological Classifieds Mushrooms in Their Natural Habitats Book Sale to Benefit the MSA Images Needed Mold Testing and Identification Services Mycology On-Line Calendar of Events Sustaining Members — Important Dates — December 15, 2008 Deadline for Submission to Inoculum 60(1) November 10-13, 2008 VI Latin American Mycology Congress (ALM) Mar del Plata, Argentina November 13-14, 2008 CBS Symposium: Fungi and Health Trippenhuis, KNAW Amsterdam. Fungal Art November 17-21, 2008 Second African Conference on Edible and Medicinal Mushrooms (2nd ACEMM) This month’s fungal art is of the bird’s nest Accra, Ghana February 19-25, 2009 fungus, Cyathus stercoreus . The fungus is grow - FNQ Mycoblitz: First fungal foray in Far North Queensland ing in Dr Clausz’s back yard in an area where a Lake Tinaroo, Queensland, Australia silver maple stump was ground up after felling Editor — Jinx Campbell the tree. Dept. of Coastal Sciences, Gulf Coast Research Lab —John Clausz University of Southern Mississippi Professor Emeritus 703 East Beach Drive, Ocean Springs, MS 39564 Telephone: (228) 818-8878, Fax: (228) 872-4264 Carroll College Email: [email protected] [email protected] MYCOLOGY FEATURE Integrating DNA Barcoding into the Mycological Sciences Introduction CODE keyword will be removed, with or Mycology has a proud taxonomic tra - without the authority of the original deposi - dition, and mycologists were early to tor. When this happens, the original se - adopt molecular techniques such as DNA quence record remains otherwise un - sequencing for identifying fungi. The re - changed, but it is excluded from BLAST or cently completed Assembling the Fungal other searches restricted to the BARCODE Tree of Life (AFTOL) project was a com - keyword. This is presently the only permit - munity effort, and provided a robust phy - ted third-party alteration of GenBank logenetic framework for mycologists records. The decision to remove the key - wishing to ‘leaf out the tree’ of species. word can be made by GenBank staff, or by The Fungi are a huge kingdom, with chal - the CBOL Scientific Advisory Board. lenges that parallel those of the inverte - DNA barcoding markers brate animal world that has given us DNA barcoding. Many fungi are pleomorphic; The Consortium for the Barcode of many are miniscule and morphologically Life (CBOL, not to be confused with the similar; there are few trained taxonomists Canadian Barcode of Life Network, BOL - to identify them; and there is a large reser - NET) is an international body with more voir of undescribed species awaiting dis - than 160 members, with offices in the covery. Mycologists should be enthusiastic proponents Smithsonian Institution in Washington, D.C. CBOL of DNA barcoding. Why has this not happened? promotes DNA barcoding internationally, and facili - Mycological barcoding discussions are preoccupied tates the development of DNA barcoding projects. It with selection of the most appropriate barcode marker. regulates the barcode standard through its Scientific This is not a trivial matter, but my observation is that Advisory Board. CBOL has the authority, negotiated mycologists generally overlook other aspects of the with GenBank, to sanction DNA barcode markers for all emerging barcode standards (Lorenz et al . 2005), un - kingdoms of life, and thus oversees the application of aware of important details and nuances that will affect the BARCODE keyword. CBOL adopted the mitochon - common practice far more in the long term. ‘DNA bar - drial gene cytochrome oxidase I, Cox1 (also known as coding’ is no longer a vague phrase to be tossed around CO1), as the default barcode for animals, where it has as a marketing device in grant applications. The term received a lot of attention, particularly with inverte - has precise meanings and implications for those who in - brates. Other markers may be proposed as DNA bar - tend to conduct this kind of research. codes for particular taxonomic groups. First, proponents The most critical detail is the acceptance of the must demonstrate that Cox1 is ineffective for the taxo - BARCODE keyword in GenBank (Hanner & Gregory nomic group in question. Then, the utility of the alter - 2007). To qualify for this keyword, a DNA sequence native marker must be demonstrated. The procedures must meet the following criteria: and requirements for these proposals, and the detailed (1) It must represent the DNA barcode marker ac - barcoding standards, are published on the CBOL web - cepted for the taxonomic group in question. site (http://www.barcoding.si.edu/). As reviewed in the last part of this article, Cox1 has (2) A voucher for the barcode must be available. hardly been studied in mycology, and it was not includ - (3) The organism that the barcode represents must ed among the genes sequenced for the AFTOL project. be correctly identified. The majority of mycologists clearly favor the nuclear ri - (4) The DNA sequence itself must be correct, bosomal internal transcribed spacer (ITS) for DNA bar - which is assured by storing sequence chro - coding of fungi, with a smaller constituency, especially matograms in on-line repositories. yeast specialists, favoring the D1/D2 region of the nu - clear large ribosomal subunit (LSU, or 28S). A formal These criteria are discussed below. If any are not met, proposal to CBOL to designate the ITS as the primary the BARCODE keyword will not be appended to a Gen - fungal barcode is expected shortly (see below), and if it Bank accession. If the conditions associated with any of is accepted, the BARCODE keyword will begin to be these criteria change, for example if either the identifica - tion or sequence is shown to be incorrect, then the BAR - Continued on following page 2 Inoculum 59(6), November 2008 applied to fungal sequences that meet the other barcode chromatogram archive ( http://www.ncbi.nlm.nih.gov/ criteria. Yeast workers, who have a more complete data - Traces/home/ ), which is open to barcode chro - base for the LSU, may independently elect to propose a matograms. The Barcode of Life Data Systems primary or secondary barcode for those fungi. (BOLD), described in more detail below, requires the Mycologists are not alone in rejecting Cox1 as a bar - deposit of chromatograms for barcode records stored in code for a kingdom. Botanists have also been searching that database. Supplementary information, such as for alternative barcodes, and will probably adopt a multi- primer sequences used to generate barcodes, may also gene approach (see Pennisi 2007). However, in this king - be required. The chromatogram archive of AFTOL dom also, formal proposals to CBOL are pending. would presumably satisfy this barcode requirement. Most taxonomically oriented mycologists would wel - Vouchering and identification come on-line accessibility of chromatograms. Mycolo - Maintenance of voucher specimens is already com - gists have been vocal critics of the GenBank policy of for - mon practice for most taxonomic mycologists, and bar - bidding third-party annotation of sequence records, coding vouchering requirements are similar to those en - generating various statistics that indicate a high error rate forced by AFTOL. The preservation of vouchers allows either in sequences themselves, or in the identification of identifications associated with barcode records to be re - the organisms from which they originate (Bridge et al. assessed, and this will probably be the most important 2007, Bidartondo et al. 2008). At least when using Gen - factor for the eventual removal of the BARCODE key - Bank as an identification tool, the possibility of removing word from GenBank records. the BARCODE keyword will be an effective method of The barcode standard allows flexibility in the defi - policing sequencing and identification errors. nition of a voucher. In mycology, a voucher normally The issue of legacy data and sequence traces is con - would be a culture or a herbarium specimen deposited sidered near the end of this article. in a recognized collection. In some circumstances, the voucher could be a photograph. The main requirement Other aspects of DNA is that the voucher should allow determinations to be barcoding and mycology verified, long after an initial identification